Starting phenix.real_space_refine on Thu Mar 21 14:13:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tkd_41347/03_2024/8tkd_41347_trim_updated.pdb" } resolution = 3.7 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= 0.159 sd= 1.690 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: 7 Type Number sf(0) Gaussians 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 ASP 54": "OD1" <-> "OD2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 658": "OD1" <-> "OD2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1747": "OE1" <-> "OE2" Residue "A TYR 2033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2048": "OE1" <-> "OE2" Residue "A PHE 2138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 2183": "OE1" <-> "OE2" Residue "A GLU 2531": "OE1" <-> "OE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1747": "OE1" <-> "OE2" Residue "B TYR 2033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2048": "OE1" <-> "OE2" Residue "B PHE 2138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 2183": "OE1" <-> "OE2" Residue "B GLU 2531": "OE1" <-> "OE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 203": "OD1" <-> "OD2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 658": "OD1" <-> "OD2" Residue "C GLU 714": "OE1" <-> "OE2" Residue "C GLU 723": "OE1" <-> "OE2" Residue "C TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 805": "OE1" <-> "OE2" Residue "C GLU 847": "OE1" <-> "OE2" Residue "C GLU 854": "OE1" <-> "OE2" Residue "C TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1747": "OE1" <-> "OE2" Residue "C TYR 2033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2048": "OE1" <-> "OE2" Residue "C PHE 2138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 2183": "OE1" <-> "OE2" Residue "C GLU 2531": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 409": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 658": "OD1" <-> "OD2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D GLU 723": "OE1" <-> "OE2" Residue "D TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D GLU 854": "OE1" <-> "OE2" Residue "D TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1747": "OE1" <-> "OE2" Residue "D TYR 2033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2048": "OE1" <-> "OE2" Residue "D PHE 2138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 2183": "OE1" <-> "OE2" Residue "D GLU 2531": "OE1" <-> "OE2" Time to flip residues: 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144368 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34462 SG CYS A2538 141.571 125.477 104.640 1.00 58.76 S ATOM 34511 SG CYS A2541 139.185 126.420 101.794 1.00 52.21 S ATOM 70498 SG CYS B2538 116.817 141.815 104.654 1.00 58.76 S ATOM 70547 SG CYS B2541 115.852 139.431 101.815 1.00 52.21 S ATOM A051I SG CYS C2538 100.510 117.398 104.490 1.00 58.76 S ATOM A052V SG CYS C2541 102.891 116.430 101.649 1.00 52.21 S ATOM A0WUI SG CYS D2538 125.122 100.900 104.548 1.00 58.76 S ATOM A0WVV SG CYS D2541 126.085 103.276 101.701 1.00 52.21 S Time building chain proxies: 46.92, per 1000 atoms: 0.33 Number of scatterers: 144368 At special positions: 0 Unit cell: (242.794, 242.794, 188.071, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 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=0, symmetry=0 Time building additional restraints: 89.87 Conformation dependent library (CDL) restraints added in 10.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2541 " pdb="ZN ZN A3001 " - pdb=" SG CYS A2538 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B3001 " - pdb=" ND1 HIS B2563 " 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 D2541 " pdb="ZN ZN D3001 " - pdb=" SG CYS D2538 " 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: 404 helices and 44 sheets defined 71.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 34.90 Creating SS restraints... 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: 3.567A pdb=" N HIS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 231' Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.080A pdb=" N ALA A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.450A 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: 3.597A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.579A pdb=" N GLN A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 4.217A 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 544 removed outlier: 4.592A pdb=" N SER A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 565 removed outlier: 5.902A pdb=" N TYR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.435A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 5.387A 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: 4.559A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 5.661A 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 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.845A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 removed outlier: 3.561A pdb=" N LEU A 657 " --> pdb=" O CYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 666 removed outlier: 3.656A pdb=" N SER A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 665 " --> pdb=" O ASN A 661 " (cutoff:3.500A) removed outlier: 5.263A 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: 3.596A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 removed outlier: 3.699A pdb=" N ILE A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 770 through 784 Processing helix chain 'A' and resid 811 through 824 removed outlier: 3.634A pdb=" N ASN A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 5.404A pdb=" N ALA A 848 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 874 removed outlier: 3.869A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 961 through 1002 removed outlier: 3.794A pdb=" N LYS A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 980 " --> pdb=" O GLN A 976 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1037 removed outlier: 3.767A pdb=" N MET A1035 " --> pdb=" O GLN A1031 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLY A1037 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1066 removed outlier: 5.397A pdb=" N ASP A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.651A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.781A pdb=" N GLN A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1128 removed outlier: 5.242A pdb=" N GLU A1125 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP A1127 " --> pdb=" O LYS A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1184 removed outlier: 4.416A pdb=" N GLY A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1202 through 1212 Processing helix chain 'A' and resid 1218 through 1237 Processing helix chain 'A' and resid 1239 through 1250 removed outlier: 4.091A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 4.224A 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 removed outlier: 4.153A pdb=" N CYS A1275 " --> pdb=" O ASN A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1293 removed outlier: 3.817A pdb=" N LEU A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1309 removed outlier: 3.979A pdb=" N LEU A1300 " --> pdb=" O HIS A1296 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1329 removed outlier: 3.815A 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: 4.125A 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 1401 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1429 through 1434 removed outlier: 3.761A pdb=" N THR A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1458 Processing helix chain 'A' and resid 1461 through 1482 removed outlier: 3.878A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1511 removed outlier: 3.555A pdb=" N CYS A1511 " --> pdb=" O ARG A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1537 removed outlier: 3.523A 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 removed outlier: 3.505A pdb=" N LYS A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Proline residue: A1608 - end of helix removed outlier: 3.929A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Proline residue: A1624 - end of helix Processing helix chain 'A' and resid 1632 through 1641 removed outlier: 4.003A pdb=" N GLY A1641 " --> pdb=" O ARG A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1655 removed outlier: 3.821A pdb=" N LYS A1652 " --> pdb=" O ILE A1648 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP A1653 " --> pdb=" O GLN A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1675 removed outlier: 3.561A pdb=" N LEU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A1674 " --> pdb=" O GLN A1670 " (cutoff:3.500A) removed outlier: 5.547A 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 removed outlier: 3.738A pdb=" N ILE A1721 " --> pdb=" O ASP A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1744 removed outlier: 3.554A 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: 3.768A pdb=" N GLN A1769 " --> pdb=" O ASN A1765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A1770 " --> pdb=" O THR A1766 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A1779 " --> pdb=" O LEU A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1804 removed outlier: 5.241A pdb=" N PHE A1785 " --> pdb=" O LYS A1781 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A1786 " --> pdb=" O SER A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1864 through 1882 removed outlier: 3.759A pdb=" N ILE A1869 " --> pdb=" O THR A1865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) removed outlier: 4.302A 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: 4.514A pdb=" N GLU A1906 " --> pdb=" O ASN A1902 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1923 removed outlier: 3.839A pdb=" N GLY A1923 " --> pdb=" O THR A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 3.913A pdb=" N TYR A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1931 through 1950 removed outlier: 4.679A pdb=" N GLY A1935 " --> pdb=" O GLU A1931 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A1936 " --> pdb=" O ASP A1932 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY A1950 " --> pdb=" O GLU A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1962 Processing helix chain 'A' and resid 1966 through 1976 removed outlier: 3.837A pdb=" N ILE A1970 " --> pdb=" O GLY A1966 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A1974 " --> pdb=" O ILE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 removed outlier: 3.849A pdb=" N LYS A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A1984 " --> pdb=" O PRO A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 2005 Processing helix chain 'A' and resid 2009 through 2021 removed outlier: 4.931A pdb=" N ALA A2013 " --> pdb=" O ASP A2009 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG A2021 " --> pdb=" O LEU A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2036 Processing helix chain 'A' and resid 2038 through 2043 removed outlier: 3.791A pdb=" N SER A2042 " --> pdb=" O GLU A2038 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU A2043 " --> pdb=" O ARG A2039 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2038 through 2043' Processing helix chain 'A' and resid 2045 through 2062 removed outlier: 3.986A pdb=" N VAL A2049 " --> pdb=" O SER A2045 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2064 through 2073 Proline residue: A2073 - end of helix Processing helix chain 'A' and resid 2112 through 2122 removed outlier: 3.695A pdb=" N TYR A2117 " --> pdb=" O PRO A2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A2121 " --> pdb=" O TYR A2117 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N SER A2122 " --> pdb=" O GLU A2118 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2147 removed outlier: 3.945A pdb=" N GLN A2145 " --> pdb=" O PRO A2141 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A2146 " --> pdb=" O GLY A2142 " (cutoff:3.500A) removed outlier: 4.523A 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: 4.612A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.562A 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 2222 removed outlier: 3.736A pdb=" N ARG A2200 " --> pdb=" O TRP A2196 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N THR A2202 " --> pdb=" O SER A2198 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A2203 " --> pdb=" O ARG A2199 " (cutoff:3.500A) Processing helix chain 'A' and resid 2260 through 2276 Processing helix chain 'A' and resid 2277 through 2310 removed outlier: 6.382A pdb=" N THR A2306 " --> pdb=" O GLY A2302 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N PHE A2307 " --> pdb=" O ASN A2303 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG A2309 " --> pdb=" O GLY A2305 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A2310 " --> pdb=" O THR A2306 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2318 removed outlier: 5.755A pdb=" N MET A2318 " --> pdb=" O MET A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2319 through 2336 Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 4.893A pdb=" N TYR A2341 " --> pdb=" O HIS A2337 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER A2342 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE A2343 " --> pdb=" O LEU A2339 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A2344 " --> pdb=" O PHE A2340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A2345 " --> pdb=" O TYR A2341 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A2346 " --> pdb=" O SER A2342 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A2348 " --> pdb=" O LEU A2344 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A2349 " --> pdb=" O LEU A2345 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A2350 " --> pdb=" O PHE A2346 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2364 removed outlier: 3.678A pdb=" N SER A2361 " --> pdb=" O ASN A2357 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.664A pdb=" N PHE A2395 " --> pdb=" O LEU A2391 " (cutoff:3.500A) removed outlier: 5.487A 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: 3.593A pdb=" N ARG A2471 " --> pdb=" O ASN A2467 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A2472 " --> pdb=" O HIS A2468 " (cutoff:3.500A) Processing helix chain 'A' and resid 2475 through 2481 removed outlier: 4.544A pdb=" N ILE A2479 " --> pdb=" O GLY A2475 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2480 " --> pdb=" O VAL A2476 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A2481 " --> pdb=" O GLY A2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2475 through 2481' Processing helix chain 'A' and resid 2489 through 2504 Processing helix chain 'A' and resid 2508 through 2537 removed outlier: 3.577A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A2515 " --> pdb=" O LEU A2511 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2550 removed outlier: 4.044A pdb=" N PHE A2548 " --> pdb=" O GLU A2544 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A2549 " --> pdb=" O ARG A2545 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN A2550 " --> pdb=" O ASP A2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2544 through 2550' 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: 4.199A pdb=" N ASN A2613 " --> pdb=" O SER A2609 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU A2614 " --> pdb=" O LEU A2610 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A2615 " --> pdb=" O VAL A2611 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A2616 " --> pdb=" O SER A2612 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A2617 " --> pdb=" O ASN A2613 " (cutoff:3.500A) 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: 3.567A pdb=" N HIS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 231' Processing helix chain 'B' and resid 272 through 277 removed outlier: 4.079A pdb=" N ALA B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 5.451A 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: 3.597A pdb=" N ILE B 439 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 485 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.579A pdb=" N GLN B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 4.216A 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 544 removed outlier: 4.593A pdb=" N SER B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 565 removed outlier: 5.902A pdb=" N TYR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 579 removed outlier: 4.435A pdb=" N GLN B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 5.387A 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: 4.559A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 5.662A 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 Processing helix chain 'B' and resid 627 through 640 removed outlier: 3.843A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 removed outlier: 3.562A pdb=" N LEU B 657 " --> pdb=" O CYS B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 666 removed outlier: 3.657A pdb=" N SER B 662 " --> pdb=" O ASP B 658 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 665 " --> pdb=" O ASN B 661 " (cutoff:3.500A) removed outlier: 5.262A 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: 3.595A pdb=" N LEU B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 removed outlier: 3.699A pdb=" N ILE B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) removed outlier: 4.295A 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 784 Processing helix chain 'B' and resid 811 through 824 removed outlier: 3.634A pdb=" N ASN B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 848 removed outlier: 5.405A pdb=" N ALA B 848 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 874 removed outlier: 3.869A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 874 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 893 Processing helix chain 'B' and resid 961 through 1002 removed outlier: 3.794A pdb=" N LYS B 968 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 980 " --> pdb=" O GLN B 976 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 981 " --> pdb=" O PHE B 977 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1037 removed outlier: 3.769A pdb=" N MET B1035 " --> pdb=" O GLN B1031 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY B1037 " --> pdb=" O GLU B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 removed outlier: 5.396A pdb=" N ASP B1066 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1084 removed outlier: 3.651A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1095 removed outlier: 3.781A pdb=" N GLN B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1128 removed outlier: 5.242A pdb=" N GLU B1125 " --> pdb=" O VAL B1121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B1126 " --> pdb=" O GLU B1122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TRP B1127 " --> pdb=" O LYS B1123 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1184 removed outlier: 4.416A pdb=" N GLY B1184 " --> pdb=" O ASN B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1201 Processing helix chain 'B' and resid 1202 through 1212 Processing helix chain 'B' and resid 1218 through 1237 Processing helix chain 'B' and resid 1239 through 1250 removed outlier: 4.091A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 4.225A 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 removed outlier: 4.153A pdb=" N CYS B1275 " --> pdb=" O ASN B1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1293 removed outlier: 3.818A pdb=" N LEU B1283 " --> pdb=" O SER B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1296 through 1309 removed outlier: 3.979A pdb=" N LEU B1300 " --> pdb=" O HIS B1296 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA B1309 " --> pdb=" O THR B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1329 removed outlier: 3.814A 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: 4.126A pdb=" N GLY B1378 " --> pdb=" O ALA B1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1392 Proline residue: B1392 - end of helix Processing helix chain 'B' and resid 1393 through 1401 Processing helix chain 'B' and resid 1406 through 1420 Processing helix chain 'B' and resid 1429 through 1434 removed outlier: 3.760A pdb=" N THR B1433 " --> pdb=" O LYS B1429 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1458 Processing helix chain 'B' and resid 1461 through 1482 removed outlier: 3.878A pdb=" N VAL B1472 " --> pdb=" O VAL B1468 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B1473 " --> pdb=" O LEU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1491 through 1511 removed outlier: 3.555A pdb=" N CYS B1511 " --> pdb=" O ARG B1507 " (cutoff:3.500A) Processing helix chain 'B' and resid 1516 through 1537 removed outlier: 3.522A 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 removed outlier: 3.505A pdb=" N LYS B1607 " --> pdb=" O GLU B1603 " (cutoff:3.500A) Proline residue: B1608 - end of helix removed outlier: 3.928A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1632 through 1641 removed outlier: 4.003A pdb=" N GLY B1641 " --> pdb=" O ARG B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1655 removed outlier: 3.821A pdb=" N LYS B1652 " --> pdb=" O ILE B1648 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1658 through 1675 removed outlier: 3.561A pdb=" N LEU B1673 " --> pdb=" O LEU B1669 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B1674 " --> pdb=" O GLN B1670 " (cutoff:3.500A) removed outlier: 5.547A 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 removed outlier: 3.738A pdb=" N ILE B1721 " --> pdb=" O ASP B1717 " (cutoff:3.500A) Processing helix chain 'B' and resid 1733 through 1744 removed outlier: 3.555A 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: 3.767A pdb=" N GLN B1769 " --> pdb=" O ASN B1765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B1770 " --> pdb=" O THR B1766 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B1779 " --> pdb=" O LEU B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 1781 through 1804 removed outlier: 5.240A pdb=" N PHE B1785 " --> pdb=" O LYS B1781 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B1786 " --> pdb=" O SER B1782 " (cutoff:3.500A) Processing helix chain 'B' and resid 1864 through 1882 removed outlier: 3.759A pdb=" N ILE B1869 " --> pdb=" O THR B1865 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) removed outlier: 4.302A 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: 4.514A pdb=" N GLU B1906 " --> pdb=" O ASN B1902 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1923 removed outlier: 3.838A pdb=" N GLY B1923 " --> pdb=" O THR B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1924 through 1930 removed outlier: 3.912A pdb=" N TYR B1928 " --> pdb=" O LEU B1924 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1931 through 1950 removed outlier: 4.680A pdb=" N GLY B1935 " --> pdb=" O GLU B1931 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B1936 " --> pdb=" O ASP B1932 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY B1950 " --> pdb=" O GLU B1946 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1962 Processing helix chain 'B' and resid 1966 through 1976 removed outlier: 3.836A pdb=" N ILE B1970 " --> pdb=" O GLY B1966 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B1974 " --> pdb=" O ILE B1970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1978 through 1985 removed outlier: 3.849A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1986 through 2005 Processing helix chain 'B' and resid 2009 through 2021 removed outlier: 4.931A pdb=" N ALA B2013 " --> pdb=" O ASP B2009 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2036 Processing helix chain 'B' and resid 2038 through 2043 removed outlier: 3.791A pdb=" N SER B2042 " --> pdb=" O GLU B2038 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU B2043 " --> pdb=" O ARG B2039 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2038 through 2043' Processing helix chain 'B' and resid 2045 through 2062 removed outlier: 3.985A pdb=" N VAL B2049 " --> pdb=" O SER B2045 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2073 Proline residue: B2073 - end of helix Processing helix chain 'B' and resid 2112 through 2122 removed outlier: 3.694A pdb=" N TYR B2117 " --> pdb=" O PRO B2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B2121 " --> pdb=" O TYR B2117 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER B2122 " --> pdb=" O GLU B2118 " (cutoff:3.500A) Processing helix chain 'B' and resid 2141 through 2147 removed outlier: 3.945A pdb=" N GLN B2145 " --> pdb=" O PRO B2141 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE B2146 " --> pdb=" O GLY B2142 " (cutoff:3.500A) removed outlier: 4.523A 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: 4.612A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.562A 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 2222 removed outlier: 3.736A pdb=" N ARG B2200 " --> pdb=" O TRP B2196 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR B2202 " --> pdb=" O SER B2198 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B2203 " --> pdb=" O ARG B2199 " (cutoff:3.500A) Processing helix chain 'B' and resid 2260 through 2276 Processing helix chain 'B' and resid 2277 through 2310 removed outlier: 6.382A pdb=" N THR B2306 " --> pdb=" O GLY B2302 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N PHE B2307 " --> pdb=" O ASN B2303 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE B2308 " --> pdb=" O ARG B2304 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG B2309 " --> pdb=" O GLY B2305 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B2310 " --> pdb=" O THR B2306 " (cutoff:3.500A) Processing helix chain 'B' and resid 2311 through 2318 removed outlier: 5.756A pdb=" N MET B2318 " --> pdb=" O MET B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2336 Processing helix chain 'B' and resid 2337 through 2352 removed outlier: 4.893A pdb=" N TYR B2341 " --> pdb=" O HIS B2337 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER B2342 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B2343 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B2344 " --> pdb=" O PHE B2340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B2345 " --> pdb=" O TYR B2341 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE B2346 " --> pdb=" O SER B2342 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP B2347 " --> pdb=" O ILE B2343 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU B2348 " --> pdb=" O LEU B2344 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B2349 " --> pdb=" O LEU B2345 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR B2350 " --> pdb=" O PHE B2346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2364 removed outlier: 3.678A pdb=" N SER B2361 " --> pdb=" O ASN B2357 " (cutoff:3.500A) removed outlier: 4.307A 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: 4.663A pdb=" N PHE B2395 " --> pdb=" O LEU B2391 " (cutoff:3.500A) removed outlier: 5.488A 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: 3.593A pdb=" N ARG B2471 " --> pdb=" O ASN B2467 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN B2472 " --> pdb=" O HIS B2468 " (cutoff:3.500A) Processing helix chain 'B' and resid 2475 through 2481 removed outlier: 4.543A pdb=" N ILE B2479 " --> pdb=" O GLY B2475 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B2480 " --> pdb=" O VAL B2476 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG B2481 " --> pdb=" O GLY B2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2475 through 2481' Processing helix chain 'B' and resid 2489 through 2504 Processing helix chain 'B' and resid 2508 through 2537 removed outlier: 3.576A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B2515 " --> pdb=" O LEU B2511 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B2516 " --> pdb=" O ILE B2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2550 removed outlier: 4.044A pdb=" N PHE B2548 " --> pdb=" O GLU B2544 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B2549 " --> pdb=" O ARG B2545 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASN B2550 " --> pdb=" O ASP B2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2544 through 2550' 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: 4.199A pdb=" N ASN B2613 " --> pdb=" O SER B2609 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B2614 " --> pdb=" O LEU B2610 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B2615 " --> pdb=" O VAL B2611 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU B2616 " --> pdb=" O SER B2612 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B2617 " --> pdb=" O ASN B2613 " (cutoff:3.500A) 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: 3.567A pdb=" N HIS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 231' Processing helix chain 'C' and resid 272 through 277 removed outlier: 4.079A pdb=" N ALA C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 5.450A 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: 3.597A pdb=" N ILE C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 447 " --> pdb=" O ASP C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 485 Processing helix chain 'C' and resid 502 through 513 removed outlier: 3.579A pdb=" N GLN C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 4.216A 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 544 removed outlier: 4.593A pdb=" N SER C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP C 543 " --> pdb=" O GLU C 539 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 565 removed outlier: 5.903A pdb=" N TYR C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU C 565 " --> pdb=" O ARG C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.435A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) removed outlier: 5.387A 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: 4.559A pdb=" N ASN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 5.661A 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: 3.844A pdb=" N LEU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 657 removed outlier: 3.560A pdb=" N LEU C 657 " --> pdb=" O CYS C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 666 removed outlier: 3.657A pdb=" N SER C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 665 " --> pdb=" O ASN C 661 " (cutoff:3.500A) removed outlier: 5.262A 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: 3.597A pdb=" N LEU C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 755 removed outlier: 3.699A pdb=" N ILE C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) removed outlier: 4.295A 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 784 Processing helix chain 'C' and resid 811 through 824 removed outlier: 3.635A pdb=" N ASN C 818 " --> pdb=" O ASP C 814 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP C 824 " --> pdb=" O ASN C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 848 removed outlier: 5.404A pdb=" N ALA C 848 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 874 removed outlier: 3.870A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 874 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 877 through 893 Processing helix chain 'C' and resid 961 through 1002 removed outlier: 3.794A pdb=" N LYS C 968 " --> pdb=" O VAL C 964 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN C 980 " --> pdb=" O GLN C 976 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 981 " --> pdb=" O PHE C 977 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1037 removed outlier: 3.768A pdb=" N MET C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1052 through 1066 removed outlier: 5.397A pdb=" N ASP C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1084 removed outlier: 3.652A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1095 removed outlier: 3.781A pdb=" N GLN C1094 " --> pdb=" O HIS C1090 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C1095 " --> pdb=" O THR C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1128 removed outlier: 5.241A pdb=" N GLU C1125 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C1126 " --> pdb=" O GLU C1122 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C1127 " --> pdb=" O LYS C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1184 removed outlier: 4.416A pdb=" N GLY C1184 " --> pdb=" O ASN C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1201 Processing helix chain 'C' and resid 1202 through 1212 Processing helix chain 'C' and resid 1218 through 1237 Processing helix chain 'C' and resid 1239 through 1250 removed outlier: 4.092A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 4.225A 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 removed outlier: 4.153A pdb=" N CYS C1275 " --> pdb=" O ASN C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1293 removed outlier: 3.818A pdb=" N LEU C1283 " --> pdb=" O SER C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1309 removed outlier: 3.979A pdb=" N LEU C1300 " --> pdb=" O HIS C1296 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA C1309 " --> pdb=" O THR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1314 through 1329 removed outlier: 3.815A 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: 4.125A 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 1401 Processing helix chain 'C' and resid 1406 through 1420 Processing helix chain 'C' and resid 1429 through 1434 removed outlier: 3.760A pdb=" N THR C1433 " --> pdb=" O LYS C1429 " (cutoff:3.500A) Processing helix chain 'C' and resid 1435 through 1458 Processing helix chain 'C' and resid 1461 through 1482 removed outlier: 3.879A pdb=" N VAL C1472 " --> pdb=" O VAL C1468 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C1473 " --> pdb=" O LEU C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1491 through 1511 removed outlier: 3.554A pdb=" N CYS C1511 " --> pdb=" O ARG C1507 " (cutoff:3.500A) Processing helix chain 'C' and resid 1516 through 1537 removed outlier: 3.522A 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 removed outlier: 3.506A pdb=" N LYS C1607 " --> pdb=" O GLU C1603 " (cutoff:3.500A) Proline residue: C1608 - end of helix removed outlier: 3.928A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) Proline residue: C1624 - end of helix Processing helix chain 'C' and resid 1632 through 1641 removed outlier: 4.003A pdb=" N GLY C1641 " --> pdb=" O ARG C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1655 removed outlier: 3.822A pdb=" N LYS C1652 " --> pdb=" O ILE C1648 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C1653 " --> pdb=" O GLN C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1658 through 1675 removed outlier: 3.561A pdb=" N LEU C1673 " --> pdb=" O LEU C1669 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C1674 " --> pdb=" O GLN C1670 " (cutoff:3.500A) removed outlier: 5.547A 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 removed outlier: 3.738A pdb=" N ILE C1721 " --> pdb=" O ASP C1717 " (cutoff:3.500A) Processing helix chain 'C' and resid 1733 through 1744 removed outlier: 3.555A 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 removed outlier: 3.767A pdb=" N GLN C1769 " --> pdb=" O ASN C1765 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C1770 " --> pdb=" O THR C1766 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C1779 " --> pdb=" O LEU C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 1781 through 1804 removed outlier: 5.240A pdb=" N PHE C1785 " --> pdb=" O LYS C1781 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE C1786 " --> pdb=" O SER C1782 " (cutoff:3.500A) Processing helix chain 'C' and resid 1864 through 1882 removed outlier: 3.759A pdb=" N ILE C1869 " --> pdb=" O THR C1865 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) removed outlier: 4.302A 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: 4.514A pdb=" N GLU C1906 " --> pdb=" O ASN C1902 " (cutoff:3.500A) Processing helix chain 'C' and resid 1917 through 1923 removed outlier: 3.838A pdb=" N GLY C1923 " --> pdb=" O THR C1919 " (cutoff:3.500A) Processing helix chain 'C' and resid 1924 through 1930 removed outlier: 3.912A pdb=" N TYR C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASN C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1931 through 1950 removed outlier: 4.680A pdb=" N GLY C1935 " --> pdb=" O GLU C1931 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU C1936 " --> pdb=" O ASP C1932 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY C1950 " --> pdb=" O GLU C1946 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1962 Processing helix chain 'C' and resid 1966 through 1976 removed outlier: 3.837A pdb=" N ILE C1970 " --> pdb=" O GLY C1966 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C1974 " --> pdb=" O ILE C1970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1978 through 1985 removed outlier: 3.849A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1986 through 2005 Processing helix chain 'C' and resid 2009 through 2021 removed outlier: 4.931A pdb=" N ALA C2013 " --> pdb=" O ASP C2009 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG C2021 " --> pdb=" O LEU C2017 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2036 Processing helix chain 'C' and resid 2038 through 2043 removed outlier: 3.790A pdb=" N SER C2042 " --> pdb=" O GLU C2038 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU C2043 " --> pdb=" O ARG C2039 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2038 through 2043' Processing helix chain 'C' and resid 2045 through 2062 removed outlier: 3.986A pdb=" N VAL C2049 " --> pdb=" O SER C2045 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2064 through 2073 Proline residue: C2073 - end of helix Processing helix chain 'C' and resid 2112 through 2122 removed outlier: 3.695A pdb=" N TYR C2117 " --> pdb=" O PRO C2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C2121 " --> pdb=" O TYR C2117 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER C2122 " --> pdb=" O GLU C2118 " (cutoff:3.500A) Processing helix chain 'C' and resid 2141 through 2147 removed outlier: 3.945A pdb=" N GLN C2145 " --> pdb=" O PRO C2141 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C2146 " --> pdb=" O GLY C2142 " (cutoff:3.500A) removed outlier: 4.523A 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: 4.612A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.562A 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 2222 removed outlier: 3.736A pdb=" N ARG C2200 " --> pdb=" O TRP C2196 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR C2202 " --> pdb=" O SER C2198 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU C2203 " --> pdb=" O ARG C2199 " (cutoff:3.500A) Processing helix chain 'C' and resid 2260 through 2276 Processing helix chain 'C' and resid 2277 through 2310 removed outlier: 6.382A pdb=" N THR C2306 " --> pdb=" O GLY C2302 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N PHE C2307 " --> pdb=" O ASN C2303 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C2308 " --> pdb=" O ARG C2304 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG C2309 " --> pdb=" O GLY C2305 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY C2310 " --> pdb=" O THR C2306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2311 through 2318 removed outlier: 5.755A pdb=" N MET C2318 " --> pdb=" O MET C2314 " (cutoff:3.500A) Processing helix chain 'C' and resid 2319 through 2336 Processing helix chain 'C' and resid 2337 through 2352 removed outlier: 4.893A pdb=" N TYR C2341 " --> pdb=" O HIS C2337 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER C2342 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU C2344 " --> pdb=" O PHE C2340 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C2345 " --> pdb=" O TYR C2341 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE C2346 " --> pdb=" O SER C2342 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP C2347 " --> pdb=" O ILE C2343 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C2348 " --> pdb=" O LEU C2344 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE C2349 " --> pdb=" O LEU C2345 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR C2350 " --> pdb=" O PHE C2346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2353 through 2364 removed outlier: 3.678A pdb=" N SER C2361 " --> pdb=" O ASN C2357 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.663A pdb=" N PHE C2395 " --> pdb=" O LEU C2391 " (cutoff:3.500A) removed outlier: 5.488A 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: 3.593A pdb=" N ARG C2471 " --> pdb=" O ASN C2467 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN C2472 " --> pdb=" O HIS C2468 " (cutoff:3.500A) Processing helix chain 'C' and resid 2475 through 2481 removed outlier: 4.543A pdb=" N ILE C2479 " --> pdb=" O GLY C2475 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C2480 " --> pdb=" O VAL C2476 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG C2481 " --> pdb=" O GLY C2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2475 through 2481' Processing helix chain 'C' and resid 2489 through 2504 Processing helix chain 'C' and resid 2508 through 2537 removed outlier: 3.575A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C2515 " --> pdb=" O LEU C2511 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C2516 " --> pdb=" O ILE C2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2550 removed outlier: 4.044A pdb=" N PHE C2548 " --> pdb=" O GLU C2544 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C2549 " --> pdb=" O ARG C2545 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN C2550 " --> pdb=" O ASP C2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2544 through 2550' 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: 4.198A pdb=" N ASN C2613 " --> pdb=" O SER C2609 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C2614 " --> pdb=" O LEU C2610 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY C2615 " --> pdb=" O VAL C2611 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU C2616 " --> pdb=" O SER C2612 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C2617 " --> pdb=" O ASN C2613 " (cutoff:3.500A) 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: 3.567A pdb=" N HIS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 226 through 231' Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.080A pdb=" N ALA D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 