Starting phenix.real_space_refine on Thu Mar 21 16:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tke_41348/03_2024/8tke_41348_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.152 sd= 1.648 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 24 5.49 5 S 444 5.16 5 C 46052 2.51 5 N 12376 2.21 5 O 13416 1.98 5 H 72052 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A ASP 814": "OD1" <-> "OD2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1630": "OE1" <-> "OE2" Residue "A ASP 1653": "OD1" <-> "OD2" Residue "A GLU 1783": "OE1" <-> "OE2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A PHE 2490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 814": "OD1" <-> "OD2" Residue "B TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B GLU 1384": "OE1" <-> "OE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B PHE 1480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1630": "OE1" <-> "OE2" Residue "B GLU 1656": "OE1" <-> "OE2" Residue "B GLU 1783": "OE1" <-> "OE2" Residue "B TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 2347": "OD1" <-> "OD2" Residue "B PHE 2356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C ASP 566": "OD1" <-> "OD2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 698": "OD1" <-> "OD2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C GLU 1087": "OE1" <-> "OE2" Residue "C GLU 1125": "OE1" <-> "OE2" Residue "C ASP 1208": "OD1" <-> "OD2" Residue "C PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1331": "OD1" <-> "OD2" Residue "C TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1384": "OE1" <-> "OE2" Residue "C ASP 1395": "OD1" <-> "OD2" Residue "C GLU 1403": "OE1" <-> "OE2" Residue "C GLU 1603": "OE1" <-> "OE2" Residue "C GLU 1630": "OE1" <-> "OE2" Residue "C ASP 1653": "OD1" <-> "OD2" Residue "C GLU 1783": "OE1" <-> "OE2" Residue "C GLU 1882": "OE1" <-> "OE2" Residue "C TYR 1901": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1946": "OE1" <-> "OE2" Residue "C TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2118": "OE1" <-> "OE2" Residue "C ASP 2347": "OD1" <-> "OD2" Residue "C PHE 2356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 2486": "OD1" <-> "OD2" Residue "C ASP 2546": "OD1" <-> "OD2" Residue "C PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D GLU 408": "OE1" <-> "OE2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D ASP 566": "OD1" <-> "OD2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 814": "OD1" <-> "OD2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D TYR 876": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1177": "OE1" <-> "OE2" Residue "D TYR 1227": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1403": "OE1" <-> "OE2" Residue "D GLU 1604": "OE1" <-> "OE2" Residue "D PHE 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1630": "OE1" <-> "OE2" Residue "D GLU 1783": "OE1" <-> "OE2" Residue "D GLU 2150": "OE1" <-> "OE2" Residue "D GLU 2163": "OE1" <-> "OE2" Residue "D TYR 2326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2338": "OE1" <-> "OE2" Residue "D PHE 2548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144372 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 36036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2249, 36036 Classifications: {'peptide': 2249} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2185} Chain breaks: 14 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 36036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2249, 36036 Classifications: {'peptide': 2249} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2185} Chain breaks: 14 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 36036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2249, 36036 Classifications: {'peptide': 2249} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2185} Chain breaks: 14 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 36036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2249, 36036 Classifications: {'peptide': 2249} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 2185} Chain breaks: 14 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34462 SG CYS A2538 140.394 124.631 104.064 1.00 82.43 S ATOM 34511 SG CYS A2541 138.669 125.932 101.127 1.00 71.31 S ATOM 70498 SG CYS B2538 116.960 140.397 104.115 1.00 83.38 S ATOM 70547 SG CYS B2541 115.781 138.570 101.195 1.00 73.65 S ATOM A051I SG CYS C2538 101.458 117.260 104.014 1.00 83.62 S ATOM A052V SG CYS C2541 103.171 115.908 101.131 1.00 73.26 S ATOM A0WUI SG CYS D2538 124.858 101.188 104.088 1.00 82.95 S ATOM A0WVV SG CYS D2541 125.926 103.223 101.223 1.00 70.99 S Time building chain proxies: 45.65, per 1000 atoms: 0.32 Number of scatterers: 144372 At special positions: 0 Unit cell: (242.165, 242.165, 187.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 444 16.00 P 24 15.00 O 13416 8.00 N 12376 7.00 C 46052 6.00 H 72052 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 95.20 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2541 " pdb="ZN ZN B3001 " - pdb=" SG CYS B2538 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C3001 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2541 " pdb="ZN ZN C3001 " - pdb=" SG CYS C2538 " pdb=" ZN D3001 " pdb="ZN ZN D3001 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D3001 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2541 " Number of angles added : 7 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17240 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 412 helices and 40 sheets defined 71.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.78 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 removed outlier: 4.676A pdb=" N CYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 56' Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 86 through 112 Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.672A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.883A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 277' Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.511A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.915A pdb=" N ASN A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 537 through 542 removed outlier: 4.944A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 565 Proline residue: A 548 - end of helix removed outlier: 3.539A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.321A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N GLY A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 590 through 603 removed outlier: 4.279A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ARG A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 610 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.527A pdb=" N VAL A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.871A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.709A pdb=" N SER A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ILE A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 666' Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 719 through 741 removed outlier: 3.727A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 removed outlier: 4.269A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.533A pdb=" N ASP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 811 through 824 removed outlier: 5.287A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 5.339A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 874 removed outlier: 3.541A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 removed outlier: 3.779A pdb=" N ARG A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 887 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 1002 Processing helix chain 'A' and resid 1024 through 1036 removed outlier: 3.815A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1065 removed outlier: 3.576A pdb=" N MET A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS A1065 " --> pdb=" O HIS A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.816A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.853A pdb=" N GLN A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 3.818A pdb=" N SER A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.037A pdb=" N GLN A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1201 removed outlier: 3.766A pdb=" N LYS A1192 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 3.784A pdb=" N ALA A1237 " --> pdb=" O GLN A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 4.079A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1271 through 1278 Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 4.000A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 4.505A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.762A pdb=" N GLY A1329 " --> pdb=" O LEU A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 Processing helix chain 'A' and resid 1360 through 1378 removed outlier: 3.932A pdb=" N GLY A1378 " --> pdb=" O ALA A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 Proline residue: A1392 - end of helix Processing helix chain 'A' and resid 1393 through 1402 removed outlier: 3.759A pdb=" N HIS A1402 " --> pdb=" O SER A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1421 Processing helix chain 'A' and resid 1429 through 1434 removed outlier: 3.580A pdb=" N THR A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1429 through 1434' Processing helix chain 'A' and resid 1435 through 1458 removed outlier: 4.248A pdb=" N THR A1439 " --> pdb=" O ASN A1435 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1440 " --> pdb=" O HIS A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.849A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1489 removed outlier: 4.053A pdb=" N SER A1488 " --> pdb=" O PHE A1484 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A1489 " --> pdb=" O SER A1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1484 through 1489' Processing helix chain 'A' and resid 1491 through 1511 removed outlier: 3.846A pdb=" N CYS A1511 " --> pdb=" O ARG A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1537 removed outlier: 3.702A pdb=" N SER A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1557 Processing helix chain 'A' and resid 1587 through 1624 Proline residue: A1608 - end of helix removed outlier: 3.914A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A1612 " --> pdb=" O PRO A1608 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A1617 " --> pdb=" O GLU A1613 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP A1623 " --> pdb=" O ASP A1619 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 3.519A pdb=" N SER A1640 " --> pdb=" O GLN A1636 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 removed outlier: 3.788A pdb=" N LYS A1652 " --> pdb=" O ILE A1648 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A1653 " --> pdb=" O GLN A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.510A pdb=" N CYS A1662 " --> pdb=" O GLU A1658 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1680 through 1695 Processing helix chain 'A' and resid 1717 through 1732 Processing helix chain 'A' and resid 1733 through 1744 removed outlier: 3.858A pdb=" N THR A1744 " --> pdb=" O LEU A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1762 Processing helix chain 'A' and resid 1765 through 1779 removed outlier: 3.543A pdb=" N GLN A1769 " --> pdb=" O ASN A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1804 removed outlier: 4.279A pdb=" N VAL A1804 " --> pdb=" O THR A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.768A pdb=" N GLN A1871 " --> pdb=" O VAL A1867 " (cutoff:3.500A) Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1885 through 1894 Processing helix chain 'A' and resid 1902 through 1916 removed outlier: 4.387A pdb=" N GLU A1906 " --> pdb=" O ASN A1902 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A1907 " --> pdb=" O LEU A1903 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A1908 " --> pdb=" O VAL A1904 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 4.161A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 4.261A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A1929 " --> pdb=" O LEU A1925 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1924 through 1930' Processing helix chain 'A' and resid 1931 through 1950 removed outlier: 5.068A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A1950 " --> pdb=" O GLU A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 removed outlier: 3.602A pdb=" N GLN A1956 " --> pdb=" O CYS A1952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1965 through 1976 removed outlier: 4.051A pdb=" N ILE A1969 " --> pdb=" O ASN A1965 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 4.521A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 removed outlier: 3.678A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2020 removed outlier: 4.377A pdb=" N ALA A2013 " --> pdb=" O ASP A2009 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2040 removed outlier: 4.678A pdb=" N GLU A2036 " --> pdb=" O ALA A2032 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU A2037 " --> pdb=" O TYR A2033 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A2038 " --> pdb=" O LEU A2034 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A2039 " --> pdb=" O GLN A2035 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU A2040 " --> pdb=" O GLU A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2045 through 2063 removed outlier: 3.563A pdb=" N VAL A2049 " --> pdb=" O SER A2045 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2072 removed outlier: 3.541A pdb=" N GLN A2068 " --> pdb=" O ASN A2064 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A2072 " --> pdb=" O GLN A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2112 through 2121 removed outlier: 4.428A pdb=" N TYR A2116 " --> pdb=" O ASP A2112 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A2117 " --> pdb=" O PRO A2113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A2118 " --> pdb=" O LEU A2114 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A2120 " --> pdb=" O TYR A2116 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A2121 " --> pdb=" O TYR A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 3.739A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A2147 " --> pdb=" O ILE A2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2141 through 2147' Processing helix chain 'A' and resid 2148 through 2159 Processing helix chain 'A' and resid 2167 through 2192 removed outlier: 3.574A pdb=" N SER A2175 " --> pdb=" O PHE A2171 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A2191 " --> pdb=" O LYS A2187 " (cutoff:3.500A) Proline residue: A2192 - end of helix Processing helix chain 'A' and resid 2193 through 2201 removed outlier: 3.849A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2223 Processing helix chain 'A' and resid 2260 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 5.898A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2317 Processing helix chain 'A' and resid 2318 through 2336 Processing helix chain 'A' and resid 2337 through 2353 removed outlier: 4.681A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A2353 " --> pdb=" O ILE A2349 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2364 removed outlier: 3.909A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2390 Processing helix chain 'A' and resid 2391 through 2396 removed outlier: 3.821A pdb=" N PHE A2395 " --> pdb=" O LEU A2391 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE A2396 " --> pdb=" O LYS A2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2391 through 2396' Processing helix chain 'A' and resid 2457 through 2472 removed outlier: 3.977A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN A2472 " --> pdb=" O HIS A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.075A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 Processing helix chain 'A' and resid 2544 through 2549 removed outlier: 4.200A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2549' Processing helix chain 'A' and resid 2554 through 2561 Processing helix chain 'A' and resid 2564 through 2578 Processing helix chain 'A' and resid 2584 through 2597 Processing helix chain 'A' and resid 2609 through 2657 removed outlier: 4.660A pdb=" N ASN A2613 " --> pdb=" O SER A2609 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 4.686A pdb=" N CYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 86 through 112 Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.697A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.874A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 277' Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.579A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 removed outlier: 4.156A pdb=" N ASN B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 527 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 537 through 542 removed outlier: 4.784A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 565 Proline residue: B 548 - end of helix removed outlier: 4.799A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.394A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 590 through 603 removed outlier: 4.203A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.600A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.959A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 658 through 666 removed outlier: 3.628A pdb=" N SER B 662 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 658 through 666' Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 719 through 741 removed outlier: 3.784A pdb=" N LEU B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 4.446A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 770 through 785 Processing helix chain 'B' and resid 811 through 824 removed outlier: 5.351A pdb=" N ASP B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 5.317A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 874 removed outlier: 