5.450A 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: 3.597A pdb=" N ILE D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP D 447 " --> pdb=" O ASP D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 485 Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.579A pdb=" N GLN D 506 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 4.216A 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 544 removed outlier: 4.592A pdb=" N SER D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP D 543 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 565 removed outlier: 5.903A pdb=" N TYR D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.435A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 5.387A 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: 4.558A pdb=" N ASN D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 5.662A 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 Processing helix chain 'D' and resid 627 through 640 removed outlier: 3.844A pdb=" N LEU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 657 removed outlier: 3.561A pdb=" N LEU D 657 " --> pdb=" O CYS D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 666 removed outlier: 3.656A pdb=" N SER D 662 " --> pdb=" O ASP D 658 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) removed outlier: 5.263A 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: 3.597A pdb=" N LEU D 741 " --> pdb=" O ALA D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 755 removed outlier: 3.699A pdb=" N ILE D 748 " --> pdb=" O GLN D 744 " (cutoff:3.500A) removed outlier: 4.295A 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 784 Processing helix chain 'D' and resid 811 through 824 removed outlier: 3.633A pdb=" N ASN D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP D 824 " --> pdb=" O ASN D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 848 removed outlier: 5.404A pdb=" N ALA D 848 " --> pdb=" O VAL D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 874 removed outlier: 3.869A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 874 " --> pdb=" O LEU D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 877 through 893 Processing helix chain 'D' and resid 961 through 1002 removed outlier: 3.794A pdb=" N LYS D 968 " --> pdb=" O VAL D 964 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN D 980 " --> pdb=" O GLN D 976 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 981 " --> pdb=" O PHE D 977 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 982 " --> pdb=" O ILE D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1037 removed outlier: 3.768A pdb=" N MET D1035 " --> pdb=" O GLN D1031 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY D1037 " --> pdb=" O GLU D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1052 through 1066 removed outlier: 5.398A pdb=" N ASP D1066 " --> pdb=" O LEU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1084 removed outlier: 3.651A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.781A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1128 removed outlier: 5.243A pdb=" N GLU D1125 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU D1126 " --> pdb=" O GLU D1122 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1184 removed outlier: 4.416A pdb=" N GLY D1184 " --> pdb=" O ASN D1180 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1201 Processing helix chain 'D' and resid 1202 through 1212 Processing helix chain 'D' and resid 1218 through 1237 Processing helix chain 'D' and resid 1239 through 1250 removed outlier: 4.092A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 4.224A 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 removed outlier: 4.154A pdb=" N CYS D1275 " --> pdb=" O ASN D1271 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 removed outlier: 3.817A pdb=" N LEU D1283 " --> pdb=" O SER D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1309 removed outlier: 3.978A pdb=" N LEU D1300 " --> pdb=" O HIS D1296 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA D1309 " --> pdb=" O THR D1305 " (cutoff:3.500A) Processing helix chain 'D' and resid 1314 through 1329 removed outlier: 3.814A 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: 4.125A 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 1401 Processing helix chain 'D' and resid 1406 through 1420 Processing helix chain 'D' and resid 1429 through 1434 removed outlier: 3.760A pdb=" N THR D1433 " --> pdb=" O LYS D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1435 through 1458 Processing helix chain 'D' and resid 1461 through 1482 removed outlier: 3.878A pdb=" N VAL D1472 " --> pdb=" O VAL D1468 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1491 through 1511 removed outlier: 3.554A pdb=" N CYS D1511 " --> pdb=" O ARG D1507 " (cutoff:3.500A) Processing helix chain 'D' and resid 1516 through 1537 removed outlier: 3.522A 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 removed outlier: 3.505A pdb=" N LYS D1607 " --> pdb=" O GLU D1603 " (cutoff:3.500A) Proline residue: D1608 - end of helix removed outlier: 3.928A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) Proline residue: D1624 - end of helix Processing helix chain 'D' and resid 1632 through 1641 removed outlier: 4.004A pdb=" N GLY D1641 " --> pdb=" O ARG D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1655 removed outlier: 3.821A pdb=" N LYS D1652 " --> pdb=" O ILE D1648 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1658 through 1675 removed outlier: 3.562A pdb=" N LEU D1673 " --> pdb=" O LEU D1669 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D1674 " --> pdb=" O GLN D1670 " (cutoff:3.500A) removed outlier: 5.548A 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 removed outlier: 3.738A pdb=" N ILE D1721 " --> pdb=" O ASP D1717 " (cutoff:3.500A) Processing helix chain 'D' and resid 1733 through 1744 removed outlier: 3.555A 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: 3.767A pdb=" N GLN D1769 " --> pdb=" O ASN D1765 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS D1770 " --> pdb=" O THR D1766 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D1779 " --> pdb=" O LEU D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 1781 through 1804 removed outlier: 5.241A pdb=" N PHE D1785 " --> pdb=" O LYS D1781 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE D1786 " --> pdb=" O SER D1782 " (cutoff:3.500A) Processing helix chain 'D' and resid 1864 through 1882 removed outlier: 3.758A pdb=" N ILE D1869 " --> pdb=" O THR D1865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) removed outlier: 4.302A 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: 4.514A pdb=" N GLU D1906 " --> pdb=" O ASN D1902 " (cutoff:3.500A) Processing helix chain 'D' and resid 1917 through 1923 removed outlier: 3.838A pdb=" N GLY D1923 " --> pdb=" O THR D1919 " (cutoff:3.500A) Processing helix chain 'D' and resid 1924 through 1930 removed outlier: 3.912A pdb=" N TYR D1928 " --> pdb=" O LEU D1924 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASN D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1931 through 1950 removed outlier: 4.678A pdb=" N GLY D1935 " --> pdb=" O GLU D1931 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU D1936 " --> pdb=" O ASP D1932 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLY D1950 " --> pdb=" O GLU D1946 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1962 Processing helix chain 'D' and resid 1966 through 1976 removed outlier: 3.837A pdb=" N ILE D1970 " --> pdb=" O GLY D1966 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1978 through 1985 removed outlier: 3.849A pdb=" N LYS D1983 " --> pdb=" O SER D1979 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR D1984 " --> pdb=" O PRO D1980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1986 through 2005 Processing helix chain 'D' and resid 2009 through 2021 removed outlier: 4.931A pdb=" N ALA D2013 " --> pdb=" O ASP D2009 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG D2021 " --> pdb=" O LEU D2017 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2036 Processing helix chain 'D' and resid 2038 through 2043 removed outlier: 3.791A pdb=" N SER D2042 " --> pdb=" O GLU D2038 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU D2043 " --> pdb=" O ARG D2039 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2038 through 2043' Processing helix chain 'D' and resid 2045 through 2062 removed outlier: 3.987A pdb=" N VAL D2049 " --> pdb=" O SER D2045 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) Processing helix chain 'D' and resid 2064 through 2073 Proline residue: D2073 - end of helix Processing helix chain 'D' and resid 2112 through 2122 removed outlier: 3.694A pdb=" N TYR D2117 " --> pdb=" O PRO D2113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D2121 " --> pdb=" O TYR D2117 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER D2122 " --> pdb=" O GLU D2118 " (cutoff:3.500A) Processing helix chain 'D' and resid 2141 through 2147 removed outlier: 3.945A pdb=" N GLN D2145 " --> pdb=" O PRO D2141 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE D2146 " --> pdb=" O GLY D2142 " (cutoff:3.500A) removed outlier: 4.523A 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: 4.613A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.563A 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 2222 removed outlier: 3.736A pdb=" N ARG D2200 " --> pdb=" O TRP D2196 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N THR D2202 " --> pdb=" O SER D2198 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D2203 " --> pdb=" O ARG D2199 " (cutoff:3.500A) Processing helix chain 'D' and resid 2260 through 2276 Processing helix chain 'D' and resid 2277 through 2310 removed outlier: 6.382A pdb=" N THR D2306 " --> pdb=" O GLY D2302 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N PHE D2307 " --> pdb=" O ASN D2303 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D2308 " --> pdb=" O ARG D2304 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG D2309 " --> pdb=" O GLY D2305 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY D2310 " --> pdb=" O THR D2306 " (cutoff:3.500A) Processing helix chain 'D' and resid 2311 through 2318 removed outlier: 5.755A pdb=" N MET D2318 " --> pdb=" O MET D2314 " (cutoff:3.500A) Processing helix chain 'D' and resid 2319 through 2336 Processing helix chain 'D' and resid 2337 through 2352 removed outlier: 4.893A pdb=" N TYR D2341 " --> pdb=" O HIS D2337 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER D2342 " --> pdb=" O GLU D2338 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE D2343 " --> pdb=" O LEU D2339 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU D2344 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D2345 " --> pdb=" O TYR D2341 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE D2346 " --> pdb=" O SER D2342 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP D2347 " --> pdb=" O ILE D2343 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU D2348 " --> pdb=" O LEU D2344 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE D2349 " --> pdb=" O LEU D2345 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR D2350 " --> pdb=" O PHE D2346 " (cutoff:3.500A) Processing helix chain 'D' and resid 2353 through 2364 removed outlier: 3.678A pdb=" N SER D2361 " --> pdb=" O ASN D2357 " (cutoff:3.500A) removed outlier: 4.308A 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: 4.663A pdb=" N PHE D2395 " --> pdb=" O LEU D2391 " (cutoff:3.500A) removed outlier: 5.487A 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: 3.593A pdb=" N ARG D2471 " --> pdb=" O ASN D2467 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN D2472 " --> pdb=" O HIS D2468 " (cutoff:3.500A) Processing helix chain 'D' and resid 2475 through 2481 removed outlier: 4.543A pdb=" N ILE D2479 " --> pdb=" O GLY D2475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D2480 " --> pdb=" O VAL D2476 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG D2481 " --> pdb=" O GLY D2477 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2475 through 2481' Processing helix chain 'D' and resid 2489 through 2504 Processing helix chain 'D' and resid 2508 through 2537 removed outlier: 3.576A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D2515 " --> pdb=" O LEU D2511 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE D2516 " --> pdb=" O ILE D2512 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2550 removed outlier: 4.045A pdb=" N PHE D2548 " --> pdb=" O GLU D2544 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D2549 " --> pdb=" O ARG D2545 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASN D2550 " --> pdb=" O ASP D2546 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2544 through 2550' 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: 4.198A pdb=" N ASN D2613 " --> pdb=" O SER D2609 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU D2614 " --> pdb=" O LEU D2610 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY D2615 " --> pdb=" O VAL D2611 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU D2616 " --> pdb=" O SER D2612 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D2617 " --> pdb=" O ASN D2613 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.725A pdb=" N SER A 15 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 24 through 28 removed outlier: 4.682A pdb=" N PHE A 25 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 39 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 57 through 61 removed outlier: 13.461A pdb=" N ILE A 122 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N VAL A 135 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU A 124 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 131 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= 5, first strand: chain 'A' and resid 194 through 198 removed outlier: 4.160A pdb=" N GLU A 209 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 262 through 265 removed outlier: 5.465A pdb=" N LEU A 243 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N CYS A 254 