3.552A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 removed outlier: 3.745A pdb=" N ARG B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 887 " --> pdb=" O ARG B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 1002 Processing helix chain 'B' and resid 1024 through 1036 removed outlier: 3.901A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1065 removed outlier: 3.578A pdb=" N MET B1064 " --> pdb=" O ILE B1060 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS B1065 " --> pdb=" O HIS B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.790A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 removed outlier: 3.793A pdb=" N GLN B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 3.828A pdb=" N SER B1124 " --> pdb=" O MET B1120 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TRP B1127 " --> pdb=" O LYS B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.081A pdb=" N GLN B1170 " --> pdb=" O SER B1166 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1201 removed outlier: 3.778A pdb=" N LYS B1192 " --> pdb=" O GLN B1188 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B1201 " --> pdb=" O LEU B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1218 through 1237 removed outlier: 3.744A pdb=" N ALA B1237 " --> pdb=" O GLN B1233 " (cutoff:3.500A) Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 3.537A pdb=" N GLN B1243 " --> pdb=" O ASN B1239 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1271 through 1278 Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.907A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 4.349A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.651A pdb=" N GLY B1329 " --> pdb=" O LEU B1325 " (cutoff:3.500A) Processing helix chain 'B' and resid 1338 through 1353 Processing helix chain 'B' and resid 1360 through 1378 removed outlier: 3.978A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 removed outlier: 3.672A pdb=" N GLU B1384 " --> pdb=" O ASN B1380 " (cutoff:3.500A) Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1402 removed outlier: 3.709A pdb=" N HIS B1402 " --> pdb=" O SER B1398 " (cutoff:3.500A) Processing helix chain 'B' and resid 1406 through 1421 Processing helix chain 'B' and resid 1429 through 1434 removed outlier: 3.601A pdb=" N THR B1433 " --> pdb=" O LYS B1429 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1429 through 1434' Processing helix chain 'B' and resid 1435 through 1458 removed outlier: 4.089A pdb=" N THR B1439 " --> pdb=" O ASN B1435 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B1440 " --> pdb=" O HIS B1436 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.772A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1484 through 1489 removed outlier: 4.058A pdb=" N SER B1488 " --> pdb=" O PHE B1484 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B1489 " --> pdb=" O SER B1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1484 through 1489' Processing helix chain 'B' and resid 1491 through 1511 removed outlier: 3.581A pdb=" N GLU B1510 " --> pdb=" O THR B1506 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1516 through 1537 removed outlier: 3.784A pdb=" N SER B1521 " --> pdb=" O GLN B1517 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1557 Processing helix chain 'B' and resid 1587 through 1624 Proline residue: B1608 - end of helix removed outlier: 3.849A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B1612 " --> pdb=" O PRO B1608 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B1617 " --> pdb=" O GLU B1613 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B1618 " --> pdb=" O LEU B1614 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP B1623 " --> pdb=" O ASP B1619 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 removed outlier: 3.509A pdb=" N SER B1640 " --> pdb=" O GLN B1636 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY B1641 " --> pdb=" O ARG B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.849A pdb=" N LYS B1652 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.510A pdb=" N CYS B1662 " --> pdb=" O GLU B1658 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS B1675 " --> pdb=" O GLN B1671 " (cutoff:3.500A) Processing helix chain 'B' and resid 1680 through 1695 Processing helix chain 'B' and resid 1717 through 1732 Processing helix chain 'B' and resid 1733 through 1744 removed outlier: 3.809A pdb=" N THR B1744 " --> pdb=" O LEU B1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 1746 through 1762 Processing helix chain 'B' and resid 1765 through 1779 removed outlier: 3.512A pdb=" N GLN B1769 " --> pdb=" O ASN B1765 " (cutoff:3.500A) Processing helix chain 'B' and resid 1781 through 1804 removed outlier: 4.401A pdb=" N VAL B1804 " --> pdb=" O THR B1800 " (cutoff:3.500A) Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.715A pdb=" N GLN B1871 " --> pdb=" O VAL B1867 " (cutoff:3.500A) Proline residue: B1872 - end of helix Processing helix chain 'B' and resid 1885 through 1894 Processing helix chain 'B' and resid 1902 through 1916 removed outlier: 4.347A pdb=" N GLU B1906 " --> pdb=" O ASN B1902 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B1908 " --> pdb=" O VAL B1904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 4.330A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 4.279A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B1929 " --> pdb=" O LEU B1925 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1924 through 1930' Processing helix chain 'B' and resid 1931 through 1950 removed outlier: 5.087A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY B1950 " --> pdb=" O GLU B1946 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 removed outlier: 3.594A pdb=" N GLN B1956 " --> pdb=" O CYS B1952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1965 through 1976 removed outlier: 4.110A pdb=" N ILE B1969 " --> pdb=" O ASN B1965 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 4.527A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 removed outlier: 3.650A pdb=" N MET B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2009 through 2020 removed outlier: 4.270A pdb=" N ALA B2013 " --> pdb=" O ASP B2009 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2040 removed outlier: 4.567A pdb=" N GLU B2036 " --> pdb=" O ALA B2032 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU B2037 " --> pdb=" O TYR B2033 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU B2038 " --> pdb=" O LEU B2034 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B2039 " --> pdb=" O GLN B2035 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B2040 " --> pdb=" O GLU B2036 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2063 removed outlier: 3.528A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2072 removed outlier: 3.591A pdb=" N GLN B2068 " --> pdb=" O ASN B2064 " (cutoff:3.500A) Processing helix chain 'B' and resid 2112 through 2121 removed outlier: 4.393A pdb=" N TYR B2116 " --> pdb=" O ASP B2112 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR B2117 " --> pdb=" O PRO B2113 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B2118 " --> pdb=" O LEU B2114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B2120 " --> pdb=" O TYR B2116 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR B2121 " --> pdb=" O TYR B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 3.806A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B2147 " --> pdb=" O ILE B2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2141 through 2147' Processing helix chain 'B' and resid 2148 through 2159 Processing helix chain 'B' and resid 2167 through 2192 removed outlier: 4.563A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B2191 " --> pdb=" O LYS B2187 " (cutoff:3.500A) Proline residue: B2192 - end of helix Processing helix chain 'B' and resid 2193 through 2201 removed outlier: 3.955A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2223 Processing helix chain 'B' and resid 2260 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 5.820A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2317 Processing helix chain 'B' and resid 2318 through 2336 Processing helix chain 'B' and resid 2337 through 2353 removed outlier: 4.825A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU B2353 " --> pdb=" O ILE B2349 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2364 removed outlier: 4.029A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2365 through 2390 Processing helix chain 'B' and resid 2391 through 2396 removed outlier: 3.810A pdb=" N PHE B2395 " --> pdb=" O LEU B2391 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE B2396 " --> pdb=" O LYS B2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2391 through 2396' Processing helix chain 'B' and resid 2457 through 2472 removed outlier: 4.004A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B2472 " --> pdb=" O HIS B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.295A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 Processing helix chain 'B' and resid 2544 through 2549 removed outlier: 4.174A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2549' Processing helix chain 'B' and resid 2554 through 2561 Processing helix chain 'B' and resid 2564 through 2578 Processing helix chain 'B' and resid 2584 through 2597 Processing helix chain 'B' and resid 2609 through 2657 removed outlier: 4.594A pdb=" N ASN B2613 " --> pdb=" O SER B2609 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B2614 " --> pdb=" O LEU B2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.706A pdb=" N CYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU C 56 " --> pdb=" O PHE C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 86 through 112 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.747A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.885A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 277' Processing helix chain 'C' and resid 435 through 462 removed outlier: 3.584A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.849A pdb=" N ASN C 513 " --> pdb=" O MET C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 527 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 537 through 542 removed outlier: 4.918A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 565 Proline residue: C 548 - end of helix removed outlier: 4.845A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.350A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLY C 579 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 590 through 603 removed outlier: 4.173A pdb=" N ASN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 610 Processing helix chain 'C' and resid 611 through 626 Processing helix chain 'C' and resid 627 through 640 removed outlier: 3.950A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 Processing helix chain 'C' and resid 658 through 666 removed outlier: 3.653A pdb=" N SER C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 658 through 666' Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 719 through 741 removed outlier: 3.753A pdb=" N LEU C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 755 removed outlier: 4.367A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 770 through 785 Processing helix chain 'C' and resid 811 through 824 removed outlier: 5.353A pdb=" N ASP C 824 " --> pdb=" O ASN C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 5.396A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 874 removed outlier: 3.537A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 removed outlier: 3.765A pdb=" N ARG C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 887 " --> pdb=" O ARG C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 1002 Processing helix chain 'C' and resid 1024 through 1036 removed outlier: 3.832A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1065 removed outlier: 3.516A pdb=" N MET C1064 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS C1065 " --> pdb=" O HIS C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.746A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 removed outlier: 3.901A pdb=" N GLN C1094 " --> pdb=" O HIS C1090 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C1095 " --> pdb=" O THR C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 3.785A pdb=" N SER C1124 " --> pdb=" O MET C1120 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.082A pdb=" N GLN C1170 " --> pdb=" O SER C1166 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1201 removed outlier: 3.772A pdb=" N LYS C1192 " --> pdb=" O GLN C1188 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C1201 " --> pdb=" O LEU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1218 through 1237 removed outlier: 3.679A pdb=" N ALA C1237 " --> pdb=" O GLN C1233 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 4.203A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1257 through 1269 Processing helix chain 'C' and resid 1271 through 1278 Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.896A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 4.331A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.680A pdb=" N GLY C1329 " --> pdb=" O LEU C1325 " (cutoff:3.500A) Processing helix chain 'C' and resid 1338 through 1353 Processing helix chain 'C' and resid 1360 through 1378 removed outlier: 3.990A pdb=" N GLY C1378 " --> pdb=" O ALA C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1380 through 1392 Proline residue: C1392 - end of helix Processing helix chain 'C' and resid 1393 through 1402 removed outlier: 3.742A pdb=" N HIS C1402 " --> pdb=" O SER C1398 " (cutoff:3.500A) Processing helix chain 'C' and resid 1406 through 1421 Processing helix chain 'C' and resid 1429 through 1434 removed outlier: 3.598A pdb=" N THR C1433 " --> pdb=" O LYS C1429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C1434 " --> pdb=" O GLU C1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1429 through 1434' Processing helix chain 'C' and resid 1435 through 1458 removed outlier: 4.047A pdb=" N THR C1439 " --> pdb=" O ASN C1435 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C1440 " --> pdb=" O HIS C1436 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.792A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1484 through 1489 removed outlier: 4.052A pdb=" N SER C1488 " --> pdb=" O PHE C1484 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C1489 " --> pdb=" O SER C1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1484 through 1489' Processing helix chain 'C' and resid 1491 through 1511 removed outlier: 3.576A pdb=" N GLU C1510 " --> pdb=" O THR C1506 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS C1511 " --> pdb=" O ARG C1507 " (cutoff:3.500A) Processing helix chain 'C' and resid 1516 through 1537 removed outlier: 3.781A pdb=" N SER C1521 " --> pdb=" O GLN C1517 " (cutoff:3.500A) Processing helix chain 'C' and resid 1541 through 1557 Processing helix chain 'C' and resid 1587 through 1624 Proline residue: C1608 - end of helix removed outlier: 3.837A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1612 " --> pdb=" O PRO C1608 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C1617 " --> pdb=" O GLU C1613 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C1618 " --> pdb=" O LEU C1614 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 removed outlier: 3.503A pdb=" N SER C1640 " --> pdb=" O GLN C1636 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY C1641 " --> pdb=" O ARG C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1655 removed outlier: 3.728A pdb=" N LYS C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C1653 " --> pdb=" O GLN C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.529A pdb=" N CYS C1662 " --> pdb=" O GLU C1658 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS C1675 " --> pdb=" O GLN C1671 " (cutoff:3.500A) Processing helix chain 'C' and resid 1680 through 1695 Processing helix chain 'C' and resid 1717 through 1732 Processing helix chain 'C' and resid 1733 through 1744 removed outlier: 3.847A pdb=" N THR C1744 " --> pdb=" O LEU C1740 " (cutoff:3.500A) Processing helix chain 'C' and resid 1746 through 1762 Processing helix chain 'C' and resid 1765 through 1779 Processing helix chain 'C' and resid 1781 through 1804 removed outlier: 4.410A pdb=" N VAL C1804 " --> pdb=" O THR C1800 " (cutoff:3.500A) Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.790A pdb=" N LEU C1868 " --> pdb=" O GLY C1864 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C1869 " --> pdb=" O THR C1865 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C1871 " --> pdb=" O VAL C1867 " (cutoff:3.500A) Proline residue: C1872 - end of helix Processing helix chain 'C' and resid 1885 through 1894 Processing helix chain 'C' and resid 1902 through 1916 removed outlier: 3.893A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C1907 " --> pdb=" O LEU C1903 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C1908 " --> pdb=" O VAL C1904 " (cutoff:3.500A) Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 4.329A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 4.244A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C1929 " --> pdb=" O LEU C1925 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1924 through 1930' Processing helix chain 'C' and resid 1931 through 1950 removed outlier: 4.941A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY C1950 " --> pdb=" O GLU C1946 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 removed outlier: 3.624A pdb=" N GLN C1956 " --> pdb=" O CYS C1952 " (cutoff:3.500A) Processing helix chain 'C' and resid 1965 through 1976 removed outlier: 4.132A pdb=" N ILE C1969 " --> pdb=" O ASN C1965 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 4.526A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 removed outlier: 3.599A pdb=" N MET C2004 " --> pdb=" O LEU C2000 " (cutoff:3.500A) Processing helix chain 'C' and resid 2009 through 2020 removed outlier: 4.257A pdb=" N ALA C2013 " --> pdb=" O ASP C2009 " (cutoff:3.500A) Processing helix chain 'C' and resid 2021 through 2040 removed outlier: 4.555A pdb=" N GLU C2036 " --> pdb=" O ALA C2032 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU C2037 " --> pdb=" O TYR C2033 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C2038 " --> pdb=" O LEU C2034 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG C2039 " --> pdb=" O GLN C2035 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU C2040 " --> pdb=" O GLU C2036 " (cutoff:3.500A) Processing helix chain 'C' and resid 2045 through 2063 removed outlier: 3.543A pdb=" N VAL C2049 " --> pdb=" O SER C2045 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2072 removed outlier: 3.541A pdb=" N GLN C2068 " --> pdb=" O ASN C2064 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C2072 " --> pdb=" O GLN C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2112 through 2121 removed outlier: 4.429A pdb=" N TYR C2116 " --> pdb=" O ASP C2112 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR C2117 " --> pdb=" O PRO C2113 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C2118 " --> pdb=" O LEU C2114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS C2120 " --> pdb=" O TYR C2116 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR C2121 " --> pdb=" O TYR C2117 " (cutoff:3.500A) Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 3.827A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C2147 " --> pdb=" O ILE C2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2141 through 2147' Processing helix chain 'C' and resid 2148 through 2159 Processing helix chain 'C' and resid 2167 through 2192 removed outlier: 4.570A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C2191 " --> pdb=" O LYS C2187 " (cutoff:3.500A) Proline residue: C2192 - end of helix Processing helix chain 'C' and resid 2193 through 2201 removed outlier: 3.877A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2223 Processing helix chain 'C' and resid 2260 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 5.832A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2317 Processing helix chain 'C' and resid 2318 through 2336 Processing helix chain 'C' and resid 2337 through 2353 removed outlier: 4.686A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU C2353 " --> pdb=" O ILE C2349 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 removed outlier: 4.027A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2365 through 2390 Processing helix chain 'C' and resid 2391 through 2396 removed outlier: 3.775A pdb=" N PHE C2395 " --> pdb=" O LEU C2391 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE C2396 " --> pdb=" O LYS C2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2391 through 2396' Processing helix chain 'C' and resid 2457 through 2472 removed outlier: 3.548A pdb=" N LEU C2470 " --> pdb=" O MET C2466 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN C2472 " --> pdb=" O HIS C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.262A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 Processing helix chain 'C' and resid 2544 through 2549 removed outlier: 4.198A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2549' Processing helix chain 'C' and resid 2554 through 2561 Processing helix chain 'C' and resid 2564 through 2578 Processing helix chain 'C' and resid 2584 through 2597 Processing helix chain 'C' and resid 2609 through 2657 removed outlier: 4.601A pdb=" N ASN C2613 " --> pdb=" O SER C2609 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.674A pdb=" N CYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 56 " --> pdb=" O PHE D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 86 through 112 Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.695A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 3.876A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 277' Processing helix chain 'D' and resid 435 through 462 removed outlier: 3.578A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 removed outlier: 4.113A pdb=" N ASN D 513 " --> pdb=" O MET D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 527 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 537 through 542 removed outlier: 4.986A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 565 Proline residue: D 548 - end of helix removed outlier: 4.803A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.370A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 590 through 603 removed outlier: 4.028A pdb=" N ASN D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 610 Processing helix chain 'D' and resid 611 through 626 removed outlier: 3.628A pdb=" N VAL D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 640 removed outlier: 4.002A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 Processing helix chain 'D' and resid 658 through 666 removed outlier: 3.728A pdb=" N SER D 662 " --> pdb=" O ASP D 658 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 658 through 666' Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 719 through 741 removed outlier: 3.749A pdb=" N LEU D 741 " --> pdb=" O ALA D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 755 removed outlier: 4.419A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 766 Processing helix chain 'D' and resid 770 through 785 Processing helix chain 'D' and resid 811 through 824 removed outlier: 5.353A pdb=" N ASP D 824 " --> pdb=" O ASN D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 848 removed outlier: 5.325A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 874 removed outlier: 3.554A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 removed outlier: 3.782A pdb=" N ARG D 886 " --> pdb=" O LEU D 882 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR D 887 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 1002 Processing helix chain 'D' and resid 1024 through 1036 removed outlier: 3.916A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1065 removed outlier: 3.525A pdb=" N MET D1064 " --> pdb=" O ILE D1060 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS D1065 " --> pdb=" O HIS D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.788A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.800A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 3.804A pdb=" N SER D1124 " --> pdb=" O MET D1120 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.090A pdb=" N GLN D1170 " --> pdb=" O SER D1166 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1187 through 1201 removed outlier: 3.764A pdb=" N LYS D1192 " --> pdb=" O GLN D1188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP D1201 " --> pdb=" O LEU D1197 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1218 through 1237 removed outlier: 3.746A pdb=" N ALA D1237 " --> pdb=" O GLN D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 4.154A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) Processing helix chain 'D' and resid 1257 through 1269 Processing helix chain 'D' and resid 1271 through 1278 Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.913A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 4.314A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.682A pdb=" N GLY D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1353 Processing helix chain 'D' and resid 1360 through 1378 removed outlier: 3.980A pdb=" N GLY D1378 " --> pdb=" O ALA D1374 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1392 Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1393 through 1402 removed outlier: 3.674A pdb=" N HIS D1402 " --> pdb=" O SER D1398 " (cutoff:3.500A) Processing helix chain 'D' and resid 1406 through 1421 Processing helix chain 'D' and resid 1429 through 1434 removed outlier: 3.600A pdb=" N THR D1433 " --> pdb=" O LYS D1429 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D1434 " --> pdb=" O GLU D1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1429 through 1434' Processing helix chain 'D' and resid 1435 through 1458 removed outlier: 4.230A pdb=" N THR D1439 " --> pdb=" O ASN D1435 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D1440 " --> pdb=" O HIS D1436 " (cutoff:3.500A) Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.777A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1484 through 1489 removed outlier: 4.011A pdb=" N SER D1488 " --> pdb=" O PHE D1484 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D1489 " --> pdb=" O SER D1485 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1484 through 1489' Processing helix chain 'D' and resid 1491 through 1511 removed outlier: 3.577A pdb=" N GLU D1510 " --> pdb=" O THR D1506 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS D1511 " --> pdb=" O ARG D1507 " (cutoff:3.500A) Processing helix chain 'D' and resid 1516 through 1537 removed outlier: 3.786A pdb=" N SER D1521 " --> pdb=" O GLN D1517 " (cutoff:3.500A) Processing helix chain 'D' and resid 1541 through 1557 Processing helix chain 'D' and resid 1587 through 1624 Proline residue: D1608 - end of helix removed outlier: 3.853A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D1612 " --> pdb=" O PRO D1608 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D1617 " --> pdb=" O GLU D1613 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D1618 " --> pdb=" O LEU D1614 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D1623 " --> pdb=" O ASP D1619 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 4.166A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.778A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET D1655 " --> pdb=" O THR D1651 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.578A pdb=" N CYS D1662 " --> pdb=" O GLU D1658 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS D1675 " --> pdb=" O GLN D1671 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1695 Processing helix chain 'D' and resid 1717 through 1732 Processing helix chain 'D' and resid 1733 through 1744 removed outlier: 3.918A pdb=" N THR D1744 " --> pdb=" O LEU D1740 " (cutoff:3.500A) Processing helix chain 'D' and resid 1746 through 1762 Processing helix chain 'D' and resid 1765 through 1779 removed outlier: 3.512A pdb=" N GLN D1769 " --> pdb=" O ASN D1765 " (cutoff:3.500A) Processing helix chain 'D' and resid 1781 through 1804 removed outlier: 4.301A pdb=" N VAL D1804 " --> pdb=" O THR D1800 " (cutoff:3.500A) Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 3.718A pdb=" N GLN D1871 " --> pdb=" O VAL D1867 " (cutoff:3.500A) Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1885 through 1894 Processing helix chain 'D' and resid 1902 through 1916 removed outlier: 4.098A pdb=" N GLU D1906 " --> pdb=" O ASN D1902 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR D1907 " --> pdb=" O LEU D1903 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D1908 " --> pdb=" O VAL D1904 " (cutoff:3.500A) Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 4.260A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 4.286A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D1929 " --> pdb=" O LEU D1925 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1924 through 1930' Processing helix chain 'D' and resid 1931 through 1950 removed outlier: 4.956A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY D1950 " --> pdb=" O GLU D1946 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 removed outlier: 3.607A pdb=" N GLN D1956 " --> pdb=" O CYS D1952 " (cutoff:3.500A) Processing helix chain 'D' and resid 1965 through 1976 removed outlier: 4.124A pdb=" N ILE D1969 " --> pdb=" O ASN D1965 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 4.526A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 removed outlier: 3.623A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) Processing helix chain 'D' and resid 2009 through 2020 removed outlier: 4.356A pdb=" N ALA D2013 " --> pdb=" O ASP D2009 " (cutoff:3.500A) Processing helix chain 'D' and resid 2021 through 2040 removed outlier: 4.598A pdb=" N GLU D2036 " --> pdb=" O ALA D2032 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU D2037 " --> pdb=" O TYR D2033 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU D2038 " --> pdb=" O LEU D2034 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D2039 " --> pdb=" O GLN D2035 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU D2040 " --> pdb=" O GLU D2036 " (cutoff:3.500A) Processing helix chain 'D' and resid 2045 through 2063 removed outlier: 3.532A pdb=" N VAL D2049 " --> pdb=" O SER D2045 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) Processing helix chain 'D' and resid 2064 through 2072 removed outlier: 3.551A pdb=" N GLN D2068 " --> pdb=" O ASN D2064 " (cutoff:3.500A) Processing helix chain 'D' and resid 2112 through 2121 removed outlier: 4.428A pdb=" N TYR D2116 " --> pdb=" O ASP D2112 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR D2117 " --> pdb=" O PRO D2113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D2118 " --> pdb=" O LEU D2114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D2120 " --> pdb=" O TYR D2116 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR D2121 " --> pdb=" O TYR D2117 " (cutoff:3.500A) Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 3.804A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D2147 " --> pdb=" O ILE D2143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2141 through 2147' Processing helix chain 'D' and resid 2148 through 2159 Processing helix chain 'D' and resid 2167 through 2192 removed outlier: 4.584A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D2191 " --> pdb=" O LYS D2187 " (cutoff:3.500A) Proline residue: D2192 - end of helix Processing helix chain 'D' and resid 2193 through 2201 removed outlier: 3.882A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) Processing helix chain 'D' and resid 2202 through 2223 Processing helix chain 'D' and resid 2260 through 2276 Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 5.871A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2317 Processing helix chain 'D' and resid 2318 through 2336 Processing helix chain 'D' and resid 2337 through 2353 removed outlier: 4.741A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU D2353 " --> pdb=" O ILE D2349 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2364 removed outlier: 4.053A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2365 through 2390 Processing helix chain 'D' and resid 2391 through 2396 removed outlier: 3.850A pdb=" N PHE D2395 " --> pdb=" O LEU D2391 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE D2396 " --> pdb=" O LYS D2392 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2391 through 2396' Processing helix chain 'D' and resid 2457 through 2472 removed outlier: 4.030A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN D2472 " --> pdb=" O HIS D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.198A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 Processing helix chain 'D' and resid 2544 through 2549 removed outlier: 4.155A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2549' Processing helix chain 'D' and resid 2554 through 2561 Processing helix chain 'D' and resid 2564 through 2578 Processing helix chain 'D' and resid 2584 through 2597 Processing helix chain 'D' and resid 2609 through 2657 removed outlier: 4.588A pdb=" N ASN D2613 " --> pdb=" O SER D2609 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 20 removed outlier: 9.411A pdb=" N THR A 217 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 185 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 181 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 149 through 154 removed outlier: 3.565A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 194 through 198 removed outlier: 3.932A pdb=" N GLU A 209 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.595A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 14.475A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 239 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LEU A 282 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 309 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 303 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 15.221A pdb=" N TYR A 304 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N ALA A 317 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE A 306 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 313 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 385 through 388 removed outlier: 4.446A pdb=" N SER A 385 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 431 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 396 through 401 removed outlier: 4.311A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 667 through 672 removed outlier: 5.026A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 2122 through 2127 Processing sheet with id= 9, first strand: chain 'A' and resid 124 through 127 removed outlier: 4.947A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 241 through 245 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 14 through 20 removed outlier: 9.469A pdb=" N THR B 217 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 185 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP B 181 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 149 through 154 removed outlier: 3.563A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 194 through 198 removed outlier: 3.931A pdb=" N GLU B 209 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.551A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 14.448A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 239 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU B 282 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 309 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU B 303 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 15.228A pdb=" N TYR B 304 