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 13.993A pdb=" N VAL A 241 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 315 through 320 removed outlier: 6.533A pdb=" N LYS A 351 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 396 through 401 removed outlier: 4.037A pdb=" N MET A 416 " --> pdb=" O THR A 401 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 667 through 672 removed outlier: 5.155A pdb=" N GLU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 800 through 803 removed outlier: 3.968A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 2123 through 2128 removed outlier: 4.258A pdb=" N SER A2132 " --> pdb=" O ARG A2128 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.726A pdb=" N SER B 15 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 24 through 28 removed outlier: 4.681A pdb=" N PHE B 25 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 39 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 57 through 61 removed outlier: 13.461A pdb=" N ILE B 122 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N VAL B 135 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 124 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 131 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 162 through 166 Processing sheet with id= 16, first strand: chain 'B' and resid 194 through 198 removed outlier: 4.159A pdb=" N GLU B 209 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 262 through 265 removed outlier: 5.464A pdb=" N LEU B 243 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N CYS B 254 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 13.992A pdb=" N VAL B 241 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.533A pdb=" N LYS B 351 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 396 through 401 removed outlier: 4.038A pdb=" N MET B 416 " --> pdb=" O THR B 401 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 667 through 672 removed outlier: 5.155A pdb=" N GLU B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 800 through 803 removed outlier: 3.968A pdb=" N LEU B1098 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP B 803 " --> pdb=" O LEU B1098 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 2123 through 2128 removed outlier: 4.259A pdb=" N SER B2132 " --> pdb=" O ARG B2128 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C' and resid 14 through 18 removed outlier: 3.726A pdb=" N SER C 15 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 24 through 28 removed outlier: 4.682A pdb=" N PHE C 25 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 39 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 57 through 61 removed outlier: 13.462A pdb=" N ILE C 122 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N VAL C 135 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 124 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 131 " --> pdb=" O HIS C 126 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 162 through 166 Processing sheet with id= 27, first strand: chain 'C' and resid 194 through 198 removed outlier: 4.159A pdb=" N GLU C 209 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 262 through 265 removed outlier: 5.464A pdb=" N LEU C 243 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N CYS C 254 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 13.993A pdb=" N VAL C 241 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 315 through 320 removed outlier: 6.532A pdb=" N LYS C 351 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 396 through 401 removed outlier: 4.037A pdb=" N MET C 416 " --> pdb=" O THR C 401 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 667 through 672 removed outlier: 5.155A pdb=" N GLU C 702 " --> pdb=" O ASP C 698 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 800 through 803 removed outlier: 3.968A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'C' and resid 2123 through 2128 removed outlier: 4.258A pdb=" N SER C2132 " --> pdb=" O ARG C2128 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 14 through 18 removed outlier: 3.725A pdb=" N SER D 15 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 24 through 28 removed outlier: 4.682A pdb=" N PHE D 25 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 39 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 57 through 61 removed outlier: 13.462A pdb=" N ILE D 122 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 135 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU D 124 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 131 " --> pdb=" O HIS D 126 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'D' and resid 162 through 166 Processing sheet with id= 38, first strand: chain 'D' and resid 194 through 198 removed outlier: 4.159A pdb=" N GLU D 209 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 262 through 265 removed outlier: 5.464A pdb=" N LEU D 243 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N CYS D 254 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 13.993A pdb=" N VAL D 241 " --> pdb=" O CYS D 254 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 315 through 320 removed outlier: 6.533A pdb=" N LYS D 351 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'D' and resid 396 through 401 removed outlier: 4.037A pdb=" N MET D 416 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'D' and resid 667 through 672 removed outlier: 5.155A pdb=" N GLU D 702 " --> pdb=" O ASP D 698 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'D' and resid 800 through 803 removed outlier: 3.968A pdb=" N LEU D1098 " --> pdb=" O ARG D 801 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP D 803 " --> pdb=" O LEU D1098 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'D' and resid 2123 through 2128 removed outlier: 4.258A pdb=" N SER D2132 " --> pdb=" O ARG D2128 " (cutoff:3.500A) 4340 hydrogen bonds defined for protein. 12996 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: 68.90 Time building geometry restraints manager: 94.78 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: 170 1.23 - 1.42: 30322 1.42 - 1.62: 42596 1.62 - 1.81: 720 Bond restraints: 145696 Sorted by residual: bond pdb=" CB MET C1448 " pdb=" CG MET C1448 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.67e-01 bond pdb=" CB MET B1448 " pdb=" CG MET B1448 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.49e-01 bond pdb=" CB MET A1448 " pdb=" CG MET A1448 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" CB MET D1448 " pdb=" CG MET D1448 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.17e-01 bond pdb=" CB ASP A 772 " pdb=" CG ASP A 772 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.77e-01 ... (remaining 145691 not shown) Histogram of bond angle deviations from ideal: 99.57 - 107.63: 8634 107.63 - 115.68: 179308 115.68 - 123.74: 64217 123.74 - 131.80: 11245 131.80 - 139.86: 92 Bond angle restraints: 263496 Sorted by residual: angle pdb=" CB MET A1986 " pdb=" CG MET A1986 " pdb=" SD MET A1986 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" CB MET D1986 " pdb=" CG MET D1986 " pdb=" SD MET D1986 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.93e+00 angle pdb=" CB MET C1986 " pdb=" CG MET C1986 " pdb=" SD MET C1986 " ideal model delta sigma weight residual 112.70 121.13 -8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" CB MET B1986 " pdb=" CG MET B1986 " pdb=" SD MET B1986 " ideal model delta sigma weight residual 112.70 121.13 -8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" CB MET C1182 " pdb=" CG MET C1182 " pdb=" SD MET C1182 " ideal model delta sigma weight residual 112.70 120.96 -8.26 3.00e+00 1.11e-01 7.59e+00 ... (remaining 263491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.47: 63893 24.47 - 48.93: 3513 48.93 - 73.40: 678 73.40 - 97.86: 100 97.86 - 122.33: 16 Dihedral angle restraints: 68200 sinusoidal: 37244 harmonic: 30956 Sorted by residual: dihedral pdb=" CA ASP B 789 " pdb=" C ASP B 789 " pdb=" N PRO B 790 " pdb=" CA PRO B 790 " ideal model delta harmonic sigma weight residual 180.00 154.20 25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ASP A 789 " pdb=" C ASP A 789 " pdb=" N PRO A 790 " pdb=" CA PRO A 790 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ASP D 789 " pdb=" C ASP D 789 " pdb=" N PRO D 790 " pdb=" CA PRO D 790 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 68197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 10277 0.058 - 0.117: 1092 0.117 - 0.175: 47 0.175 - 0.234: 0 0.234 - 0.292: 12 Chirality restraints: 11428 Sorted by residual: chirality pdb=" C3' ATP C3003 " pdb=" C2' ATP C3003 " pdb=" C4' ATP C3003 " pdb=" O3' ATP C3003 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B3003 " pdb=" C1' ATP B3003 " pdb=" C3' ATP B3003 " pdb=" O2' ATP B3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP D3003 " pdb=" C1' ATP D3003 " pdb=" C3' ATP D3003 " pdb=" O2' ATP D3003 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 11425 not shown) Planarity restraints: 21340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D1455 " -0.214 9.50e-02 1.11e+02 7.16e-02 6.35e+00 pdb=" NE ARG D1455 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D1455 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D1455 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D1455 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D1455 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG D1455 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D1455 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D1455 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1455 " -0.213 9.50e-02 1.11e+02 7.14e-02 6.33e+00 pdb=" NE ARG A1455 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A1455 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1455 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A1455 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A1455 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A1455 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A1455 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1455 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1455 " 0.213 9.50e-02 1.11e+02 7.14e-02 6.33e+00 pdb=" NE ARG C1455 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C1455 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG C1455 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C1455 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C1455 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG C1455 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C1455 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C1455 " -0.000 2.00e-02 2.50e+03 ... (remaining 21337 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 4064 2.14 - 2.75: 269049 2.75 - 3.37: 411989 3.37 - 3.98: 497468 3.98 - 4.60: 794557 Nonbonded interactions: 1977127 Sorted by model distance: nonbonded pdb=" OE2 GLU A 256 " pdb=" H GLY A 259 " model vdw 1.523 1.850 nonbonded pdb=" OE2 GLU D 256 " pdb=" H GLY D 259 " model vdw 1.523 1.850 nonbonded pdb=" OE2 GLU B 256 " pdb=" H GLY B 259 " model vdw 1.523 1.850 nonbonded pdb=" OE2 GLU C 256 " pdb=" H GLY C 259 " model vdw 1.524 1.850 nonbonded pdb=" OE1 GLU D 232 " pdb=" H GLU D 232 " model vdw 1.615 1.850 ... (remaining 1977122 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: 16.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.580 Extract box with map and model: 60.590 Check model and map are aligned: 1.640 Set scattering table: 1.040 Process input model: 426.720 Find NCS groups from input model: 5.790 Set up NCS constraints: 0.650 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: 0.030 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 516.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 0.030 73644 Z= 0.129 Angle : 0.471 9.607 99580 Z= 0.241 Chirality : 0.034 0.292 11428 Planarity : 0.003 0.094 12652 Dihedral : 16.635 122.329 27596 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.21 % Rotamer: Outliers : 0.26 % Allowed : 15.03 % Favored : 84.71 % 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: 3.11 (0.07), residues: 5544 sheet: -0.13 (0.21), residues: 648 loop : 0.05 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 803 HIS 0.006 0.000 HIS C1790 PHE 0.016 0.001 PHE A 994 TYR 0.022 0.001 TYR A 65 ARG 0.014 0.000 ARG C1455 *********************** 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 1746 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1725 time to evaluate : 8.657 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 31 LEU cc_start: 0.6056 (mt) cc_final: 0.4475 (mt) REVERT: A 53 ARG cc_start: 0.7207 (mtm110) cc_final: 0.6988 (mtm110) REVERT: A 62 MET cc_start: 0.5993 (mmm) cc_final: 0.5655 (mmm) REVERT: A 388 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7992 (mtm-85) REVERT: A 656 VAL cc_start: 0.8629 (p) cc_final: 0.8344 (m) REVERT: A 714 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 753 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8423 (mt0) REVERT: A 973 GLU cc_start: 0.6437 (mt-10) cc_final: 0.6166 (mt-10) REVERT: A 1107 TYR cc_start: 0.8701 (t80) cc_final: 0.8198 (t80) REVERT: A 1189 MET cc_start: 0.8222 (tmm) cc_final: 0.7985 (tmm) REVERT: A 1363 MET cc_start: 0.8335 (ttm) cc_final: 0.8097 (ttm) REVERT: A 1688 LYS cc_start: 0.8372 (tptm) cc_final: 0.8086 (tppt) REVERT: A 1731 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7071 (mm-30) REVERT: A 1780 LYS cc_start: 0.8560 (tppt) cc_final: 0.8110 (tppt) REVERT: A 2030 LYS cc_start: 0.8197 (mttt) cc_final: 0.7905 (mttp) REVERT: A 2283 ASN cc_start: 0.8345 (m-40) cc_final: 0.8101 (m-40) REVERT: B 53 ARG cc_start: 0.7194 (mtm110) cc_final: 0.6687 (mtp180) REVERT: B 62 MET cc_start: 0.6236 (mmm) cc_final: 0.5816 (tpp) REVERT: B 70 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8590 (mm-40) REVERT: B 139 LEU cc_start: 0.7778 (mt) cc_final: 0.7548 (mt) REVERT: B 161 TRP cc_start: 0.7738 (m-10) cc_final: 0.7508 (m-10) REVERT: B 275 SER cc_start: 0.8844 (m) cc_final: 0.8392 (t) REVERT: B 552 MET cc_start: 0.7987 (ttp) cc_final: 0.7764 (ttp) REVERT: B 572 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 