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N ALA B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B 306 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN B 313 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 385 through 388 removed outlier: 4.423A pdb=" N SER B 385 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 431 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 396 through 401 removed outlier: 4.323A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 667 through 672 removed outlier: 5.016A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 2122 through 2127 Processing sheet with id= 19, first strand: chain 'B' and resid 124 through 127 removed outlier: 4.979A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 131 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 241 through 245 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'C' and resid 14 through 20 removed outlier: 9.438A pdb=" N THR C 217 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 185 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP C 181 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C' and resid 149 through 154 removed outlier: 3.534A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 194 through 198 removed outlier: 3.949A pdb=" N GLU C 209 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.508A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.842A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 14.408A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP C 239 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N LEU C 282 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 309 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU C 303 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 15.301A pdb=" N TYR C 304 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N ALA C 317 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N PHE C 306 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN C 313 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 385 through 388 removed outlier: 4.418A pdb=" N SER C 385 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 431 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 396 through 401 removed outlier: 4.344A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 667 through 672 removed outlier: 4.756A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 2122 through 2127 Processing sheet with id= 29, first strand: chain 'C' and resid 124 through 127 removed outlier: 5.020A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 131 " --> pdb=" O HIS C 126 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 241 through 245 No H-bonds generated for sheet with id= 30 Processing sheet with id= 31, first strand: chain 'D' and resid 14 through 20 removed outlier: 9.432A pdb=" N THR D 217 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 185 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP D 181 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 149 through 154 removed outlier: 3.559A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 194 through 198 removed outlier: 3.933A pdb=" N GLU D 209 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.536A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 14.397A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP D 239 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU D 282 " --> pdb=" O LEU D 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 309 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU D 303 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 15.240A pdb=" N TYR D 304 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 10.899A pdb=" N ALA D 317 " --> pdb=" O TYR D 304 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N PHE D 306 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN D 313 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 385 through 388 removed outlier: 4.421A pdb=" N SER D 385 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 431 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 396 through 401 removed outlier: 4.345A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 667 through 672 removed outlier: 5.040A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 2122 through 2127 Processing sheet with id= 39, first strand: chain 'D' and resid 124 through 127 removed outlier: 4.946A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 241 through 245 No H-bonds generated for sheet with id= 40 4410 hydrogen bonds defined for protein. 13194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 69.69 Time building geometry restraints manager: 100.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 71888 1.03 - 1.23: 419 1.23 - 1.43: 30073 1.43 - 1.62: 42596 1.62 - 1.82: 720 Bond restraints: 145696 Sorted by residual: bond pdb=" CB GLU B1630 " pdb=" CG GLU B1630 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB LYS B 73 " pdb=" CG LYS B 73 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" N LEU B 31 " pdb=" CA LEU B 31 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.30e+00 bond pdb=" N LEU D 31 " pdb=" CA LEU D 31 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.22e+00 bond pdb=" CA ASP D1048 " pdb=" CB ASP D1048 " ideal model delta sigma weight residual 1.535 1.556 -0.021 1.90e-02 2.77e+03 1.18e+00 ... (remaining 145691 not shown) Histogram of bond angle deviations from ideal: 99.30 - 107.41: 5320 107.41 - 115.53: 182316 115.53 - 123.64: 64250 123.64 - 131.76: 11517 131.76 - 139.88: 93 Bond angle restraints: 263496 Sorted by residual: angle pdb=" CB LYS B 73 " pdb=" CG LYS B 73 " pdb=" CD LYS B 73 " ideal model delta sigma weight residual 111.30 121.67 -10.37 2.30e+00 1.89e-01 2.03e+01 angle pdb=" N VAL D2362 " pdb=" CA VAL D2362 " pdb=" C VAL D2362 " ideal model delta sigma weight residual 112.96 109.45 3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" N VAL B2362 " pdb=" CA VAL B2362 " pdb=" C VAL B2362 " ideal model delta sigma weight residual 113.42 109.33 4.09 1.17e+00 7.31e-01 1.22e+01 angle pdb=" C ASN D1902 " pdb=" CA ASN D1902 " pdb=" CB ASN D1902 " ideal model delta sigma weight residual 112.03 117.47 -5.44 1.56e+00 4.11e-01 1.22e+01 angle pdb=" N VAL C2362 " pdb=" CA VAL C2362 " pdb=" C VAL C2362 " ideal model delta sigma weight residual 113.42 109.35 4.07 1.17e+00 7.31e-01 1.21e+01 ... (remaining 263491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.40: 63645 24.40 - 48.79: 3730 48.79 - 73.19: 714 73.19 - 97.58: 95 97.58 - 121.98: 16 Dihedral angle restraints: 68200 sinusoidal: 37244 harmonic: 30956 Sorted by residual: dihedral pdb=" C1 I3P D3002 " pdb=" C2 I3P D3002 " pdb=" C3 I3P D3002 " pdb=" C4 I3P D3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.17 121.98 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 I3P B3002 " pdb=" C2 I3P B3002 " pdb=" C3 I3P B3002 " pdb=" C4 I3P B3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.16 121.97 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 I3P A3002 " pdb=" C2 I3P A3002 " pdb=" C3 I3P A3002 " pdb=" C4 I3P A3002 " ideal model delta sinusoidal sigma weight residual 56.81 -65.14 121.95 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 68197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 10305 0.059 - 0.118: 1063 0.118 - 0.177: 47 0.177 - 0.236: 1 0.236 - 0.295: 12 Chirality restraints: 11428 Sorted by residual: chirality pdb=" C2' ATP B3004 " pdb=" C1' ATP B3004 " pdb=" C3' ATP B3004 " pdb=" O2' ATP B3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP D3004 " pdb=" C1' ATP D3004 " pdb=" C3' ATP D3004 " pdb=" O2' ATP D3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP C3004 " pdb=" C1' ATP C3004 " pdb=" C3' ATP C3004 " pdb=" O2' ATP C3004 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 11425 not shown) Planarity restraints: 21340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B1902 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ASN B1902 " 0.041 2.00e-02 2.50e+03 pdb=" O ASN B1902 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B1903 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1902 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C ASN A1902 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN A1902 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A1903 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 661 " 0.009 2.00e-02 2.50e+03 1.45e-02 3.15e+00 pdb=" CG ASN B 661 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 661 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 661 " 0.007 2.00e-02 2.50e+03 pdb="HD21 ASN B 661 " 0.003 2.00e-02 2.50e+03 pdb="HD22 ASN B 661 " 0.001 2.00e-02 2.50e+03 ... (remaining 21337 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 2371 2.10 - 2.72: 245107 2.72 - 3.35: 422677 3.35 - 3.97: 505052 3.97 - 4.60: 806895 Nonbonded interactions: 1982102 Sorted by model distance: nonbonded pdb=" OE1 GLU D 539 " pdb=" H GLU D 539 " model vdw 1.470 1.850 nonbonded pdb=" OE1 GLU A 539 " pdb=" H GLU A 539 " model vdw 1.470 1.850 nonbonded pdb=" OE1 GLU D1633 " pdb=" H GLU D1633 " model vdw 1.486 1.850 nonbonded pdb=" OE1 GLU B1633 " pdb=" H GLU B1633 " model vdw 1.488 1.850 nonbonded pdb=" OE1 GLU B 614 " pdb=" H GLU B 614 " model vdw 1.501 1.850 ... (remaining 1982097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.550 Extract box with map and model: 60.570 Check model and map are aligned: 1.570 Set scattering table: 1.030 Process input model: 424.910 Find NCS groups from input model: 5.650 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 515.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 73644 Z= 0.129 Angle : 0.456 10.371 99580 Z= 0.240 Chirality : 0.034 0.295 11428 Planarity : 0.002 0.060 12652 Dihedral : 16.851 121.978 27596 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.13 % Allowed : 14.97 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.09), residues: 8876 helix: 3.46 (0.07), residues: 5664 sheet: 0.55 (0.20), residues: 708 loop : 0.55 (0.13), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C2566 HIS 0.011 0.001 HIS D1203 PHE 0.017 0.001 PHE A2490 TYR 0.022 0.001 TYR B 71 ARG 0.011 0.000 ARG C2154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1966 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1956 time to evaluate : 8.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8126 (t) cc_final: 0.7926 (p) REVERT: A 203 ASP cc_start: 0.7998 (t0) cc_final: 0.7773 (t0) REVERT: A 612 LYS cc_start: 0.8914 (tttm) cc_final: 0.8566 (ttpp) REVERT: A 616 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6871 (mm-30) REVERT: A 636 ASP cc_start: 0.7999 (t0) cc_final: 0.7640 (t0) REVERT: A 1243 GLN cc_start: 0.8375 (mt0) cc_final: 0.8091 (mt0) REVERT: A 1273 GLN cc_start: 0.8411 (tp40) cc_final: 0.8056 (tp-100) REVERT: A 1280 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 1613 GLU cc_start: 0.7053 (tt0) cc_final: 0.6651 (tt0) REVERT: A 1947 TYR cc_start: 0.7372 (m-10) cc_final: 0.7151 (m-10) REVERT: B 93 LEU cc_start: 0.8394 (mm) cc_final: 0.8124 (mt) REVERT: B 181 ASP cc_start: 0.7528 (m-30) cc_final: 0.7292 (m-30) REVERT: B 275 SER cc_start: 0.9221 (m) cc_final: 0.9010 (t) REVERT: B 315 LEU cc_start: 0.8595 (tp) cc_final: 0.8238 (tt) REVERT: B 636 ASP cc_start: 0.7858 (t0) cc_final: 0.7480 (t0) REVERT: B 643 ILE cc_start: 0.8459 (mm) cc_final: 0.7920 (pt) REVERT: B 691 GLU cc_start: 0.5186 (pm20) cc_final: 0.4982 (pm20) REVERT: B 716 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8228 (ttp-110) REVERT: B 1280 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 1312 LYS cc_start: 0.8345 (ptpt) cc_final: 0.8138 (pttm) REVERT: B 1344 HIS cc_start: 0.7714 (t-90) cc_final: 0.7146 (t-170) REVERT: B 1370 ASP cc_start: 0.7916 (m-30) cc_final: 0.7523 (m-30) REVERT: B 1421 TYR cc_start: 0.7502 (m-10) cc_final: 0.6791 (m-10) REVERT: B 1613 GLU cc_start: 0.7119 (tt0) cc_final: 0.6737 (tt0) REVERT: B 1625 GLU cc_start: 0.7418 (pt0) cc_final: 0.6639 (pt0) REVERT: B 1942 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6800 (mt-10) REVERT: B 2016 ILE cc_start: 0.8993 (tp) cc_final: 0.8735 (mt) REVERT: B 2035 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7811 (tp-100) REVERT: B 2047 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.7894 (mtt180) REVERT: B 2154 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8180 (tmm-80) REVERT: B 2472 ASN cc_start: 0.7840 (m-40) cc_final: 0.7509 (m110) REVERT: C 468 ASP cc_start: 0.7443 (m-30) cc_final: 0.7027 (m-30) REVERT: C 476 LEU cc_start: 0.7701 (mm) cc_final: 0.7497 (mt) REVERT: C 600 HIS cc_start: 0.6518 (t70) cc_final: 0.6158 (t70) REVERT: C 614 GLU cc_start: 0.7675 (mp0) cc_final: 0.7425 (mp0) REVERT: C 710 GLN cc_start: 0.7757 (mm-40) cc_final: 0.6818 (tp40) REVERT: C 714 GLU cc_start: 0.7246 (mp0) cc_final: 0.6919 (mp0) REVERT: C 1064 MET cc_start: 0.7660 (mtp) cc_final: 0.7453 (mtp) REVERT: C 1227 TYR cc_start: 0.8881 (m-10) cc_final: 0.8538 (m-80) REVERT: C 1271 ASN cc_start: 0.8066 (t0) cc_final: 0.7712 (t0) REVERT: C 1619 ASP cc_start: 0.7909 (t0) cc_final: 0.7687 (t0) REVERT: C 1689 MET cc_start: 0.6557 (tmm) cc_final: 0.6315 (tmt) REVERT: C 1693 ASN cc_start: 0.7974 (t0) cc_final: 0.7669 (t0) REVERT: C 1909 GLN cc_start: 0.7935 (mt0) cc_final: 0.7264 (mt0) REVERT: C 2201 MET cc_start: 0.7864 (mmm) cc_final: 0.7588 (mmt) REVERT: C 2489 LEU cc_start: 0.7523 (mm) cc_final: 0.6907 (tp) REVERT: C 2497 ASP cc_start: 0.7597 (m-30) cc_final: 0.7298 (m-30) REVERT: C 2518 ASP cc_start: 0.8218 (t70) cc_final: 0.7908 (t0) REVERT: D 253 THR cc_start: 0.8299 (m) cc_final: 0.8024 (p) REVERT: D 291 ASP cc_start: 0.8009 (t0) cc_final: 0.7762 (t0) REVERT: D 657 LEU cc_start: 0.8562 (mm) cc_final: 0.8327 (mm) REVERT: D 710 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8099 (mm-40) REVERT: D 776 SER cc_start: 0.8434 (m) cc_final: 0.8073 (p) REVERT: D 791 GLN cc_start: 0.8256 (mp10) cc_final: 0.8017 (mp10) REVERT: D 814 ASP cc_start: 0.7725 (m-30) cc_final: 0.7513 (m-30) REVERT: D 860 THR cc_start: 0.7994 (m) cc_final: 0.7262 (p) REVERT: D 1116 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8265 (ttp-170) REVERT: D 1248 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8441 (mttp) REVERT: D 1271 ASN cc_start: 0.7590 (t0) cc_final: 0.7283 (t0) REVERT: D 1383 THR cc_start: 0.8940 (m) cc_final: 0.8601 (p) REVERT: D 1998 LYS cc_start: 0.8722 (mttt) cc_final: 0.8457 (mtmm) REVERT: D 2031 LYS cc_start: 0.9031 (mttm) cc_final: 0.8621 (mtmm) REVERT: D 2154 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8112 (ttt180) REVERT: D 2285 LEU cc_start: 0.7800 (mt) cc_final: 0.7594 (mt) REVERT: D 2493 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7214 (tpt-90) REVERT: D 2510 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8231 (t0) outliers start: 10 outliers final: 4 residues processed: 1958 average time/residue: 1.6371 time to fit residues: 5448.0051 Evaluate side-chains 1796 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1791 time to evaluate : 8.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 1210 LEU Chi-restraints excluded: chain D residue 1367 SER Chi-restraints excluded: chain D residue 2510 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 756 optimal weight: 0.9990 chunk 679 optimal weight: 9.9990 chunk 376 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 458 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 702 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 chunk 813 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 601 ASN A 602 ASN A1084 GLN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2145 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 546 ASN B 602 ASN B1084 GLN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 GLN ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2145 GLN B2210 ASN ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN C 601 ASN C1084 GLN ** C1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2145 GLN C2472 ASN D 192 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN D 602 ASN D 869 ASN D1084 GLN D1327 ASN D1487 ASN D1790 HIS D1955 ASN D2145 GLN D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2472 ASN D2550 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 73644 Z= 0.387 Angle : 0.555 7.475 99580 Z= 0.299 Chirality : 0.038 0.210 11428 Planarity : 0.003 0.089 12652 Dihedral : 5.483 89.643 9925 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.89 % Allowed : 13.63 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.09), residues: 8876 helix: 2.93 (0.07), residues: 5732 sheet: 0.12 (0.20), residues: 696 loop : 0.22 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 219 HIS 0.011 0.001 HIS A 868 PHE 0.019 0.002 PHE B1286 TYR 0.040 0.001 TYR A2341 ARG 0.007 0.001 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 2056 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1905 time to evaluate : 8.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 SER cc_start: 0.8844 (t) cc_final: 0.8579 (p) REVERT: A 232 GLU cc_start: 0.7103 (tp30) cc_final: 0.6809 (tp30) REVERT: A 399 GLN cc_start: 0.7663 (tt0) cc_final: 0.7292 (mt0) REVERT: A 476 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7555 (mt) REVERT: A 614 GLU cc_start: 0.7503 (mp0) cc_final: 0.7076 (mp0) REVERT: A 616 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 714 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6816 (mp0) REVERT: A 753 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: A 1271 ASN cc_start: 0.8073 (t0) cc_final: 0.7861 (t0) REVERT: A 1448 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7828 (mtm) REVERT: A 1509 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7823 (pp) REVERT: A 1613 GLU cc_start: 0.7143 (tt0) cc_final: 0.6740 (tt0) REVERT: A 1647 LEU cc_start: 0.8005 (tp) cc_final: 0.7668 (tt) REVERT: A 1648 ILE cc_start: 0.8654 (mm) cc_final: 0.8439 (mt) REVERT: A 1988 LEU cc_start: 0.8428 (mt) cc_final: 0.8227 (mt) REVERT: A 2346 PHE cc_start: 0.8070 (m-10) cc_final: 0.7863 (m-10) REVERT: A 2528 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8073 (tt0) REVERT: A 2604 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6861 (ttt90) REVERT: B 93 LEU cc_start: 0.8390 (mm) cc_final: 0.8164 (mt) REVERT: B 262 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: B 399 GLN cc_start: 0.7533 (mt0) cc_final: 0.7330 (mt0) REVERT: B 713 GLN cc_start: 0.8690 (mm110) cc_final: 0.8239 (mt0) REVERT: B 730 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7025 (ttm110) REVERT: B 767 GLU cc_start: 0.7669 (pt0) cc_final: 0.7468 (pt0) REVERT: B 1206 MET cc_start: 0.9105 (mmt) cc_final: 0.8694 (mmt) REVERT: B 1280 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8086 (mm-30) REVERT: B 1344 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: B 1363 MET cc_start: 0.6924 (ptm) cc_final: 0.6567 (ptm) REVERT: B 1370 ASP cc_start: 0.8025 (m-30) cc_final: 0.7676 (m-30) REVERT: B 1448 MET cc_start: 0.8111 (mtm) cc_final: 0.7620 (mtm) REVERT: B 1613 GLU cc_start: 0.7111 (tt0) cc_final: 0.6750 (tt0) REVERT: B 1798 GLN cc_start: 0.8485 (tp40) cc_final: 0.8212 (tp-100) REVERT: B 1879 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 2035 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8009 (tp-100) REVERT: B 2047 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.8104 (mtt180) REVERT: B 2324 VAL cc_start: 0.7455 (m) cc_final: 0.7207 (p) REVERT: B 2332 LEU cc_start: 0.8825 (mt) cc_final: 0.8559 (mp) REVERT: B 2513 PHE cc_start: 0.8366 (t80) cc_final: 0.8029 (t80) REVERT: C 468 ASP cc_start: 0.7488 (m-30) cc_final: 0.7091 (m-30) REVERT: C 476 LEU cc_start: 0.7941 (mm) cc_final: 0.7713 (mt) REVERT: C 1115 ASP cc_start: 0.8016 (m-30) cc_final: 0.7801 (m-30) REVERT: C 1208 ASP cc_start: 0.7351 (m-30) cc_final: 0.7005 (m-30) REVERT: C 1245 LEU cc_start: 0.8975 (tp) cc_final: 0.8730 (tp) REVERT: C 1448 MET cc_start: 0.8187 (mtm) cc_final: 0.7926 (mtm) REVERT: C 1647 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7657 (tt) REVERT: C 1671 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7821 (mm-40) REVERT: C 1693 ASN cc_start: 0.8374 (t0) cc_final: 0.8090 (t0) REVERT: C 1930 ASN cc_start: 0.7586 (p0) cc_final: 0.7277 (p0) REVERT: C 1955 ASN cc_start: 0.8634 (m-40) cc_final: 0.8433 (m-40) REVERT: C 2035 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7942 (tp-100) REVERT: C 2118 GLU cc_start: 0.7829 (tp30) cc_final: 0.7621 (tp30) REVERT: C 2457 THR cc_start: 0.8931 (t) cc_final: 0.8613 (p) REVERT: D 73 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8752 (tppt) REVERT: D 100 GLU cc_start: 0.7762 (tp30) cc_final: 0.7549 (tp30) REVERT: D 291 ASP cc_start: 0.8290 (t0) cc_final: 0.8079 (t0) REVERT: D 657 LEU cc_start: 0.8550 (mm) cc_final: 0.8345 (mm) REVERT: D 753 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: D 1116 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8262 (ttp-170) REVERT: D 1798 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8277 (tp-100) REVERT: D 1902 ASN cc_start: 0.7649 (p0) cc_final: 0.7439 (p0) REVERT: D 1906 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6917 (mm-30) REVERT: D 1939 GLN cc_start: 0.8374 (tp40) cc_final: 0.8011 (tp40) REVERT: D 1955 ASN cc_start: 0.8492 (m-40) cc_final: 0.8210 (m110) REVERT: D 2293 LYS cc_start: 0.8201 (tptp) cc_final: 0.7836 (tptm) REVERT: D 2326 TYR cc_start: 0.6960 (t80) cc_final: 0.6718 (t80) outliers start: 151 outliers final: 79 residues processed: 1990 average time/residue: 1.6485 time to fit residues: 5627.7071 Evaluate side-chains 1891 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1803 time to evaluate : 8.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1448 MET Chi-restraints excluded: chain A residue 1487 ASN Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2343 ILE Chi-restraints excluded: chain A residue 2363 THR Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1367 SER Chi-restraints excluded: chain B residue 1389 SER Chi-restraints excluded: chain B residue 1487 ASN Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1894 CYS Chi-restraints excluded: chain B residue 2133 MET Chi-restraints excluded: chain B residue 2327 ILE Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1487 ASN Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2210 ASN Chi-restraints excluded: chain C residue 2546 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 565 GLU Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 590 LEU Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1674 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2479 ILE Chi-restraints excluded: chain D residue 2538 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 452 optimal weight: 0.4980 chunk 252 optimal weight: 2.9990 chunk 677 optimal weight: 0.5980 chunk 554 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 815 optimal weight: 0.3980 chunk 880 optimal weight: 1.9990 chunk 725 optimal weight: 0.9980 chunk 808 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 653 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1203 HIS A1327 ASN A1790 HIS ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2135 GLN A2145 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 ASN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1436 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2550 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN C 601 ASN C1650 HIS ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2472 ASN D 601 ASN D 642 HIS D1327 ASN D2123 GLN D2135 GLN D2216 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 73644 Z= 0.163 Angle : 0.442 7.247 99580 Z= 0.234 Chirality : 0.034 0.157 11428 Planarity : 0.003 0.099 12652 Dihedral : 4.688 87.242 9918 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.43 % Allowed : 14.46 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.09), residues: 8876 helix: 3.18 (0.07), residues: 5736 sheet: 0.15 (0.20), residues: 700 loop : 0.29 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2196 HIS 0.011 0.001 HIS C1650 PHE 0.014 0.001 PHE A2209 TYR 0.019 0.001 TYR C1432 ARG 0.005 0.000 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1952 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1838 time to evaluate : 8.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.7071 (tp30) cc_final: 0.6814 (tp30) REVERT: A 616 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 636 ASP cc_start: 0.7985 (t0) cc_final: 0.7604 (t0) REVERT: A 714 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6766 (mp0) REVERT: A 753 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 1271 ASN cc_start: 0.8119 (t0) cc_final: 0.7839 (t0) REVERT: A 1464 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 1648 ILE cc_start: 0.8668 (mm) cc_final: 0.8447 (mt) REVERT: A 1671 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7555 (mm-40) REVERT: A 1910 PHE cc_start: 0.7864 (t80) cc_final: 0.7596 (t80) REVERT: A 1947 TYR cc_start: 0.8058 (m-10) cc_final: 0.7787 (m-10) REVERT: A 2528 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8120 (tt0) REVERT: A 2604 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6844 (ttt90) REVERT: B 93 LEU cc_start: 0.8366 (mm) cc_final: 0.8153 (mt) REVERT: B 554 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7627 (mtt180) REVERT: B 1116 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8416 (ttp80) REVERT: B 1280 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 1344 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6956 (t-170) REVERT: B 1363 MET cc_start: 0.6828 (ptm) cc_final: 0.6441 (ptm) REVERT: B 1448 MET cc_start: 0.8082 (mtm) cc_final: 0.7625 (mtm) REVERT: B 1613 GLU cc_start: 0.7057 (tt0) cc_final: 0.6689 (tt0) REVERT: B 1798 GLN cc_start: 0.8484 (tp40) cc_final: 0.8189 (tp-100) REVERT: B 2016 ILE cc_start: 0.8975 (tp) cc_final: 0.8677 (mt) REVERT: B 2035 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7929 (tp-100) REVERT: B 2293 LYS cc_start: 0.8338 (tppt) cc_final: 0.8101 (tptm) REVERT: B 2324 VAL cc_start: 0.7388 (m) cc_final: 0.7065 (p) REVERT: B 2332 LEU cc_start: 0.8789 (mt) cc_final: 0.8515 (mp) REVERT: B 2513 PHE cc_start: 0.8329 (t80) cc_final: 0.8106 (t80) REVERT: C 62 MET cc_start: 0.7918 (ttp) cc_final: 0.7707 (ttm) REVERT: C 172 SER cc_start: 0.8543 (p) cc_final: 0.8337 (m) REVERT: C 249 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 476 LEU cc_start: 0.7921 (mm) cc_final: 0.7670 (mt) REVERT: C 614 GLU cc_start: 0.7700 (mp0) cc_final: 0.7398 (mp0) REVERT: C 713 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8178 (mt0) REVERT: C 1115 ASP cc_start: 0.8068 (m-30) cc_final: 0.7821 (m-30) REVERT: C 1208 ASP cc_start: 0.7496 (m-30) cc_final: 0.6926 (m-30) REVERT: C 1448 MET cc_start: 0.8175 (mtm) cc_final: 0.7888 (mtm) REVERT: C 1647 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7562 (tt) REVERT: C 1693 ASN cc_start: 0.8382 (t0) cc_final: 0.8081 (t0) REVERT: C 1879 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8001 (mm) REVERT: C 1909 GLN cc_start: 0.8289 (mt0) cc_final: 0.7610 (mt0) REVERT: C 1930 ASN cc_start: 0.7707 (p0) cc_final: 0.7236 (p0) REVERT: C 2035 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7878 (tp-100) REVERT: C 2154 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8121 (ttt-90) REVERT: C 2457 THR cc_start: 0.8914 (t) cc_final: 0.8662 (p) REVERT: D 73 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8766 (tppt) REVERT: D 93 LEU cc_start: 0.8350 (mm) cc_final: 0.8008 (mp) REVERT: D 636 ASP cc_start: 0.8083 (t0) cc_final: 0.7666 (t0) REVERT: D 657 LEU cc_start: 0.8500 (mm) cc_final: 0.8289 (mm) REVERT: D 753 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: D 1116 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8280 (ttp-170) REVERT: D 1122 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 1395 ASP cc_start: 0.7793 (t0) cc_final: 0.7572 (m-30) REVERT: D 1798 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8257 (tp-100) REVERT: D 1879 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 1955 ASN cc_start: 0.8409 (m-40) cc_final: 0.8208 (m110) outliers start: 114 outliers final: 70 residues processed: 1889 average time/residue: 1.5730 time to fit residues: 5041.7499 Evaluate side-chains 1880 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1803 time to evaluate : 8.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 1208 ASP Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2546 ASP Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1252 LEU Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1389 SER Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1625 GLU Chi-restraints excluded: chain B residue 1674 LEU Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2133 MET Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1614 LEU Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 1982 CYS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1913 ILE Chi-restraints excluded: chain D residue 1938 ILE Chi-restraints excluded: chain D residue 1982 CYS Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2538 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 805 optimal weight: 9.9990 chunk 612 optimal weight: 1.9990 chunk 423 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 389 optimal weight: 1.9990 chunk 547 optimal weight: 9.9990 chunk 818 optimal weight: 6.9990 chunk 866 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 775 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 601 ASN A 661 ASN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN A1622 HIS ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1419 HIS B1436 HIS B1622 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2120 HIS B2135 GLN ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN C 562 HIS C 601 ASN C 602 ASN ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2135 GLN C2472 ASN D 195 HIS ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 HIS D 869 ASN D1622 HIS ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 73644 Z= 0.454 Angle : 0.540 6.619 99580 Z= 0.296 Chirality : 0.038 0.175 11428 Planarity : 0.004 0.066 12652 Dihedral : 4.888 87.890 9918 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.22 % Allowed : 14.46 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.09), residues: 8876 helix: 2.80 (0.07), residues: 5732 sheet: -0.29 (0.20), residues: 708 loop : -0.07 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 219 HIS 0.012 0.001 HIS D 868 PHE 0.021 0.002 PHE C2602 TYR 0.026 0.001 TYR C2381 ARG 0.009 0.001 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 2041 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1864 time to evaluate : 8.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 697 THR cc_start: 0.8180 (m) cc_final: 0.7843 (p) REVERT: A 714 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6783 (mp0) REVERT: A 753 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: A 1305 THR cc_start: 0.8351 (m) cc_final: 0.8150 (p) REVERT: A 1464 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 1626 LEU cc_start: 0.8844 (mp) cc_final: 0.8623 (mm) REVERT: A 1658 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6500 (mt-10) REVERT: A 1891 PHE cc_start: 0.7017 (t80) cc_final: 0.6807 (t80) REVERT: A 2035 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 2285 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7758 (tt) REVERT: A 2388 PHE cc_start: 0.8228 (t80) cc_final: 0.8027 (t80) REVERT: A 2510 ASN cc_start: 0.8562 (m-40) cc_final: 0.8310 (m110) REVERT: A 2522 ASP cc_start: 0.8721 (t0) cc_final: 0.8483 (t0) REVERT: A 2528 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8190 (tt0) REVERT: B 93 LEU cc_start: 0.8433 (mm) cc_final: 0.8206 (mt) REVERT: B 100 GLU cc_start: 0.8029 (tp30) cc_final: 0.7524 (tp30) REVERT: B 402 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8139 (t0) REVERT: B 600 HIS cc_start: 0.7012 (t70) cc_final: 0.6414 (t70) REVERT: B 730 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7057 (ttm110) REVERT: B 1116 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8481 (ttp80) REVERT: B 1230 GLN cc_start: 0.8764 (mt0) cc_final: 0.8480 (mt0) REVERT: B 1344 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7289 (t-90) REVERT: B 1363 MET cc_start: 0.6904 (ptm) cc_final: 0.6481 (ptm) REVERT: B 1798 GLN cc_start: 0.8541 (tp40) cc_final: 0.8306 (tp-100) REVERT: B 1879 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8024 (mm) REVERT: B 2016 ILE cc_start: 0.8988 (tp) cc_final: 0.8706 (mt) REVERT: B 2035 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7962 (tm-30) REVERT: B 2293 LYS cc_start: 0.8357 (tppt) cc_final: 0.8021 (tptp) REVERT: B 2332 LEU cc_start: 0.8892 (mt) cc_final: 0.8605 (mp) REVERT: B 2513 PHE cc_start: 0.8457 (t80) cc_final: 0.7933 (t80) REVERT: C 441 ASP cc_start: 0.7664 (m-30) cc_final: 0.7444 (m-30) REVERT: C 468 ASP cc_start: 0.7482 (m-30) cc_final: 0.7062 (m-30) REVERT: C 476 LEU cc_start: 0.7928 (mm) cc_final: 0.7717 (mt) REVERT: C 614 GLU cc_start: 0.7779 (mp0) cc_final: 0.7501 (mp0) REVERT: C 713 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8269 (mt0) REVERT: C 1044 MET cc_start: 0.7730 (mmm) cc_final: 0.7492 (mmm) REVERT: C 1046 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 1048 ASP cc_start: 0.6785 (p0) cc_final: 0.6546 (p0) REVERT: C 1208 ASP cc_start: 0.7604 (m-30) cc_final: 0.7021 (m-30) REVERT: C 1245 LEU cc_start: 0.8970 (tp) cc_final: 0.8746 (tp) REVERT: C 1658 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6209 (mt-10) REVERT: C 1693 ASN cc_start: 0.8451 (t0) cc_final: 0.8155 (t0) REVERT: C 1798 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7969 (tp-100) REVERT: C 1870 MET cc_start: 0.8337 (tpt) cc_final: 0.7601 (tpt) REVERT: C 1930 ASN cc_start: 0.7800 (p0) cc_final: 0.7398 (p0) REVERT: C 2035 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8140 (tp-100) REVERT: C 2498 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 93 LEU cc_start: 0.8382 (mm) cc_final: 0.8092 (mt) REVERT: D 476 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7635 (mt) REVERT: D 504 GLU cc_start: 0.7858 (mp0) cc_final: 0.7641 (mp0) REVERT: D 636 ASP cc_start: 0.8128 (t0) cc_final: 0.7690 (t0) REVERT: D 657 LEU cc_start: 0.8524 (mm) cc_final: 0.8311 (mm) REVERT: D 753 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: D 795 THR cc_start: 0.9163 (m) cc_final: 0.8935 (t) REVERT: D 1116 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8312 (ttp-170) REVERT: D 1122 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 1280 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8026 (mm-30) REVERT: D 1395 ASP cc_start: 0.7888 (t0) cc_final: 0.7642 (m-30) REVERT: D 2035 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7845 (tp-100) REVERT: D 2117 TYR cc_start: 0.6835 (m-10) cc_final: 0.6600 (m-10) REVERT: D 2196 TRP cc_start: 0.8656 (t60) cc_final: 0.8445 (t-100) REVERT: D 2484 SER cc_start: 0.8795 (t) cc_final: 0.8541 (p) REVERT: D 2522 ASP cc_start: 0.8696 (t0) cc_final: 0.8436 (t0) outliers start: 177 outliers final: 117 residues processed: 1961 average time/residue: 1.6407 time to fit residues: 5504.3853 Evaluate side-chains 1927 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1801 time to evaluate : 7.