660 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9013 (tppp) REVERT: B 763 CYS cc_start: 0.7703 (m) cc_final: 0.7449 (m) REVERT: B 803 TRP cc_start: 0.6986 (t60) cc_final: 0.6773 (t60) REVERT: B 841 LEU cc_start: 0.5685 (mp) cc_final: 0.5233 (mt) REVERT: B 1190 ARG cc_start: 0.8778 (tpt170) cc_final: 0.8489 (tpt-90) REVERT: B 1363 MET cc_start: 0.8118 (ttm) cc_final: 0.7888 (ttm) REVERT: B 1364 TYR cc_start: 0.8441 (t80) cc_final: 0.7614 (t80) REVERT: B 1411 MET cc_start: 0.7320 (ttt) cc_final: 0.6925 (tpt) REVERT: B 1594 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8446 (mmtm) REVERT: B 1689 MET cc_start: 0.7547 (mtm) cc_final: 0.7159 (mtm) REVERT: B 1731 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6985 (mm-30) REVERT: B 1780 LYS cc_start: 0.8620 (tppt) cc_final: 0.8202 (tppt) REVERT: B 1884 HIS cc_start: 0.8385 (m-70) cc_final: 0.8139 (m-70) REVERT: B 2027 ASP cc_start: 0.8152 (m-30) cc_final: 0.7503 (m-30) REVERT: B 2513 PHE cc_start: 0.8188 (t80) cc_final: 0.7828 (t80) REVERT: C 62 MET cc_start: 0.6533 (mmm) cc_final: 0.6324 (tpp) REVERT: C 98 GLN cc_start: 0.8231 (mt0) cc_final: 0.7990 (mm110) REVERT: C 388 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7986 (mtm-85) REVERT: C 552 MET cc_start: 0.8094 (ttp) cc_final: 0.7834 (ttp) REVERT: C 745 TYR cc_start: 0.7435 (m-80) cc_final: 0.7183 (m-80) REVERT: C 763 CYS cc_start: 0.7868 (m) cc_final: 0.7651 (m) REVERT: C 1206 MET cc_start: 0.8859 (mmp) cc_final: 0.8643 (mmp) REVERT: C 1364 TYR cc_start: 0.8553 (t80) cc_final: 0.8305 (t80) REVERT: C 1411 MET cc_start: 0.7455 (ttt) cc_final: 0.7105 (tpt) REVERT: C 1780 LYS cc_start: 0.8741 (tppt) cc_final: 0.8251 (tppt) REVERT: C 1869 ILE cc_start: 0.8822 (tp) cc_final: 0.8540 (tp) REVERT: C 2027 ASP cc_start: 0.8102 (m-30) cc_final: 0.7440 (m-30) REVERT: C 2030 LYS cc_start: 0.8638 (mttt) cc_final: 0.8332 (mttp) REVERT: C 2345 LEU cc_start: 0.7787 (mt) cc_final: 0.7578 (mt) REVERT: D 62 MET cc_start: 0.6625 (mmm) cc_final: 0.6284 (mmm) REVERT: D 98 GLN cc_start: 0.8165 (mt0) cc_final: 0.7891 (mm-40) REVERT: D 552 MET cc_start: 0.8094 (ttp) cc_final: 0.7854 (ttp) REVERT: D 656 VAL cc_start: 0.8712 (p) cc_final: 0.8507 (m) REVERT: D 753 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8458 (mt0) REVERT: D 834 MET cc_start: 0.8604 (mtt) cc_final: 0.8348 (mtm) REVERT: D 1249 HIS cc_start: 0.8535 (m-70) cc_final: 0.8309 (m-70) REVERT: D 1411 MET cc_start: 0.7589 (ttt) cc_final: 0.7172 (tpt) REVERT: D 1658 GLU cc_start: 0.6905 (mp0) cc_final: 0.6682 (mp0) REVERT: D 1870 MET cc_start: 0.7764 (tpp) cc_final: 0.7309 (tpp) REVERT: D 1885 ASN cc_start: 0.8679 (t0) cc_final: 0.8444 (t0) REVERT: D 2027 ASP cc_start: 0.8135 (m-30) cc_final: 0.7545 (m-30) REVERT: D 2030 LYS cc_start: 0.8619 (mttt) cc_final: 0.8362 (mttp) outliers start: 21 outliers final: 13 residues processed: 1727 average time/residue: 1.7324 time to fit residues: 4991.6741 Evaluate side-chains 1596 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1583 time to evaluate : 8.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1797 GLN Chi-restraints excluded: chain B residue 1531 MET Chi-restraints excluded: chain B residue 1797 GLN Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1797 GLN Chi-restraints excluded: chain D residue 758 ASP Chi-restraints excluded: chain D residue 1531 MET Chi-restraints excluded: chain D residue 1797 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 756 optimal weight: 0.3980 chunk 679 optimal weight: 8.9990 chunk 376 optimal weight: 2.9990 chunk 231 optimal weight: 8.9990 chunk 458 optimal weight: 1.9990 chunk 362 optimal weight: 10.0000 chunk 702 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 chunk 427 optimal weight: 1.9990 chunk 522 optimal weight: 8.9990 chunk 813 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN A 869 ASN B 248 GLN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2164 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2164 GLN D2210 ASN D2592 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 73644 Z= 0.329 Angle : 0.546 7.377 99580 Z= 0.291 Chirality : 0.036 0.206 11428 Planarity : 0.004 0.071 12652 Dihedral : 5.708 79.387 9950 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 1.80 % Allowed : 14.05 % Favored : 84.15 % 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: 2.77 (0.09), residues: 8876 helix: 2.90 (0.07), residues: 5684 sheet: -0.37 (0.20), residues: 716 loop : -0.05 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 219 HIS 0.009 0.001 HIS A 868 PHE 0.021 0.001 PHE C 244 TYR 0.016 0.001 TYR B 17 ARG 0.008 0.001 ARG B1455 *********************** 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 1781 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1637 time to evaluate : 7.849 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 ARG cc_start: 0.7367 (mtm110) cc_final: 0.6514 (mtp180) REVERT: A 388 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8321 (mtm-85) REVERT: A 714 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7557 (mt-10) REVERT: A 754 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8543 (mm-40) REVERT: A 816 ASP cc_start: 0.7852 (m-30) cc_final: 0.7503 (m-30) REVERT: A 973 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6334 (mt-10) REVERT: A 1105 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 1107 TYR cc_start: 0.8733 (t80) cc_final: 0.8495 (t80) REVERT: A 1363 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8160 (ttm) REVERT: A 1402 HIS cc_start: 0.7965 (t70) cc_final: 0.7293 (t-90) REVERT: A 1455 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7948 (mtp-110) REVERT: A 1531 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: A 1731 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7006 (mm-30) REVERT: A 1780 LYS cc_start: 0.8592 (tppt) cc_final: 0.8154 (tppt) REVERT: A 2053 ILE cc_start: 0.8425 (mm) cc_final: 0.8035 (mt) REVERT: A 2283 ASN cc_start: 0.8345 (m-40) cc_final: 0.8074 (m-40) REVERT: B 62 MET cc_start: 0.6741 (mmm) cc_final: 0.6505 (tpp) REVERT: B 211 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7759 (p0) REVERT: B 441 ASP cc_start: 0.7908 (m-30) cc_final: 0.7671 (m-30) REVERT: B 552 MET cc_start: 0.7925 (ttp) cc_final: 0.7702 (ttp) REVERT: B 816 ASP cc_start: 0.8066 (m-30) cc_final: 0.7859 (m-30) REVERT: B 841 LEU cc_start: 0.6214 (mp) cc_final: 0.5804 (mt) REVERT: B 1096 GLN cc_start: 0.7154 (tp40) cc_final: 0.6898 (mt0) REVERT: B 1105 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 1206 MET cc_start: 0.8741 (mmp) cc_final: 0.8344 (mmp) REVERT: B 1363 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: B 1411 MET cc_start: 0.7456 (ttt) cc_final: 0.7050 (tpt) REVERT: B 1448 MET cc_start: 0.7548 (tmm) cc_final: 0.7348 (tmm) REVERT: B 1531 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7376 (mmm) REVERT: B 1633 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 1731 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 2027 ASP cc_start: 0.8229 (m-30) cc_final: 0.7584 (m-30) REVERT: B 2030 LYS cc_start: 0.8469 (mttt) cc_final: 0.8156 (mttp) REVERT: C 388 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8286 (mtm-85) REVERT: C 457 GLU cc_start: 0.8670 (tt0) cc_final: 0.8444 (tp30) REVERT: C 494 LEU cc_start: 0.8160 (mp) cc_final: 0.7792 (mt) REVERT: C 552 MET cc_start: 0.8038 (ttp) cc_final: 0.7757 (ttp) REVERT: C 778 CYS cc_start: 0.7941 (t) cc_final: 0.7580 (t) REVERT: C 984 ASP cc_start: 0.7601 (t0) cc_final: 0.7361 (t0) REVERT: C 1105 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 1190 ARG cc_start: 0.8850 (tpt170) cc_final: 0.8358 (tpt170) REVERT: C 1264 MET cc_start: 0.8665 (ttm) cc_final: 0.8461 (ttp) REVERT: C 1270 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8643 (t0) REVERT: C 1411 MET cc_start: 0.7583 (ttt) cc_final: 0.7205 (tpt) REVERT: C 1736 LEU cc_start: 0.8720 (tp) cc_final: 0.8469 (tt) REVERT: C 1780 LYS cc_start: 0.8791 (tppt) cc_final: 0.8306 (tppt) REVERT: C 1869 ILE cc_start: 0.8946 (tp) cc_final: 0.8689 (tp) REVERT: C 1906 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6619 (mm-30) REVERT: C 2030 LYS cc_start: 0.8661 (mttt) cc_final: 0.8376 (mttp) REVERT: C 2338 GLU cc_start: 0.8075 (mp0) cc_final: 0.7572 (mt-10) REVERT: D 62 MET cc_start: 0.6991 (mmm) cc_final: 0.6661 (mmm) REVERT: D 98 GLN cc_start: 0.8159 (mt0) cc_final: 0.7853 (mm-40) REVERT: D 211 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8084 (p0) REVERT: D 552 MET cc_start: 0.8034 (ttp) cc_final: 0.7805 (ttp) REVERT: D 656 VAL cc_start: 0.8779 (p) cc_final: 0.8520 (m) REVERT: D 714 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7747 (mt-10) REVERT: D 965 MET cc_start: 0.6975 (tpp) cc_final: 0.6656 (tpp) REVERT: D 984 ASP cc_start: 0.7542 (t0) cc_final: 0.7231 (t0) REVERT: D 1064 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7638 (ttt) REVERT: D 1411 MET cc_start: 0.7700 (ttt) cc_final: 0.7265 (tpt) REVERT: D 1531 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: D 1791 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7666 (p0) REVERT: D 1906 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6849 (mm-30) REVERT: D 1986 MET cc_start: 0.8183 (tpp) cc_final: 0.7633 (tpp) REVERT: D 2027 ASP cc_start: 0.8235 (m-30) cc_final: 0.7620 (m-30) REVERT: D 2030 LYS cc_start: 0.8652 (mttt) cc_final: 0.8388 (mttp) REVERT: D 2145 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8058 (tm-30) outliers start: 144 outliers final: 100 residues processed: 1702 average time/residue: 1.6711 time to fit residues: 4787.6354 Evaluate side-chains 1672 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1561 time to evaluate : 8.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 854 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1588 TYR Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1221 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1531 MET Chi-restraints excluded: chain B residue 1588 TYR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1997 SER Chi-restraints excluded: chain B residue 2061 SER Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 752 SER Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 973 GLU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1388 THR Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1588 TYR Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1531 MET Chi-restraints excluded: chain D residue 1588 TYR Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 2061 SER Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2143 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 452 optimal weight: 0.0470 chunk 252 optimal weight: 2.9990 chunk 677 optimal weight: 0.9980 chunk 554 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 815 optimal weight: 3.9990 chunk 880 optimal weight: 0.9990 chunk 725 optimal weight: 6.9990 chunk 808 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 653 optimal weight: 0.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS B 783 HIS B 869 ASN B2510 ASN C 869 ASN C1065 HIS D 562 HIS D 869 ASN D1065 HIS ** D1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2164 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 73644 Z= 0.213 Angle : 0.472 7.150 99580 Z= 0.250 Chirality : 0.034 0.197 11428 Planarity : 0.003 0.047 12652 Dihedral : 5.014 88.323 9928 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 1.59 % Allowed : 14.25 % Favored : 84.16 % 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: 3.01 (0.07), residues: 5688 sheet: -0.34 (0.20), residues: 716 loop : -0.07 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 219 HIS 0.005 0.001 HIS A 562 PHE 0.023 0.001 PHE B 761 TYR 0.013 0.001 TYR C 257 ARG 0.004 0.000 ARG D2524 *********************** 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 1731 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1604 time to evaluate : 8.785 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 388 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8238 (mtm-85) REVERT: A 714 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 816 ASP cc_start: 0.7792 (m-30) cc_final: 0.7412 (m-30) REVERT: A 840 TYR cc_start: 0.7544 (t80) cc_final: 0.7302 (t80) REVERT: A 973 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6329 (mt-10) REVERT: A 1107 TYR cc_start: 0.8743 (t80) cc_final: 0.8487 (t80) REVERT: A 1221 MET cc_start: 0.8660 (ttm) cc_final: 0.8397 (ttm) REVERT: A 1363 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8126 (ttm) REVERT: A 1402 HIS cc_start: 0.7942 (t70) cc_final: 0.7278 (t-90) REVERT: A 1411 MET cc_start: 0.7513 (tmt) cc_final: 0.6968 (tpt) REVERT: A 1474 ASP cc_start: 0.8339 (t0) cc_final: 0.8132 (t0) REVERT: A 1671 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7697 (mm-40) REVERT: A 1674 LEU cc_start: 0.8251 (mt) cc_final: 0.8046 (mt) REVERT: A 1731 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6995 (mm-30) REVERT: A 1780 LYS cc_start: 0.8576 (tppt) cc_final: 0.8231 (tppt) REVERT: A 1986 MET cc_start: 0.8272 (tpp) cc_final: 0.7694 (tpp) REVERT: A 1990 LEU cc_start: 0.8689 (mt) cc_final: 0.8249 (mt) REVERT: A 2035 GLN cc_start: 0.7400 (tp40) cc_final: 0.6834 (tm-30) REVERT: A 2053 ILE cc_start: 0.8420 (mm) cc_final: 0.8055 (mt) REVERT: A 2283 ASN cc_start: 0.8346 (m-40) cc_final: 0.8071 (m-40) REVERT: B 53 ARG cc_start: 0.7477 (mtm110) cc_final: 0.7217 (mtm110) REVERT: B 65 TYR cc_start: 0.6121 (m-80) cc_final: 0.5817 (m-80) REVERT: B 284 GLU cc_start: 0.6849 (tt0) cc_final: 0.6599 (tt0) REVERT: B 399 GLN cc_start: 0.7690 (tt0) cc_final: 0.7475 (tt0) REVERT: B 441 ASP cc_start: 0.7907 (m-30) cc_final: 0.7681 (m-30) REVERT: B 457 GLU cc_start: 0.8610 (tt0) cc_final: 0.8194 (tp30) REVERT: B 552 MET cc_start: 0.7968 (ttp) cc_final: 0.7718 (ttp) REVERT: B 816 ASP cc_start: 0.8058 (m-30) cc_final: 0.7704 (m-30) REVERT: B 1056 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.7006 (tt) REVERT: B 1105 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 1190 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8399 (tpt170) REVERT: B 1206 MET cc_start: 0.8741 (mmp) cc_final: 0.8113 (mmp) REVERT: B 1363 