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1487 ASN Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1622 HIS Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1918 THR Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2225 TYR Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2363 THR Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1487 ASN Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1622 HIS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1894 CYS Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2133 MET Chi-restraints excluded: chain B residue 2225 TYR Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2363 THR Chi-restraints excluded: chain B residue 2479 ILE Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1487 ASN Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1730 LYS Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 1971 THR Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2546 ASP Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 869 ASN Chi-restraints excluded: chain D residue 990 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1210 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1622 HIS Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1938 ILE Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2289 ASN Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 721 optimal weight: 4.9990 chunk 491 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 644 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 739 optimal weight: 2.9990 chunk 598 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 442 optimal weight: 1.9990 chunk 777 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 ASN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 HIS A1327 ASN A1419 HIS A1622 HIS ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2510 ASN B 63 ASN B 108 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS B1622 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2023 GLN C2510 ASN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN D1622 HIS ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 73644 Z= 0.240 Angle : 0.467 7.957 99580 Z= 0.250 Chirality : 0.035 0.163 11428 Planarity : 0.003 0.064 12652 Dihedral : 4.731 86.239 9918 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.90 % Allowed : 15.64 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.09), residues: 8876 helix: 2.96 (0.07), residues: 5752 sheet: -0.14 (0.20), residues: 692 loop : -0.09 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C2204 HIS 0.014 0.001 HIS A1622 PHE 0.015 0.001 PHE C2513 TYR 0.020 0.001 TYR D1432 ARG 0.007 0.000 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1946 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1794 time to evaluate : 8.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7504 (mt) REVERT: A 616 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 636 ASP cc_start: 0.8033 (t0) cc_final: 0.7625 (t0) REVERT: A 691 GLU cc_start: 0.5839 (pm20) cc_final: 0.5322 (pm20) REVERT: A 714 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6774 (mp0) REVERT: A 730 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7093 (ttm110) REVERT: A 753 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: A 795 THR cc_start: 0.9108 (m) cc_final: 0.8560 (p) REVERT: A 1305 THR cc_start: 0.8341 (m) cc_final: 0.8115 (p) REVERT: A 1464 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 2035 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7835 (tm-30) REVERT: A 2285 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7602 (tt) REVERT: A 2388 PHE cc_start: 0.8185 (t80) cc_final: 0.7952 (t80) REVERT: A 2520 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: A 2522 ASP cc_start: 0.8702 (t0) cc_final: 0.8469 (t0) REVERT: A 2528 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8162 (tt0) REVERT: B 93 LEU cc_start: 0.8435 (mm) cc_final: 0.8174 (mt) REVERT: B 100 GLU cc_start: 0.7931 (tp30) cc_final: 0.7434 (tp30) REVERT: B 402 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8093 (t0) REVERT: B 600 HIS cc_start: 0.7008 (t70) cc_final: 0.6367 (t70) REVERT: B 713 GLN cc_start: 0.8655 (mm110) cc_final: 0.8188 (mt0) REVERT: B 730 ARG cc_start: 0.7446 (ttp80) cc_final: 0.7088 (ttm110) REVERT: B 1116 ARG cc_start: 0.8789 (ttp-170) cc_final: 0.8482 (ttp80) REVERT: B 1344 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7196 (t-90) REVERT: B 1798 GLN cc_start: 0.8556 (tp40) cc_final: 0.8344 (tp-100) REVERT: B 1879 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8031 (mm) REVERT: B 2016 ILE cc_start: 0.8992 (tp) cc_final: 0.8720 (mt) REVERT: B 2026 VAL cc_start: 0.8749 (p) cc_final: 0.8447 (m) REVERT: B 2035 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8038 (tp-100) REVERT: B 2332 LEU cc_start: 0.8879 (mt) cc_final: 0.8584 (mp) REVERT: B 2513 PHE cc_start: 0.8359 (t80) cc_final: 0.8026 (t80) REVERT: B 2528 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7965 (mt0) REVERT: C 468 ASP cc_start: 0.7463 (m-30) cc_final: 0.7052 (m-30) REVERT: C 476 LEU cc_start: 0.7932 (mm) cc_final: 0.7654 (mt) REVERT: C 614 GLU cc_start: 0.7759 (mp0) cc_final: 0.7514 (mp0) REVERT: C 671 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7606 (mtm180) REVERT: C 713 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8249 (mt0) REVERT: C 753 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: C 1046 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6952 (mm-30) REVERT: C 1048 ASP cc_start: 0.6772 (p0) cc_final: 0.6450 (p0) REVERT: C 1208 ASP cc_start: 0.7635 (m-30) cc_final: 0.7043 (m-30) REVERT: C 1509 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (pp) REVERT: C 1658 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6208 (mt-10) REVERT: C 1689 MET cc_start: 0.6844 (tmm) cc_final: 0.6587 (tmt) REVERT: C 1693 ASN cc_start: 0.8462 (t0) cc_final: 0.8140 (t0) REVERT: C 1798 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7963 (tp-100) REVERT: C 1879 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8200 (mm) REVERT: C 1930 ASN cc_start: 0.7825 (p0) cc_final: 0.7389 (p0) REVERT: C 2035 GLN cc_start: 0.8361 (tp-100) cc_final: 0.8079 (tp-100) REVERT: C 2204 TRP cc_start: 0.8455 (m100) cc_final: 0.8172 (m100) REVERT: C 2384 SER cc_start: 0.8523 (t) cc_final: 0.8245 (p) REVERT: D 93 LEU cc_start: 0.8362 (mm) cc_final: 0.8090 (mt) REVERT: D 636 ASP cc_start: 0.8116 (t0) cc_final: 0.7663 (t0) REVERT: D 753 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7049 (mp10) REVERT: D 795 THR cc_start: 0.9121 (m) cc_final: 0.8891 (t) REVERT: D 1122 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7994 (mm-30) REVERT: D 1262 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8120 (mt-10) REVERT: D 1344 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7093 (t70) REVERT: D 1395 ASP cc_start: 0.7867 (t0) cc_final: 0.7628 (m-30) REVERT: D 1433 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 1798 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8200 (tp-100) REVERT: D 1879 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8174 (mm) REVERT: D 2035 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7836 (tp-100) REVERT: D 2484 SER cc_start: 0.8782 (t) cc_final: 0.8531 (p) REVERT: D 2522 ASP cc_start: 0.8640 (t0) cc_final: 0.8251 (t0) outliers start: 152 outliers final: 111 residues processed: 1870 average time/residue: 1.6087 time to fit residues: 5138.9203 Evaluate side-chains 1902 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1775 time to evaluate : 8.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 1222 MET Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 789 ASP Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1674 LEU Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2400 ASP Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2565 MET Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 869 ASN Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1803 THR Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 742 ASP Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1047 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1252 LEU Chi-restraints excluded: chain D residue 1288 HIS Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1433 THR Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1955 ASN Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2398 GLU Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2520 PHE Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 291 optimal weight: 2.9990 chunk 779 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 508 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 866 optimal weight: 3.9990 chunk 719 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 286 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN C1515 GLN C1622 HIS ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN D1327 ASN ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 73644 Z= 0.393 Angle : 0.505 7.163 99580 Z= 0.274 Chirality : 0.036 0.165 11428 Planarity : 0.003 0.065 12652 Dihedral : 4.820 87.412 9918 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.31 % Allowed : 16.10 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.09), residues: 8876 helix: 2.85 (0.07), residues: 5740 sheet: -0.43 (0.20), residues: 708 loop : -0.22 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D2601 HIS 0.011 0.001 HIS C 868 PHE 0.016 0.001 PHE C2602 TYR 0.028 0.001 TYR A2341 ARG 0.009 0.000 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 2008 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1824 time to evaluate : 8.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.7675 (mp0) cc_final: 0.7424 (mp0) REVERT: A 616 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7626 (mm-30) REVERT: A 636 ASP cc_start: 0.8049 (t0) cc_final: 0.7625 (t0) REVERT: A 691 GLU cc_start: 0.5876 (pm20) cc_final: 0.5502 (pm20) REVERT: A 697 THR cc_start: 0.8295 (m) cc_final: 0.7955 (p) REVERT: A 714 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6814 (mp0) REVERT: A 730 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7105 (ttm110) REVERT: A 753 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: A 795 THR cc_start: 0.9131 (m) cc_final: 0.8568 (p) REVERT: A 1305 THR cc_start: 0.8320 (m) cc_final: 0.8099 (p) REVERT: A 1433 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 1464 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 1798 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8079 (tp-100) REVERT: A 2285 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 2388 PHE cc_start: 0.8215 (t80) cc_final: 0.7890 (t80) REVERT: A 2457 THR cc_start: 0.8601 (m) cc_final: 0.8367 (t) REVERT: A 2520 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: A 2522 ASP cc_start: 0.8744 (t0) cc_final: 0.8505 (t0) REVERT: A 2528 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8176 (tt0) REVERT: B 100 GLU cc_start: 0.7993 (tp30) cc_final: 0.7467 (tp30) REVERT: B 402 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8195 (t0) REVERT: B 600 HIS cc_start: 0.7050 (t70) cc_final: 0.6395 (t70) REVERT: B 713 GLN cc_start: 0.8677 (mm110) cc_final: 0.8220 (mt0) REVERT: B 730 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7063 (ttm110) REVERT: B 1103 ASP cc_start: 0.8246 (m-30) cc_final: 0.7833 (m-30) REVERT: B 1116 ARG cc_start: 0.8792 (ttp-170) cc_final: 0.8501 (ttp80) REVERT: B 1344 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: B 1363 MET cc_start: 0.6898 (ptm) cc_final: 0.6469 (ptm) REVERT: B 1799 GLU cc_start: 0.7724 (tp30) cc_final: 0.7378 (tp30) REVERT: B 1879 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (mm) REVERT: B 2016 ILE cc_start: 0.9003 (tp) cc_final: 0.8734 (mt) REVERT: B 2026 VAL cc_start: 0.8764 (p) cc_final: 0.8470 (m) REVERT: B 2035 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8108 (tp-100) REVERT: B 2214 PHE cc_start: 0.7523 (m-80) cc_final: 0.7179 (m-80) REVERT: B 2332 LEU cc_start: 0.8904 (mt) cc_final: 0.8611 (mp) REVERT: B 2513 PHE cc_start: 0.8462 (t80) cc_final: 0.8079 (t80) REVERT: B 2528 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7990 (mt0) REVERT: C 441 ASP cc_start: 0.7646 (m-30) cc_final: 0.7433 (m-30) REVERT: C 468 ASP cc_start: 0.7492 (m-30) cc_final: 0.7085 (m-30) REVERT: C 476 LEU cc_start: 0.7920 (mm) cc_final: 0.7689 (mt) REVERT: C 671 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (mtm180) REVERT: C 713 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8293 (mt0) REVERT: C 753 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: C 1046 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6969 (mm-30) REVERT: C 1048 ASP cc_start: 0.6998 (p0) cc_final: 0.6714 (p0) REVERT: C 1208 ASP cc_start: 0.7645 (m-30) cc_final: 0.7070 (m-30) REVERT: C 1509 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7847 (pp) REVERT: C 1648 ILE cc_start: 0.8759 (mm) cc_final: 0.8516 (mt) REVERT: C 1689 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6640 (tmt) REVERT: C 1693 ASN cc_start: 0.8495 (t0) cc_final: 0.8189 (t0) REVERT: C 1798 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7986 (tp-100) REVERT: C 1930 ASN cc_start: 0.7836 (p0) cc_final: 0.7407 (p0) REVERT: C 2035 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8164 (tp-100) REVERT: C 2117 TYR cc_start: 0.6874 (m-10) cc_final: 0.6636 (m-10) REVERT: C 2384 SER cc_start: 0.8592 (t) cc_final: 0.8292 (p) REVERT: C 2498 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8369 (tt) REVERT: C 2593 MET cc_start: 0.7792 (mmm) cc_final: 0.7532 (mmm) REVERT: D 93 LEU cc_start: 0.8424 (mm) cc_final: 0.8144 (mt) REVERT: D 636 ASP cc_start: 0.8124 (t0) cc_final: 0.7678 (t0) REVERT: D 753 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: D 795 THR cc_start: 0.9123 (m) cc_final: 0.8882 (t) REVERT: D 1103 ASP cc_start: 0.8303 (m-30) cc_final: 0.7918 (m-30) REVERT: D 1208 ASP cc_start: 0.7651 (m-30) cc_final: 0.7104 (m-30) REVERT: D 1262 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8138 (mt-10) REVERT: D 1344 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7275 (t70) REVERT: D 1395 ASP cc_start: 0.7881 (t0) cc_final: 0.7630 (m-30) REVERT: D 1658 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6384 (mt-10) REVERT: D 1798 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8048 (tp-100) REVERT: D 2035 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7940 (tp-100) REVERT: D 2196 TRP cc_start: 0.8583 (t-100) cc_final: 0.8355 (t-100) REVERT: D 2293 LYS cc_start: 0.8303 (tptm) cc_final: 0.7909 (tppp) REVERT: D 2295 VAL cc_start: 0.8556 (t) cc_final: 0.8326 (p) REVERT: D 2350 TYR cc_start: 0.7542 (t80) cc_final: 0.7272 (m-80) REVERT: D 2484 SER cc_start: 0.8840 (t) cc_final: 0.8577 (p) REVERT: D 2522 ASP cc_start: 0.8658 (t0) cc_final: 0.8306 (t0) outliers start: 184 outliers final: 134 residues processed: 1921 average time/residue: 1.5299 time to fit residues: 4998.4669 Evaluate side-chains 1943 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1794 time to evaluate : 8.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2120 HIS Chi-restraints excluded: chain A residue 2225 TYR Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2363 THR Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2557 GLU Chi-restraints excluded: chain A residue 2565 MET Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 1208 ASP Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1894 CYS Chi-restraints excluded: chain B residue 1955 ASN Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2225 TYR Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2400 ASP Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2554 SER Chi-restraints excluded: chain B residue 2565 MET Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 353 CYS Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1626 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1803 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1210 LEU Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1955 ASN Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 835 optimal weight: 5.9990 chunk 97 optimal weight: 0.0470 chunk 493 optimal weight: 0.9980 chunk 633 optimal weight: 6.9990 chunk 490 optimal weight: 0.9980 chunk 729 optimal weight: 5.9990 chunk 484 optimal weight: 0.0370 chunk 863 optimal weight: 5.9990 chunk 540 optimal weight: 2.9990 chunk 526 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN A1419 HIS ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 ASN ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 ASN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 HIS D1327 ASN ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 73644 Z= 0.203 Angle : 0.461 7.637 99580 Z= 0.245 Chirality : 0.034 0.177 11428 Planarity : 0.003 0.054 12652 Dihedral : 4.625 89.488 9918 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.95 % Allowed : 16.73 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.09), residues: 8876 helix: 2.99 (0.07), residues: 5756 sheet: -0.30 (0.20), residues: 700 loop : -0.14 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C2204 HIS 0.012 0.001 HIS C1622 PHE 0.020 0.001 PHE C2513 TYR 0.025 0.001 TYR D 71 ARG 0.008 0.000 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1959 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1803 time to evaluate : 8.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.7672 (mp0) cc_final: 0.7439 (mp0) REVERT: A 616 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 636 ASP cc_start: 0.8023 (t0) cc_final: 0.7611 (t0) REVERT: A 691 GLU cc_start: 0.5936 (pm20) cc_final: 0.5566 (pm20) REVERT: A 697 THR cc_start: 0.8302 (m) cc_final: 0.7967 (p) REVERT: A 714 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6771 (mp0) REVERT: A 730 ARG cc_start: 0.7429 (ttp80) cc_final: 0.7108 (ttm110) REVERT: A 753 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: A 795 THR cc_start: 0.9097 (m) cc_final: 0.8550 (p) REVERT: A 1206 MET cc_start: 0.9114 (tpp) cc_final: 0.8901 (mmt) REVERT: A 1210 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8952 (tp) REVERT: A 1305 THR cc_start: 0.8302 (m) cc_final: 0.8077 (p) REVERT: A 1433 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 1464 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8759 (tt) REVERT: A 1619 ASP cc_start: 0.8248 (t0) cc_final: 0.7733 (t0) REVERT: A 1798 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8068 (tp-100) REVERT: A 2035 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7877 (tp-100) REVERT: A 2285 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 2388 PHE cc_start: 0.8213 (t80) cc_final: 0.7969 (t80) REVERT: A 2457 THR cc_start: 0.8619 (m) cc_final: 0.8387 (t) REVERT: A 2520 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: A 2522 ASP cc_start: 0.8728 (t0) cc_final: 0.8453 (t0) REVERT: A 2528 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8151 (tt0) REVERT: B 100 GLU cc_start: 0.7918 (tp30) cc_final: 0.7418 (tp30) REVERT: B 402 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 600 HIS cc_start: 0.7021 (t70) cc_final: 0.6379 (t70) REVERT: B 713 GLN cc_start: 0.8650 (mm110) cc_final: 0.8196 (mt0) REVERT: B 730 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7060 (ttm110) REVERT: B 1103 ASP cc_start: 0.8235 (m-30) cc_final: 0.7823 (m-30) REVERT: B 1116 ARG cc_start: 0.8780 (ttp-170) cc_final: 0.8495 (ttp80) REVERT: B 1344 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7263 (t-90) REVERT: B 1363 MET cc_start: 0.6833 (ptm) cc_final: 0.6408 (ptm) REVERT: B 1879 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 2016 ILE cc_start: 0.8997 (tp) cc_final: 0.8736 (mt) REVERT: B 2026 VAL cc_start: 0.8757 (p) cc_final: 0.8462 (m) REVERT: B 2035 GLN cc_start: 0.8260 (tp-100) cc_final: 0.8058 (tp-100) REVERT: B 2332 LEU cc_start: 0.8881 (mt) cc_final: 0.8580 (mp) REVERT: B 2384 SER cc_start: 0.8515 (t) cc_final: 0.8200 (p) REVERT: B 2513 PHE cc_start: 0.8360 (t80) cc_final: 0.8075 (t80) REVERT: B 2528 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7974 (mt0) REVERT: C 468 ASP cc_start: 0.7439 (m-30) cc_final: 0.7055 (m-30) REVERT: C 476 LEU cc_start: 0.7919 (mm) cc_final: 0.7623 (mt) REVERT: C 713 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8261 (mt0) REVERT: C 753 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: C 1046 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6848 (mm-30) REVERT: C 1048 ASP cc_start: 0.6947 (p0) cc_final: 0.6548 (p0) REVERT: C 1208 ASP cc_start: 0.7659 (m-30) cc_final: 0.7088 (m-30) REVERT: C 1222 MET cc_start: 0.7397 (mtt) cc_final: 0.7146 (mtt) REVERT: C 1509 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7824 (pp) REVERT: C 1648 ILE cc_start: 0.8746 (mm) cc_final: 0.8506 (mt) REVERT: C 1689 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6635 (tmt) REVERT: C 1693 ASN cc_start: 0.8489 (t0) cc_final: 0.8175 (t0) REVERT: C 1798 GLN cc_start: 0.8217 (tp-100) cc_final: 0.8005 (tp-100) REVERT: C 1870 MET cc_start: 0.8323 (tpt) cc_final: 0.7628 (tpt) REVERT: C 1930 ASN cc_start: 0.7800 (p0) cc_final: 0.7347 (p0) REVERT: C 2035 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8141 (tp-100) REVERT: C 2154 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8336 (tmm-80) REVERT: C 2332 LEU cc_start: 0.8904 (mt) cc_final: 0.8590 (mp) REVERT: C 2384 SER cc_start: 0.8557 (t) cc_final: 0.8264 (p) REVERT: C 2593 MET cc_start: 0.7763 (mmm) cc_final: 0.7528 (mmm) REVERT: D 93 LEU cc_start: 0.8402 (mm) cc_final: 0.8144 (mt) REVERT: D 636 ASP cc_start: 0.8111 (t0) cc_final: 0.7657 (t0) REVERT: D 642 HIS cc_start: 0.8115 (t70) cc_final: 0.7691 (t70) REVERT: D 753 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: D 795 THR cc_start: 0.9096 (m) cc_final: 0.8815 (t) REVERT: D 1262 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8123 (mt-10) REVERT: D 1297 VAL cc_start: 0.8346 (p) cc_final: 0.8142 (t) REVERT: D 1344 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7256 (t70) REVERT: D 1395 ASP cc_start: 0.7853 (t0) cc_final: 0.7613 (m-30) REVERT: D 1433 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8494 (p) REVERT: D 1798 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8036 (tp-100) REVERT: D 2035 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7910 (tp-100) REVERT: D 2350 TYR cc_start: 0.7546 (t80) cc_final: 0.7295 (m-80) REVERT: D 2370 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8689 (mm) REVERT: D 2484 SER cc_start: 0.8822 (t) cc_final: 0.8571 (p) REVERT: D 2522 ASP cc_start: 0.8611 (t0) cc_final: 0.8240 (t0) REVERT: D 2545 ARG cc_start: 0.8645 (tpp-160) cc_final: 0.8403 (ttt-90) outliers start: 156 outliers final: 121 residues processed: 1885 average time/residue: 1.5916 time to fit residues: 5146.1565 Evaluate side-chains 1929 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1792 time to evaluate : 8.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2120 HIS Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2565 MET Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1602 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1674 LEU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2210 ASN Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2400 ASP Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2554 SER Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1730 LYS Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1803 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 990 LEU Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1433 THR Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1982 CYS Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2398 GLU Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2520 PHE Chi-restraints excluded: chain D residue 2541 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 534 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 515 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 549 optimal weight: 0.0060 chunk 588 optimal weight: 1.9990 chunk 426 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 678 optimal weight: 4.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1622 HIS ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 73644 Z= 0.235 Angle : 0.466 9.260 99580 Z= 0.248 Chirality : 0.035 0.162 11428 Planarity : 0.003 0.055 12652 Dihedral : 4.590 89.580 9918 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.99 % Allowed : 17.12 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.09), residues: 8876 helix: 3.03 (0.07), residues: 5756 sheet: -0.27 (0.20), residues: 692 loop : -0.17 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C2204 HIS 0.021 0.001 HIS A2120 PHE 0.017 0.001 PHE C2513 TYR 0.026 0.001 TYR D 71 ARG 0.010 0.000 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1973 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1814 time to evaluate : 8.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 LEU cc_start: 0.7709 (mm) cc_final: 0.7495 (mt) REVERT: A 504 GLU cc_start: 0.7693 (mp0) cc_final: 0.7460 (mp0) REVERT: A 616 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 636 ASP cc_start: 0.8018 (t0) cc_final: 0.7604 (t0) REVERT: A 691 GLU cc_start: 0.6004 (pm20) cc_final: 0.5695 (pm20) REVERT: A 697 THR cc_start: 0.8316 (m) cc_final: 0.7986 (p) REVERT: A 714 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6746 (mp0) REVERT: A 730 ARG cc_start: 0.7424 (ttp80) cc_final: 0.7100 (ttm110) REVERT: A 753 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: A 795 THR cc_start: 0.9096 (m) cc_final: 0.8550 (p) REVERT: A 1122 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7239 (tm-30) REVERT: A 1206 MET cc_start: 0.9099 (tpp) cc_final: 0.8887 (mmt) REVERT: A 1222 MET cc_start: 0.8019 (mmm) cc_final: 0.7784 (mmm) REVERT: A 1305 THR cc_start: 0.8300 (m) cc_final: 0.8072 (p) REVERT: A 1433 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 1464 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8763 (tt) REVERT: A 1619 ASP cc_start: 0.8241 (t0) cc_final: 0.7754 (t0) REVERT: A 1798 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8097 (tp-100) REVERT: A 2035 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7894 (tp-100) REVERT: A 2285 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 2457 THR cc_start: 0.8644 (m) cc_final: 0.8419 (t) REVERT: A 2520 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: A 2522 ASP cc_start: 0.8717 (t0) cc_final: 0.8448 (t0) REVERT: A 2528 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8178 (tt0) REVERT: B 100 GLU cc_start: 0.7907 (tp30) cc_final: 0.7445 (tp30) REVERT: B 402 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8141 (t0) REVERT: B 600 HIS cc_start: 0.7038 (t70) cc_final: 0.6379 (t70) REVERT: B 713 GLN cc_start: 0.8650 (mm110) cc_final: 0.8201 (mt0) REVERT: B 730 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7053 (ttm110) REVERT: B 1103 ASP cc_start: 0.8233 (m-30) cc_final: 0.7829 (m-30) REVERT: B 1116 ARG cc_start: 0.8780 (ttp-170) cc_final: 0.8493 (ttp80) REVERT: B 1344 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7289 (t-90) REVERT: B 1363 MET cc_start: 0.6827 (ptm) cc_final: 0.6399 (ptm) REVERT: B 1879 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8105 (mm) REVERT: B 2016 ILE cc_start: 0.8996 (tp) cc_final: 0.8735 (mt) REVERT: B 2026 VAL cc_start: 0.8750 (p) cc_final: 0.8456 (m) REVERT: B 2332 LEU cc_start: 0.8893 (mt) cc_final: 0.8591 (mp) REVERT: B 2384 SER cc_start: 0.8526 (t) cc_final: 0.8239 (p) REVERT: B 2513 PHE cc_start: 0.8368 (t80) cc_final: 0.8128 (t80) REVERT: B 2528 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7990 (mt0) REVERT: C 100 GLU cc_start: 0.7945 (tp30) cc_final: 0.7477 (tp30) REVERT: C 468 ASP cc_start: 0.7423 (m-30) cc_final: 0.7067 (m-30) REVERT: C 476 LEU cc_start: 0.7917 (mm) cc_final: 0.7621 (mt) REVERT: C 713 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8233 (mt0) REVERT: C 753 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: C 1046 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6901 (mm-30) REVERT: C 1048 ASP cc_start: 0.6964 (p0) cc_final: 0.6598 (p0) REVERT: C 1208 ASP cc_start: 0.7666 (m-30) cc_final: 0.7099 (m-30) REVERT: C 1222 MET cc_start: 0.7390 (mtt) cc_final: 0.7135 (mtt) REVERT: C 1509 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7827 (pp) REVERT: C 1648 ILE cc_start: 0.8751 (mm) cc_final: 0.8520 (mt) REVERT: C 1689 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6646 (tmt) REVERT: C 1693 ASN cc_start: 0.8500 (t0) cc_final: 0.8185 (t0) REVERT: C 1798 GLN cc_start: 0.8250 (tp-100) cc_final: 0.8026 (tp-100) REVERT: C 1930 ASN cc_start: 0.7781 (p0) cc_final: 0.7321 (p0) REVERT: C 2035 GLN cc_start: 0.8382 (tp-100) cc_final: 0.8160 (tp-100) REVERT: C 2332 LEU cc_start: 0.8919 (mt) cc_final: 0.8587 (mp) REVERT: C 2384 SER cc_start: 0.8578 (t) cc_final: 0.8276 (p) REVERT: C 2458 LEU cc_start: 0.8716 (tp) cc_final: 0.8473 (tt) REVERT: D 93 LEU cc_start: 0.8390 (mm) cc_final: 0.8163 (mt) REVERT: D 636 ASP cc_start: 0.8107 (t0) cc_final: 0.7653 (t0) REVERT: D 642 HIS cc_start: 0.8144 (t70) cc_final: 0.7738 (t70) REVERT: D 751 ILE cc_start: 0.8910 (mm) cc_final: 0.8520 (mt) REVERT: D 753 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: D 795 THR cc_start: 0.9092 (m) cc_final: 0.8809 (t) REVERT: D 1262 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8130 (mt-10) REVERT: D 1297 VAL cc_start: 0.8335 (p) cc_final: 0.8121 (t) REVERT: D 1344 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7274 (t70) REVERT: D 1395 ASP cc_start: 0.7860 (t0) cc_final: 0.7642 (m-30) REVERT: D 1433 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8522 (p) REVERT: D 1798 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8030 (tp-100) REVERT: D 2035 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7909 (tp-100) REVERT: D 2350 TYR cc_start: 0.7570 (t80) cc_final: 0.7319 (m-80) REVERT: D 2370 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8704 (mm) REVERT: D 2484 SER cc_start: 0.8812 (t) cc_final: 0.8548 (p) REVERT: D 2522 ASP cc_start: 0.8606 (t0) cc_final: 0.8240 (t0) REVERT: D 2545 ARG cc_start: 0.8657 (tpp-160) cc_final: 0.8406 (ttt-90) outliers start: 159 outliers final: 128 residues processed: 1898 average time/residue: 1.5237 time to fit residues: 4915.9963 Evaluate side-chains 1937 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1794 time to evaluate : 8.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2120 HIS Chi-restraints excluded: chain A residue 2225 TYR Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2565 MET Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 1210 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1614 LEU Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 GLU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2400 ASP Chi-restraints excluded: chain B residue 2520 PHE Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2554 SER Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1033 GLU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1622 HIS Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1658 GLU Chi-restraints excluded: chain C residue 1689 MET Chi-restraints excluded: chain C residue 1730 LYS Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1803 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2210 ASN Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2520 PHE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 990 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1433 THR Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1982 CYS Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2541 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 785 optimal weight: 5.9990 chunk 827 optimal weight: 5.9990 chunk 754 optimal weight: 1.9990 chunk 804 optimal weight: 9.9990 chunk 484 optimal weight: 2.9990 chunk 350 optimal weight: 20.0000 chunk 631 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 727 optimal weight: 5.9990 chunk 761 optimal weight: 3.9990 chunk 801 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 195 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN A 601 ASN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 HIS ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 73644 Z= 0.528 Angle : 0.564 9.981 99580 Z= 0.309 Chirality : 0.039 0.215 11428 Planarity : 0.004 0.051 12652 Dihedral : 5.003 85.669 9918 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.18 % Allowed : 17.13 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.09), residues: 8876 helix: 2.73 (0.07), residues: 5724 sheet: -0.63 (0.19), residues: 708 loop : -0.40 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C1623 HIS 0.037 0.001 HIS A2120 PHE 0.029 0.002 PHE D2602 TYR 0.045 0.002 TYR A2341 ARG 0.010 0.001 ARG D2154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 2030 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1856 time to evaluate : 8.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.7776 (mp0) cc_final: 0.7511 (mp0) REVERT: A 616 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 636 ASP cc_start: 0.8039 (t0) cc_final: 0.7623 (t0) REVERT: A 691 GLU cc_start: 0.6173 (pm20) cc_final: 0.5829 (pm20) REVERT: A 697 THR cc_start: 0.8369 (m) cc_final: 0.8085 (p) REVERT: A 714 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6806 (mp0) REVERT: A 730 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7144 (ttm110) REVERT: A 753 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: A 795 THR cc_start: 0.9136 (m) cc_final: 0.8587 (p) REVERT: A 1122 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7309 (tm-30) REVERT: A 1222 MET cc_start: 0.8064 (mmm) cc_final: 0.7817 (mmm) REVERT: A 1305 THR cc_start: 0.8349 (m) cc_final: 0.8119 (p) REVERT: A 1433 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 1464 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 1619 ASP cc_start: 0.8268 (t0) cc_final: 0.7778 (t0) REVERT: A 1620 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7232 (t) REVERT: A 1693 ASN cc_start: 0.8331 (t0) cc_final: 0.7949 (t0) REVERT: A 1798 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8096 (tp-100) REVERT: A 2285 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 2520 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: A 2522 ASP cc_start: 0.8792 (t0) cc_final: 0.8486 (t0) REVERT: B 100 GLU cc_start: 0.8038 (tp30) cc_final: 0.7473 (tp30) REVERT: B 103 GLN cc_start: 0.8448 (tt0) cc_final: 0.8216 (tt0) REVERT: B 402 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 600 HIS cc_start: 0.7096 (t70) cc_final: 0.6417 (t70) REVERT: B 697 THR cc_start: 0.8386 (m) cc_final: 0.8015 (p) REVERT: B 713 GLN cc_start: 0.8682 (mm110) cc_final: 0.8231 (mt0) REVERT: B 730 ARG cc_start: 0.7471 (ttp80) cc_final: 0.7078 (ttm110) REVERT: B 1103 ASP cc_start: 0.8262 (m-30) cc_final: 0.7873 (m-30) REVERT: B 1116 ARG cc_start: 0.8807 (ttp-170) cc_final: 0.8519 (ttp80) REVERT: B 1344 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7454 (t-90) REVERT: B 1363 MET cc_start: 0.6990 (ptm) cc_final: 0.6541 (ptm) REVERT: B 1879 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8080 (mm) REVERT: B 2016 ILE cc_start: 0.9015 (tp) cc_final: 0.8764 (mt) REVERT: B 2026 VAL cc_start: 0.8803 (p) cc_final: 0.8504 (m) REVERT: B 2332 LEU cc_start: 0.8931 (mt) cc_final: 0.8637 (mp) REVERT: B 2384 SER cc_start: 0.8607 (t) cc_final: 0.8305 (p) REVERT: B 2513 PHE cc_start: 0.8516 (t80) cc_final: 0.8155 (t80) REVERT: B 2532 GLU cc_start: 0.8303 (tp30) cc_final: 0.8041 (tt0) REVERT: C 100 GLU cc_start: 0.8040 (tp30) cc_final: 0.7580 (tp30) REVERT: C 468 ASP cc_start: 0.7512 (m-30) cc_final: 0.7149 (m-30) REVERT: C 476 LEU cc_start: 0.7914 (mm) cc_final: 0.7683 (mt) REVERT: C 713 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8298 (mt0) REVERT: C 753 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: C 1208 ASP cc_start: 0.7740 (m-30) cc_final: 0.7179 (m-30) REVERT: C 1222 MET cc_start: 0.7445 (mtt) cc_final: 0.7202 (mtt) REVERT: C 1280 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 1297 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8354 (p) REVERT: C 1509 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7855 (pp) REVERT: C 1647 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7724 (tt) REVERT: C 1648 ILE cc_start: 0.8783 (mm) cc_final: 0.8564 (mt) REVERT: C 1693 ASN cc_start: 0.8510 (t0) cc_final: 0.8221 (t0) REVERT: C 1798 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7995 (tp-100) REVERT: C 1930 ASN cc_start: 0.7788 (p0) cc_final: 0.7354 (p0) REVERT: C 2154 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8366 (tmm-80) REVERT: C 2332 LEU cc_start: 0.8930 (mt) cc_final: 0.8600 (mp) REVERT: C 2384 SER cc_start: 0.8664 (t) cc_final: 0.8313 (p) REVERT: C 2458 LEU cc_start: 0.8750 (tp) cc_final: 0.8480 (tt) REVERT: C 2498 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8426 (tt) REVERT: C 2593 MET cc_start: 0.7792 (mmm) cc_final: 0.7574 (mmm) REVERT: D 93 LEU cc_start: 0.8432 (mm) cc_final: 0.8180 (mt) REVERT: D 103 GLN cc_start: 0.8655 (tt0) cc_final: 0.8328 (tt0) REVERT: D 636 ASP cc_start: 0.8138 (t0) cc_final: 0.7691 (t0) REVERT: D 697 THR cc_start: 0.8333 (m) cc_final: 0.8045 (p) REVERT: D 751 ILE cc_start: 0.8951 (mm) cc_final: 0.8594 (mt) REVERT: D 753 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: D 795 THR cc_start: 0.9113 (m) cc_final: 0.8540 (p) REVERT: D 1103 ASP cc_start: 0.8321 (m-30) cc_final: 0.7925 (m-30) REVERT: D 1262 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8153 (mt-10) REVERT: D 1284 GLN cc_start: 0.8691 (mt0) cc_final: 0.8452 (mt0) REVERT: D 1344 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7486 (t70) REVERT: D 1395 ASP cc_start: 0.7910 (t0) cc_final: 0.7690 (m-30) REVERT: D 1433 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8622 (p) REVERT: D 1693 ASN cc_start: 0.8464 (t0) cc_final: 0.8119 (t0) REVERT: D 1798 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8032 (tp-100) REVERT: D 1968 ASP cc_start: 0.6973 (m-30) cc_final: 0.6710 (m-30) REVERT: D 2035 GLN cc_start: 0.8279 (tp-100) cc_final: 0.7922 (tp-100) REVERT: D 2204 TRP cc_start: 0.8470 (m100) cc_final: 0.8262 (m100) REVERT: D 2350 TYR cc_start: 0.7653 (t80) cc_final: 0.7400 (m-80) REVERT: D 2484 SER cc_start: 0.8890 (t) cc_final: 0.8629 (p) REVERT: D 2522 ASP cc_start: 0.8659 (t0) cc_final: 0.8324 (t0) outliers start: 174 outliers final: 135 residues processed: 1946 average time/residue: 1.5145 time to fit residues: 5020.9743 Evaluate side-chains 1970 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1818 time to evaluate : 8.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1918 THR Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 2008 HIS Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2225 TYR Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2565 MET Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1625 GLU Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 GLU Chi-restraints excluded: chain B residue 1674 LEU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2225 TYR Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2554 SER Chi-restraints excluded: chain B residue 2565 MET Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1033 GLU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1658 GLU Chi-restraints excluded: chain C residue 1730 LYS Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 1982 CYS Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2140 VAL Chi-restraints excluded: chain C residue 2210 ASN Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2599 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1433 THR Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1955 ASN Chi-restraints excluded: chain D residue 1982 CYS Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2541 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 528 optimal weight: 0.5980 chunk 850 optimal weight: 2.9990 chunk 519 optimal weight: 0.9990 chunk 403 optimal weight: 0.5980 chunk 591 optimal weight: 0.8980 chunk 892 optimal weight: 5.9990 chunk 821 optimal weight: 0.8980 chunk 710 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 549 optimal weight: 3.9990 chunk 435 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 HIS ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 ASN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 73644 Z= 0.355 Angle : 0.599 59.196 99580 Z= 0.331 Chirality : 0.035 0.166 11428 Planarity : 0.003 0.049 12652 Dihedral : 5.012 85.152 9918 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.06 % Allowed : 17.66 % Favored : 80.29 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.09), residues: 8876 helix: 2.73 (0.07), residues: 5724 sheet: -0.65 (0.19), residues: 708 loop : -0.40 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1623 HIS 0.024 0.001 HIS C1622 PHE 0.023 0.002 PHE D2602 TYR 0.040 0.001 TYR A2341 ARG 0.025 0.000 ARG D2200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17752 Ramachandran restraints generated. 8876 Oldfield, 0 Emsley, 8876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Residue VAL 1498 is missing expected H atoms. Skipping. Residue MET 2226 is missing expected H atoms. Skipping. Residue ILE 2622 is missing expected H atoms. Skipping. Residue ILE 2624 is missing expected H atoms. Skipping. Residue LEU 2625 is missing expected H atoms. Skipping. Residue LYS 2628 is missing expected H atoms. Skipping. Residue LEU 2629 is missing expected H atoms. Skipping. Residue SER 2631 is missing expected H atoms. Skipping. Residue THR 2632 is missing expected H atoms. Skipping. Residue MET 2633 is missing expected H atoms. Skipping. Residue LYS 2634 is missing expected H atoms. Skipping. Residue LEU 2635 is missing expected H atoms. Skipping. Residue VAL 2636 is missing expected H atoms. Skipping. Residue SER 2637 is missing expected H atoms. Skipping. Residue LEU 2639 is missing expected H atoms. Skipping. Residue THR 2640 is missing expected H atoms. Skipping. Residue LEU 2643 is missing expected H atoms. Skipping. Residue LEU 2646 is missing expected H atoms. Skipping. Residue LYS 2647 is missing expected H atoms. Skipping. Residue MET 2650 is missing expected H atoms. Skipping. Residue THR 2651 is missing expected H atoms. Skipping. Residue LYS 2655 is missing expected H atoms. Skipping. Evaluate side-chains 1983 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1819 time to evaluate : 8.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 GLU cc_start: 0.7763 (mp0) cc_final: 0.7503 (mp0) REVERT: A 616 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 636 ASP cc_start: 0.8034 (t0) cc_final: 0.7609 (t0) REVERT: A 691 GLU cc_start: 0.6157 (pm20) cc_final: 0.5817 (pm20) REVERT: A 697 THR cc_start: 0.8360 (m) cc_final: 0.8078 (p) REVERT: A 714 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6783 (mp0) REVERT: A 730 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7113 (ttm110) REVERT: A 753 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: A 795 THR cc_start: 0.9113 (m) cc_final: 0.8570 (p) REVERT: A 1122 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7301 (tm-30) REVERT: A 1222 MET cc_start: 0.8046 (mmm) cc_final: 0.7800 (mmm) REVERT: A 1305 THR cc_start: 0.8335 (m) cc_final: 0.8106 (p) REVERT: A 1433 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 1464 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8774 (tt) REVERT: A 1619 ASP cc_start: 0.8246 (t0) cc_final: 0.7759 (t0) REVERT: A 1620 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7205 (t) REVERT: A 1693 ASN cc_start: 0.8315 (t0) cc_final: 0.7934 (t0) REVERT: A 1798 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8088 (tp-100) REVERT: A 2035 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7976 (tp-100) REVERT: A 2285 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 2520 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: A 2522 ASP cc_start: 0.8769 (t0) cc_final: 0.8467 (t0) REVERT: B 100 GLU cc_start: 0.8028 (tp30) cc_final: 0.7455 (tp30) REVERT: B 103 GLN cc_start: 0.8434 (tt0) cc_final: 0.8198 (tt0) REVERT: B 402 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 600 HIS cc_start: 0.7080 (t70) cc_final: 0.6401 (t70) REVERT: B 697 THR cc_start: 0.8367 (m) cc_final: 0.8002 (p) REVERT: B 713 GLN cc_start: 0.8659 (mm110) cc_final: 0.8214 (mt0) REVERT: B 730 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7069 (ttm110) REVERT: B 1103 ASP cc_start: 0.8248 (m-30) cc_final: 0.7852 (m-30) REVERT: B 1116 ARG cc_start: 0.8797 (ttp-170) cc_final: 0.8508 (ttp80) REVERT: B 1344 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7448 (t-90) REVERT: B 1363 MET cc_start: 0.6959 (ptm) cc_final: 0.6514 (ptm) REVERT: B 1879 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 2016 ILE cc_start: 0.9013 (tp) cc_final: 0.8757 (mt) REVERT: B 2026 VAL cc_start: 0.8794 (p) cc_final: 0.8493 (m) REVERT: B 2332 LEU cc_start: 0.8917 (mt) cc_final: 0.8621 (mp) REVERT: B 2384 SER cc_start: 0.8564 (t) cc_final: 0.8278 (p) REVERT: B 2513 PHE cc_start: 0.8504 (t80) cc_final: 0.8128 (t80) REVERT: B 2532 GLU cc_start: 0.8299 (tp30) cc_final: 0.8058 (tt0) REVERT: C 100 GLU cc_start: 0.8030 (tp30) cc_final: 0.7560 (tp30) REVERT: C 468 ASP cc_start: 0.7491 (m-30) cc_final: 0.7133 (m-30) REVERT: C 476 LEU cc_start: 0.7923 (mm) cc_final: 0.7681 (mt) REVERT: C 713 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8286 (mt0) REVERT: C 753 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: C 1208 ASP cc_start: 0.7728 (m-30) cc_final: 0.7162 (m-30) REVERT: C 1222 MET cc_start: 0.7433 (mtt) cc_final: 0.7186 (mtt) REVERT: C 1280 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8044 (mm-30) REVERT: C 1297 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8341 (p) REVERT: C 1509 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7845 (pp) REVERT: C 1647 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7715 (tt) REVERT: C 1648 ILE cc_start: 0.8761 (mm) cc_final: 0.8542 (mt) REVERT: C 1693 ASN cc_start: 0.8493 (t0) cc_final: 0.8208 (t0) REVERT: C 1798 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7992 (tp-100) REVERT: C 2154 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8356 (tmm-80) REVERT: C 2332 LEU cc_start: 0.8924 (mt) cc_final: 0.8589 (mp) REVERT: C 2384 SER cc_start: 0.8653 (t) cc_final: 0.8298 (p) REVERT: C 2458 LEU cc_start: 0.8720 (tp) cc_final: 0.8470 (tt) REVERT: C 2498 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 2593 MET cc_start: 0.7783 (mmm) cc_final: 0.7573 (mmm) REVERT: D 93 LEU cc_start: 0.8428 (mm) cc_final: 0.8177 (mt) REVERT: D 103 GLN cc_start: 0.8648 (tt0) cc_final: 0.8314 (tt0) REVERT: D 636 ASP cc_start: 0.8119 (t0) cc_final: 0.7668 (t0) REVERT: D 697 THR cc_start: 0.8327 (m) cc_final: 0.8038 (p) REVERT: D 751 ILE cc_start: 0.8944 (mm) cc_final: 0.8580 (mt) REVERT: D 753 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: D 795 THR cc_start: 0.9105 (m) cc_final: 0.8859 (t) REVERT: D 1103 ASP cc_start: 0.8313 (m-30) cc_final: 0.7910 (m-30) REVERT: D 1262 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8145 (mt-10) REVERT: D 1284 GLN cc_start: 0.8679 (mt0) cc_final: 0.8442 (mt0) REVERT: D 1344 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7479 (t70) REVERT: D 1395 ASP cc_start: 0.7903 (t0) cc_final: 0.7683 (m-30) REVERT: D 1433 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8613 (p) REVERT: D 1693 ASN cc_start: 0.8449 (t0) cc_final: 0.8086 (t0) REVERT: D 1798 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8024 (tp-100) REVERT: D 1968 ASP cc_start: 0.6918 (m-30) cc_final: 0.6653 (m-30) REVERT: D 2035 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7910 (tp-100) REVERT: D 2204 TRP cc_start: 0.8457 (m100) cc_final: 0.8223 (m100) REVERT: D 2350 TYR cc_start: 0.7647 (t80) cc_final: 0.7374 (m-80) REVERT: D 2484 SER cc_start: 0.8892 (t) cc_final: 0.8627 (p) REVERT: D 2522 ASP cc_start: 0.8655 (t0) cc_final: 0.8307 (t0) outliers start: 164 outliers final: 141 residues processed: 1908 average time/residue: 1.5420 time to fit residues: 5017.7020 Evaluate side-chains 1973 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1815 time to evaluate : 8.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 817 SER Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1367 SER Chi-restraints excluded: chain A residue 1433 THR Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1509 LEU Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1803 THR Chi-restraints excluded: chain A residue 1879 LEU Chi-restraints excluded: chain A residue 1918 THR Chi-restraints excluded: chain A residue 1936 LEU Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 2008 HIS Chi-restraints excluded: chain A residue 2070 LEU Chi-restraints excluded: chain A residue 2225 TYR Chi-restraints excluded: chain A residue 2285 LEU Chi-restraints excluded: chain A residue 2297 VAL Chi-restraints excluded: chain A residue 2308 ILE Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2520 PHE Chi-restraints excluded: chain A residue 2538 CYS Chi-restraints excluded: chain A residue 2554 SER Chi-restraints excluded: chain A residue 2565 MET Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 1225 LEU Chi-restraints excluded: chain B residue 1344 HIS Chi-restraints excluded: chain B residue 1431 ILE Chi-restraints excluded: chain B residue 1487 ASN Chi-restraints excluded: chain B residue 1618 VAL Chi-restraints excluded: chain B residue 1625 GLU Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 GLU Chi-restraints excluded: chain B residue 1674 LEU Chi-restraints excluded: chain B residue 1803 THR Chi-restraints excluded: chain B residue 1879 LEU Chi-restraints excluded: chain B residue 1934 VAL Chi-restraints excluded: chain B residue 2008 HIS Chi-restraints excluded: chain B residue 2020 LEU Chi-restraints excluded: chain B residue 2049 VAL Chi-restraints excluded: chain B residue 2120 HIS Chi-restraints excluded: chain B residue 2225 TYR Chi-restraints excluded: chain B residue 2285 LEU Chi-restraints excluded: chain B residue 2288 LEU Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2308 ILE Chi-restraints excluded: chain B residue 2370 LEU Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2538 CYS Chi-restraints excluded: chain B residue 2554 SER Chi-restraints excluded: chain B residue 2565 MET Chi-restraints excluded: chain B residue 2584 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 583 SER Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 753 GLN Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 991 LEU Chi-restraints excluded: chain C residue 1033 GLU Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1246 LEU Chi-restraints excluded: chain C residue 1252 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1297 VAL Chi-restraints excluded: chain C residue 1389 SER Chi-restraints excluded: chain C residue 1464 LEU Chi-restraints excluded: chain C residue 1509 LEU Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1658 GLU Chi-restraints excluded: chain C residue 1730 LYS Chi-restraints excluded: chain C residue 1766 THR Chi-restraints excluded: chain C residue 1918 THR Chi-restraints excluded: chain C residue 1982 CYS Chi-restraints excluded: chain C residue 2008 HIS Chi-restraints excluded: chain C residue 2049 VAL Chi-restraints excluded: chain C residue 2070 LEU Chi-restraints excluded: chain C residue 2210 ASN Chi-restraints excluded: chain C residue 2225 TYR Chi-restraints excluded: chain C residue 2298 VAL Chi-restraints excluded: chain C residue 2308 ILE Chi-restraints excluded: chain C residue 2461 CYS Chi-restraints excluded: chain C residue 2498 LEU Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2538 CYS Chi-restraints excluded: chain C residue 2549 ASP Chi-restraints excluded: chain C residue 2552 THR Chi-restraints excluded: chain C residue 2575 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2599 LEU Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 454 SER Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 753 GLN Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 849 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1246 LEU Chi-restraints excluded: chain D residue 1255 THR Chi-restraints excluded: chain D residue 1344 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1433 THR Chi-restraints excluded: chain D residue 1618 VAL Chi-restraints excluded: chain D residue 1626 LEU Chi-restraints excluded: chain D residue 1654 LEU Chi-restraints excluded: chain D residue 1803 THR Chi-restraints excluded: chain D residue 1955 ASN Chi-restraints excluded: chain D residue 1982 CYS Chi-restraints excluded: chain D residue 2049 VAL Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2308 ILE Chi-restraints excluded: chain D residue 2370 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2457 THR Chi-restraints excluded: chain D residue 2541 CYS Chi-restraints excluded: chain D residue 2554 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 564 optimal weight: 9.9990 chunk 757 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 655 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 711 optimal weight: 0.9990 chunk 297 optimal weight: 0.1980 chunk 731 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 ASN A 744 GLN ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 ASN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1327 ASN ** D1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1962 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114721 restraints weight = 329842.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117135 restraints weight = 165012.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118719 restraints weight = 106107.646| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 73644 Z= 0.355 Angle : 0.599 59.196 99580 Z= 0.331 Chirality : 0.035 0.166 11428 Planarity : 0.003 0.049 12652 Dihedral : 5.012 85.152 9918 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.99 % Allowed : 17.79 % Favored : 80.21 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.09), residues: 8876 helix: 2.73 (0.07), residues: 5724 sheet: -0.65 (0.19), residues: 708 loop : -0.40 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C1623 HIS 0.024 0.001 HIS C1622 PHE 0.023 0.002 PHE D2602 TYR 0.040 0.001 TYR A2341 ARG 0.025 0.000 ARG D2200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 62566.58 seconds wall clock time: 1066 minutes 50.50 seconds (64010.50 seconds total)