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.8002 (ttm) REVERT: B 1411 MET cc_start: 0.7442 (ttt) cc_final: 0.7056 (tpt) REVERT: B 1448 MET cc_start: 0.7556 (tmm) cc_final: 0.7321 (tmm) REVERT: B 1633 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7480 (tm-30) REVERT: B 1731 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 1780 LYS cc_start: 0.8650 (tppt) cc_final: 0.8320 (tppt) REVERT: B 1956 GLN cc_start: 0.8267 (mt0) cc_final: 0.7940 (mt0) REVERT: B 2027 ASP cc_start: 0.8239 (m-30) cc_final: 0.7550 (m-30) REVERT: B 2384 SER cc_start: 0.9257 (t) cc_final: 0.8934 (p) REVERT: C 388 ARG cc_start: 0.8574 (mtt90) cc_final: 0.8245 (mtm-85) REVERT: C 494 LEU cc_start: 0.8212 (mp) cc_final: 0.7859 (mt) REVERT: C 552 MET cc_start: 0.8004 (ttp) cc_final: 0.7744 (ttp) REVERT: C 562 HIS cc_start: 0.7530 (m-70) cc_final: 0.7304 (m-70) REVERT: C 778 CYS cc_start: 0.7980 (t) cc_final: 0.7616 (t) REVERT: C 965 MET cc_start: 0.6797 (tpp) cc_final: 0.6533 (tpp) REVERT: C 984 ASP cc_start: 0.7495 (t0) cc_final: 0.7269 (t0) REVERT: C 1105 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8088 (mm-30) REVERT: C 1190 ARG cc_start: 0.8847 (tpt170) cc_final: 0.8347 (tpt170) REVERT: C 1270 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8625 (t0) REVERT: C 1411 MET cc_start: 0.7580 (ttt) cc_final: 0.7209 (tpt) REVERT: C 1780 LYS cc_start: 0.8754 (tppt) cc_final: 0.8256 (tppt) REVERT: C 1906 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6584 (mm-30) REVERT: C 2030 LYS cc_start: 0.8617 (mttt) cc_final: 0.8364 (mttp) REVERT: C 2338 GLU cc_start: 0.8040 (mp0) cc_final: 0.7671 (mt-10) REVERT: D 71 TYR cc_start: 0.8055 (t80) cc_final: 0.7716 (t80) REVERT: D 94 GLN cc_start: 0.8202 (tt0) cc_final: 0.7974 (tt0) REVERT: D 98 GLN cc_start: 0.8166 (mt0) cc_final: 0.7858 (mm-40) REVERT: D 552 MET cc_start: 0.8030 (ttp) cc_final: 0.7817 (ttp) REVERT: D 714 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 965 MET cc_start: 0.6884 (tpp) cc_final: 0.6667 (tpp) REVERT: D 973 GLU cc_start: 0.6767 (tt0) cc_final: 0.6501 (tt0) REVERT: D 984 ASP cc_start: 0.7469 (t0) cc_final: 0.7204 (t0) REVERT: D 1105 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8034 (mm-30) REVERT: D 1411 MET cc_start: 0.7674 (ttt) cc_final: 0.7275 (tpt) REVERT: D 1685 GLN cc_start: 0.7043 (tp-100) cc_final: 0.6699 (tp-100) REVERT: D 1791 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7623 (p0) REVERT: D 1879 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7449 (mm) REVERT: D 1906 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6801 (mm-30) REVERT: D 1956 GLN cc_start: 0.8091 (mt0) cc_final: 0.7815 (mt0) REVERT: D 1986 MET cc_start: 0.8197 (tpp) cc_final: 0.7700 (tpp) REVERT: D 2027 ASP cc_start: 0.8216 (m-30) cc_final: 0.7562 (m-30) outliers start: 127 outliers final: 92 residues processed: 1670 average time/residue: 1.6901 time to fit residues: 4773.4623 Evaluate side-chains 1644 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1546 time to evaluate : 8.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 854 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 1065 HIS Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1588 TYR Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1938 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1531 MET Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1938 ILE Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain B residue 2155 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 973 GLU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1531 MET Chi-restraints excluded: chain D residue 1588 TYR Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1938 ILE Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2155 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 805 optimal weight: 10.0000 chunk 612 optimal weight: 1.9990 chunk 423 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 389 optimal weight: 1.9990 chunk 547 optimal weight: 8.9990 chunk 818 optimal weight: 1.9990 chunk 866 optimal weight: 0.9980 chunk 427 optimal weight: 2.9990 chunk 775 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 601 ASN A 869 ASN A2164 GLN B 869 ASN B2510 ASN C 103 GLN C 625 ASN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN ** C2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** D1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2164 GLN D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2550 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 : 0.472 6.891 99580 Z= 0.252 Chirality : 0.034 0.148 11428 Planarity : 0.003 0.037 12652 Dihedral : 4.397 81.423 9928 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 1.72 % Allowed : 14.67 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: 2.84 (0.09), residues: 8876 helix: 3.00 (0.07), residues: 5692 sheet: -0.44 (0.20), residues: 716 loop : -0.12 (0.13), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 219 HIS 0.014 0.001 HIS A1065 PHE 0.023 0.001 PHE A 761 TYR 0.012 0.001 TYR D 745 ARG 0.004 0.000 ARG A1455 *********************** 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 1726 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1589 time to evaluate : 8.768 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 388 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8309 (mtm-85) REVERT: A 714 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 816 ASP cc_start: 0.7838 (m-30) cc_final: 0.7442 (m-30) REVERT: A 840 TYR cc_start: 0.7585 (t80) cc_final: 0.7339 (t80) REVERT: A 973 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6344 (mt-10) REVERT: A 1363 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8135 (ttm) REVERT: A 1411 MET cc_start: 0.7536 (tmt) cc_final: 0.6984 (tpt) REVERT: A 1474 ASP cc_start: 0.8432 (t0) cc_final: 0.8193 (t0) REVERT: A 1674 LEU cc_start: 0.8236 (mt) cc_final: 0.8012 (mt) REVERT: A 1731 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7056 (mm-30) REVERT: A 1780 LYS cc_start: 0.8591 (tppt) cc_final: 0.8241 (tppt) REVERT: A 1986 MET cc_start: 0.8233 (tpp) cc_final: 0.7638 (tpp) REVERT: A 1990 LEU cc_start: 0.8699 (mt) cc_final: 0.8211 (mt) REVERT: A 2053 ILE cc_start: 0.8434 (mm) cc_final: 0.8096 (mt) REVERT: A 2225 TYR cc_start: 0.7106 (p90) cc_final: 0.6858 (p90) REVERT: B 53 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7038 (ttp-110) REVERT: B 107 GLU cc_start: 0.8135 (tp30) cc_final: 0.7889 (tp30) REVERT: B 211 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7643 (p0) REVERT: B 399 GLN cc_start: 0.7701 (tt0) cc_final: 0.7482 (tt0) REVERT: B 441 ASP cc_start: 0.7931 (m-30) cc_final: 0.7720 (m-30) REVERT: B 509 MET cc_start: 0.8257 (tpt) cc_final: 0.7974 (mmm) REVERT: B 552 MET cc_start: 0.7981 (ttp) cc_final: 0.7729 (ttp) REVERT: B 730 ARG cc_start: 0.7855 (ptm160) cc_final: 0.7588 (ptm160) REVERT: B 816 ASP cc_start: 0.8040 (m-30) cc_final: 0.7650 (m-30) REVERT: B 984 ASP cc_start: 0.7468 (t0) cc_final: 0.7226 (t0) REVERT: B 1056 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (tt) REVERT: B 1105 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7980 (mm-30) REVERT: B 1206 MET cc_start: 0.8760 (mmp) cc_final: 0.8109 (mmp) REVERT: B 1363 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8018 (ttm) REVERT: B 1411 MET cc_start: 0.7465 (ttt) cc_final: 0.7082 (tpt) REVERT: B 1448 MET cc_start: 0.7572 (tmm) cc_final: 0.7315 (tmm) REVERT: B 1671 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7756 (mm-40) REVERT: B 1731 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7021 (mm-30) REVERT: B 1956 GLN cc_start: 0.8282 (mt0) cc_final: 0.7929 (mt0) REVERT: B 2027 ASP cc_start: 0.8241 (m-30) cc_final: 0.7542 (m-30) REVERT: C 211 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7423 (p0) REVERT: C 352 TYR cc_start: 0.7994 (m-80) cc_final: 0.7641 (m-80) REVERT: C 388 ARG cc_start: 0.8629 (mtt90) cc_final: 0.8287 (mtm-85) REVERT: C 494 LEU cc_start: 0.8309 (mp) cc_final: 0.7987 (mt) REVERT: C 552 MET cc_start: 0.7992 (ttp) cc_final: 0.7752 (ttp) REVERT: C 778 CYS cc_start: 0.7980 (t) cc_final: 0.7614 (t) REVERT: C 816 ASP cc_start: 0.7662 (m-30) cc_final: 0.7382 (m-30) REVERT: C 984 ASP cc_start: 0.7577 (t0) cc_final: 0.7363 (t0) REVERT: C 1105 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 1120 MET cc_start: 0.8509 (mmm) cc_final: 0.8260 (mmm) REVERT: C 1190 ARG cc_start: 0.8843 (tpt170) cc_final: 0.8268 (tpt170) REVERT: C 1270 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8704 (t0) REVERT: C 1411 MET cc_start: 0.7599 (ttt) cc_final: 0.7232 (tpt) REVERT: C 1780 LYS cc_start: 0.8758 (tppt) cc_final: 0.8255 (tppt) REVERT: C 1791 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7726 (p0) REVERT: C 1870 MET cc_start: 0.8182 (tpp) cc_final: 0.7955 (tpp) REVERT: C 1906 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6692 (mm-30) REVERT: C 2338 GLU cc_start: 0.8022 (mp0) cc_final: 0.7731 (mt-10) REVERT: D 71 TYR cc_start: 0.8129 (t80) cc_final: 0.7779 (t80) REVERT: D 94 GLN cc_start: 0.8203 (tt0) cc_final: 0.7975 (tt0) REVERT: D 98 GLN cc_start: 0.8154 (mt0) cc_final: 0.7861 (mm-40) REVERT: D 270 ARG cc_start: 0.8292 (mtp85) cc_final: 0.8083 (mtt-85) REVERT: D 552 MET cc_start: 0.8005 (ttp) cc_final: 0.7801 (ttp) REVERT: D 714 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 973 GLU cc_start: 0.6786 (tt0) cc_final: 0.6526 (tt0) REVERT: D 984 ASP cc_start: 0.7554 (t0) cc_final: 0.7315 (t0) REVERT: D 1105 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8003 (mm-30) REVERT: D 1411 MET cc_start: 0.7696 (ttt) cc_final: 0.7277 (tpt) REVERT: D 1791 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7600 (p0) REVERT: D 1879 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7377 (mm) REVERT: D 1906 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 1956 GLN cc_start: 0.8141 (mt0) cc_final: 0.7915 (mt0) REVERT: D 1986 MET cc_start: 0.8229 (tpp) cc_final: 0.7768 (tpp) REVERT: D 2027 ASP cc_start: 0.8218 (m-30) cc_final: 0.7554 (m-30) REVERT: D 2145 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7951 (tm-30) outliers start: 137 outliers final: 100 residues processed: 1664 average time/residue: 1.5938 time to fit residues: 4430.6691 Evaluate side-chains 1667 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1558 time to evaluate : 8.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 854 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1531 MET Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2164 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1531 MET Chi-restraints excluded: chain B residue 1588 TYR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 2061 SER Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1531 MET Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 1997 SER Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1285 HIS Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1531 MET Chi-restraints excluded: chain D residue 1588 TYR Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2143 ILE Chi-restraints excluded: chain D residue 2155 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 721 optimal weight: 20.0000 chunk 491 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 644 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 739 optimal weight: 4.9990 chunk 598 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 442 optimal weight: 1.9990 chunk 777 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS A2059 GLN B2059 GLN B2510 ASN C 94 GLN C 460 ASN C 869 ASN ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 73644 Z= 0.402 Angle : 0.542 9.465 99580 Z= 0.296 Chirality : 0.037 0.187 11428 Planarity : 0.004 0.064 12652 Dihedral : 4.485 52.158 9928 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 15.28 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 2.47 (0.09), residues: 8876 helix: 2.74 (0.07), residues: 5672 sheet: -0.59 (0.20), residues: 708 loop : -0.32 (0.13), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 219 HIS 0.010 0.001 HIS A 868 PHE 0.030 0.002 PHE C 25 TYR 0.021 0.001 TYR A2583 ARG 0.005 0.000 ARG A 505 *********************** 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 1789 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1621 time to evaluate : 8.816 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8201 (mt0) cc_final: 0.7837 (mm110) REVERT: A 388 ARG cc_start: 0.8727 (mtt90) cc_final: 0.8468 (mtm-85) REVERT: A 714 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 816 ASP cc_start: 0.7902 (m-30) cc_final: 0.7504 (m-30) REVERT: A 840 TYR cc_start: 0.7681 (t80) cc_final: 0.7443 (t80) REVERT: A 973 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6364 (mt-10) REVERT: A 1087 GLU cc_start: 0.7983 (tt0) cc_final: 0.7747 (tt0) REVERT: A 1363 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8206 (ttm) REVERT: A 1411 MET cc_start: 0.7585 (tmt) cc_final: 0.7045 (tpt) REVERT: A 1474 ASP cc_start: 0.8506 (t0) cc_final: 0.8234 (m-30) REVERT: A 1731 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7201 (mm-30) REVERT: A 1780 LYS cc_start: 0.8607 (tppt) cc_final: 0.8173 (tppt) REVERT: A 1986 MET cc_start: 0.8173 (tpp) cc_final: 0.7771 (tpp) REVERT: A 2053 ILE cc_start: 0.8459 (mm) cc_final: 0.8197 (mt) REVERT: A 2225 TYR cc_start: 0.7217 (p90) cc_final: 0.6977 (p90) REVERT: B 53 ARG cc_start: 0.7629 (mtm110) cc_final: 0.6900 (mtp180) REVERT: B 107 GLU cc_start: 0.8158 (tp30) cc_final: 0.7915 (tp30) REVERT: B 402 ASN cc_start: 0.8427 (t0) cc_final: 0.8136 (t0) REVERT: B 441 ASP cc_start: 0.8048 (m-30) cc_final: 0.7807 (m-30) REVERT: B 509 MET cc_start: 0.8303 (tpt) cc_final: 0.8018 (mmm) REVERT: B 552 MET cc_start: 0.8015 (ttp) cc_final: 0.7783 (ttp) REVERT: B 730 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7547 (ptm-80) REVERT: B 778 CYS cc_start: 0.7927 (t) cc_final: 0.7690 (t) REVERT: B 816 ASP cc_start: 0.8068 (m-30) cc_final: 0.7647 (m-30) REVERT: B 984 ASP cc_start: 0.7674 (t0) cc_final: 0.7460 (t0) REVERT: B 1056 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7122 (tt) REVERT: B 1105 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7995 (mm-30) REVERT: B 1206 MET cc_start: 0.8824 (mmp) cc_final: 0.8231 (mmp) REVERT: B 1411 MET cc_start: 0.7573 (ttt) cc_final: 0.7161 (tpt) REVERT: B 1448 MET cc_start: 0.7658 (tmm) cc_final: 0.7368 (tmm) REVERT: B 1731 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7203 (mm-30) REVERT: B 1780 LYS cc_start: 0.8694 (tppt) cc_final: 0.8349 (tppt) REVERT: B 2003 LEU cc_start: 0.8388 (mt) cc_final: 0.8179 (mp) REVERT: B 2027 ASP cc_start: 0.8266 (m-30) cc_final: 0.7594 (m-30) REVERT: B 2046 PRO cc_start: 0.9180 (Cg_exo) cc_final: 0.8918 (Cg_endo) REVERT: B 2341 TYR cc_start: 0.8762 (m-80) cc_final: 0.8541 (m-80) REVERT: C 107 GLU cc_start: 0.7887 (tp30) cc_final: 0.7646 (mm-30) REVERT: C 352 TYR cc_start: 0.8033 (m-80) cc_final: 0.7792 (m-80) REVERT: C 388 ARG cc_start: 0.8692 (mtt90) cc_final: 0.8248 (mtm-85) REVERT: C 552 MET cc_start: 0.8011 (ttp) cc_final: 0.7794 (ttp) REVERT: C 984 ASP cc_start: 0.7750 (t0) cc_final: 0.7532 (t0) REVERT: C 1105 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8078 (mm-30) REVERT: C 1120 MET cc_start: 0.8544 (mmm) cc_final: 0.8296 (mmm) REVERT: C 1190 ARG cc_start: 0.8857 (tpt170) cc_final: 0.8318 (tpt170) REVERT: C 1270 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8807 (t0) REVERT: C 1411 MET cc_start: 0.7685 (ttt) cc_final: 0.7308 (tpt) REVERT: C 1780 LYS cc_start: 0.8790 (tppt) cc_final: 0.8290 (tppt) REVERT: C 1791 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7771 (p0) REVERT: C 1906 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6799 (mm-30) REVERT: C 2023 GLN cc_start: 0.7595 (tp40) cc_final: 0.7126 (tm-30) REVERT: C 2030 LYS cc_start: 0.8653 (mttt) cc_final: 0.8401 (mttp) REVERT: D 98 GLN cc_start: 0.8187 (mt0) cc_final: 0.7921 (mm-40) REVERT: D 714 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7676 (mt-10) REVERT: D 985 TYR cc_start: 0.7994 (t80) cc_final: 0.7490 (t80) REVERT: D 1105 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8033 (mm-30) REVERT: D 1264 MET cc_start: 0.8857 (ttm) cc_final: 0.8621 (ttm) REVERT: D 1331 ASP cc_start: 0.8316 (m-30) cc_final: 0.8049 (p0) REVERT: D 1791 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (p0) REVERT: D 1879 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 1906 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6793 (mm-30) REVERT: D 1986 MET cc_start: 0.8242 (tpp) cc_final: 0.7800 (tpp) REVERT: D 2027 ASP cc_start: 0.8226 (m-30) cc_final: 0.7570 (m-30) REVERT: D 2053 ILE cc_start: 0.8487 (mm) cc_final: 0.8217 (mt) REVERT: D 2145 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 168 outliers final: 128 residues processed: 1725 average time/residue: 1.6253 time to fit residues: 4689.8529 Evaluate side-chains 1711 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1577 time to evaluate : 8.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 854 GLU Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1938 ILE Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2130 ASP Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 2130 ASP Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 384 ASN Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1285 HIS Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1997 SER Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2130 ASP Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2329 THR Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1542 MET Chi-restraints excluded: chain D residue 1588 TYR Chi-restraints excluded: chain D residue 1648 ILE Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1997 SER Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2143 ILE Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2391 LEU Chi-restraints excluded: chain D residue 2461 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 291 optimal weight: 3.9990 chunk 779 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 508 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 866 optimal weight: 0.3980 chunk 719 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 286 optimal weight: 0.0980 chunk 455 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 562 HIS ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 HIS A1889 GLN B 460 ASN ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN C 710 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2216 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1956 GLN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 73644 Z= 0.196 Angle : 0.473 7.406 99580 Z= 0.251 Chirality : 0.034 0.148 11428 Planarity : 0.003 0.051 12652 Dihedral : 4.222 55.754 9916 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 1.59 % Allowed : 16.17 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 2.66 (0.09), residues: 8876 helix: 2.91 (0.07), residues: 5688 sheet: -0.78 (0.20), residues: 716 loop : -0.20 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2601 HIS 0.006 0.001 HIS A 868 PHE 0.031 0.001 PHE B 761 TYR 0.018 0.001 TYR A2583 ARG 0.009 0.000 ARG D 64 *********************** 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 1727 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1600 time to evaluate : 8.719 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8145 (mt0) cc_final: 0.7788 (mm110) REVERT: A 352 TYR cc_start: 0.7909 (m-80) cc_final: 0.7637 (m-10) REVERT: A 714 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 745 TYR cc_start: 0.7718 (m-80) cc_final: 0.7319 (m-80) REVERT: A 816 ASP cc_start: 0.7814 (m-30) cc_final: 0.7414 (m-30) REVERT: A 840 TYR cc_start: 0.7629 (t80) cc_final: 0.7357 (t80) REVERT: A 973 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6364 (mt-10) REVERT: A 1087 GLU cc_start: 0.7887 (tt0) cc_final: 0.7641 (tt0) REVERT: A 1474 ASP cc_start: 0.8516 (t0) cc_final: 0.8263 (m-30) REVERT: A 1731 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 1780 LYS cc_start: 0.8594 (tppt) cc_final: 0.8129 (tppt) REVERT: A 1986 MET cc_start: 0.8118 (tpp) cc_final: 0.7704 (tpp) REVERT: A 2053 ILE cc_start: 0.8439 (mm) cc_final: 0.8161 (mt) REVERT: A 2225 TYR cc_start: 0.7162 (p90) cc_final: 0.6908 (p90) REVERT: B 53 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7079 (ttp-110) REVERT: B 107 GLU cc_start: 0.8110 (tp30) cc_final: 0.7879 (tp30) REVERT: B 370 ASP cc_start: 0.7528 (m-30) cc_final: 0.7298 (m-30) REVERT: B 402 ASN cc_start: 0.8372 (t0) cc_final: 0.8051 (t0) REVERT: B 441 ASP cc_start: 0.7976 (m-30) cc_final: 0.7747 (m-30) REVERT: B 509 MET cc_start: 0.8277 (tpt) cc_final: 0.7973 (mmm) REVERT: B 552 MET cc_start: 0.7993 (ttp) cc_final: 0.7756 (ttp) REVERT: B 778 CYS cc_start: 0.7963 (t) cc_final: 0.7685 (t) REVERT: B 816 ASP cc_start: 0.7991 (m-30) cc_final: 0.7547 (m-30) REVERT: B 984 ASP cc_start: 0.7554 (t0) cc_final: 0.7335 (t0) REVERT: B 1105 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7979 (mm-30) REVERT: B 1190 ARG cc_start: 0.8852 (tpt170) cc_final: 0.8274 (tpt170) REVERT: B 1411 MET cc_start: 0.7567 (ttt) cc_final: 0.7158 (tpt) REVERT: B 1448 MET cc_start: 0.7645 (tmm) cc_final: 0.7338 (tmm) REVERT: B 1531 MET cc_start: 0.7770 (mmt) cc_final: 0.7570 (mmt) REVERT: B 1731 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 1780 LYS cc_start: 0.8665 (tppt) cc_final: 0.8315 (tppt) REVERT: B 2046 PRO cc_start: 0.9188 (Cg_exo) cc_final: 0.8928 (Cg_endo) REVERT: B 2341 TYR cc_start: 0.8712 (m-80) cc_final: 0.8482 (m-80) REVERT: C 388 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8255 (mtm-85) REVERT: C 552 MET cc_start: 0.7975 (ttp) cc_final: 0.7774 (ttp) REVERT: C 816 ASP cc_start: 0.7577 (m-30) cc_final: 0.7273 (m-30) REVERT: C 1105 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8063 (mm-30) REVERT: C 1120 MET cc_start: 0.8553 (mmm) cc_final: 0.8296 (mmm) REVERT: C 1190 ARG cc_start: 0.8826 (tpt170) cc_final: 0.8344 (tpt170) REVERT: C 1270 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8775 (t0) REVERT: C 1411 MET cc_start: 0.7679 (ttt) cc_final: 0.7298 (tpt) REVERT: C 1780 LYS cc_start: 0.8773 (tppt) cc_final: 0.8271 (tppt) REVERT: C 1791 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7710 (p0) REVERT: C 1906 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6679 (mm-30) REVERT: C 1931 GLU cc_start: 0.7808 (mp0) cc_final: 0.7526 (mp0) REVERT: C 2023 GLN cc_start: 0.7546 (tp40) cc_final: 0.7072 (tm-30) REVERT: D 53 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6876 (mtp-110) REVERT: D 98 GLN cc_start: 0.8157 (mt0) cc_final: 0.7921 (mm-40) REVERT: D 714 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 973 GLU cc_start: 0.6822 (tt0) cc_final: 0.6566 (tt0) REVERT: D 985 TYR cc_start: 0.7963 (t80) cc_final: 0.7469 (t80) REVERT: D 1064 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7765 (ttt) REVERT: D 1105 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8008 (mm-30) REVERT: D 1264 MET cc_start: 0.8834 (ttm) cc_final: 0.8580 (ttm) REVERT: D 1331 ASP cc_start: 0.8282 (m-30) cc_final: 0.8035 (p0) REVERT: D 1411 MET cc_start: 0.7710 (ttt) cc_final: 0.7307 (tpt) REVERT: D 1791 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7591 (p0) REVERT: D 1906 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6726 (mm-30) REVERT: D 1956 GLN cc_start: 0.8253 (mt0) cc_final: 0.8036 (mt0) REVERT: D 1986 MET cc_start: 0.8189 (tpp) cc_final: 0.7749 (tpp) REVERT: D 2027 ASP cc_start: 0.8187 (m-30) cc_final: 0.7499 (m-30) REVERT: D 2145 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7947 (tm-30) outliers start: 127 outliers final: 110 residues processed: 1665 average time/residue: 1.6328 time to fit residues: 4546.9390 Evaluate side-chains 1671 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1557 time to evaluate : 8.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1285 HIS Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1938 ILE Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2219 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 973 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1997 SER Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1285 HIS Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1542 MET Chi-restraints excluded: chain D residue 1588 TYR Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1888 LEU Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2466 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 835 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 493 optimal weight: 1.9990 chunk 633 optimal weight: 7.9990 chunk 490 optimal weight: 20.0000 chunk 729 optimal weight: 7.9990 chunk 484 optimal weight: 0.5980 chunk 863 optimal weight: 3.9990 chunk 540 optimal weight: 1.9990 chunk 526 optimal weight: 0.7980 chunk 398 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 ASN B 710 GLN B2510 ASN B2592 GLN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN C1285 HIS C1939 GLN ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 ASN D 474 GLN D 562 HIS D 783 HIS D1270 ASN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 73644 Z= 0.324 Angle : 0.515 8.095 99580 Z= 0.277 Chirality : 0.036 0.202 11428 Planarity : 0.004 0.063 12652 Dihedral : 4.309 52.278 9916 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 2.01 % Allowed : 16.40 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.21 % 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: 2.48 (0.09), residues: 8876 helix: 2.79 (0.07), residues: 5688 sheet: -0.85 (0.20), residues: 708 loop : -0.35 (0.13), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 219 HIS 0.009 0.001 HIS A 868 PHE 0.025 0.001 PHE B 761 TYR 0.020 0.001 TYR A2583 ARG 0.008 0.000 ARG D 64 *********************** 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 1765 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1605 time to evaluate : 8.146 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8184 (mt0) cc_final: 0.7843 (mm110) REVERT: A 263 VAL cc_start: 0.9023 (m) cc_final: 0.8680 (p) REVERT: A 352 TYR cc_start: 0.7917 (m-80) cc_final: 0.7655 (m-10) REVERT: A 714 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 816 ASP cc_start: 0.7826 (m-30) cc_final: 0.7410 (m-30) REVERT: A 840 TYR cc_start: 0.7684 (t80) cc_final: 0.7460 (t80) REVERT: A 1087 GLU cc_start: 0.7965 (tt0) cc_final: 0.7730 (tt0) REVERT: A 1474 ASP cc_start: 0.8543 (t0) cc_final: 0.8284 (m-30) REVERT: A 1617 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6363 (tp) REVERT: A 1731 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7144 (mm-30) REVERT: A 1780 LYS cc_start: 0.8626 (tppt) cc_final: 0.8159 (tppt) REVERT: A 2053 ILE cc_start: 0.8440 (mm) cc_final: 0.8180 (mt) REVERT: A 2225 TYR cc_start: 0.7289 (p90) cc_final: 0.7010 (p90) REVERT: B 53 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7215 (ttp-110) REVERT: B 107 GLU cc_start: 0.8136 (tp30) cc_final: 0.7893 (tp30) REVERT: B 370 ASP cc_start: 0.7535 (m-30) cc_final: 0.7286 (m-30) REVERT: B 402 ASN cc_start: 0.8483 (t0) cc_final: 0.7931 (t0) REVERT: B 441 ASP cc_start: 0.8036 (m-30) cc_final: 0.7810 (m-30) REVERT: B 509 MET cc_start: 0.8268 (tpt) cc_final: 0.7970 (mmm) REVERT: B 552 MET cc_start: 0.8018 (ttp) cc_final: 0.7793 (ttp) REVERT: B 602 ASN cc_start: 0.8749 (t0) cc_final: 0.8549 (t0) REVERT: B 730 ARG cc_start: 0.7916 (ptm160) cc_final: 0.7639 (ptm160) REVERT: B 816 ASP cc_start: 0.8016 (m-30) cc_final: 0.7546 (m-30) REVERT: B 1056 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7117 (tt) REVERT: B 1105 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8005 (mm-30) REVERT: B 1190 ARG cc_start: 0.8866 (tpt170) cc_final: 0.8219 (tpt170) REVERT: B 1448 MET cc_start: 0.7704 (tmm) cc_final: 0.7370 (tmm) REVERT: B 1731 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 1780 LYS cc_start: 0.8685 (tppt) cc_final: 0.8339 (tppt) REVERT: B 2046 PRO cc_start: 0.9215 (Cg_exo) cc_final: 0.8976 (Cg_endo) REVERT: C 53 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7337 (mtm180) REVERT: C 62 MET cc_start: 0.7012 (tpp) cc_final: 0.6765 (ttm) REVERT: C 107 GLU cc_start: 0.7874 (tp30) cc_final: 0.7566 (tp30) REVERT: C 388 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8263 (mtm-85) REVERT: C 1105 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8056 (mm-30) REVERT: C 1120 MET cc_start: 0.8567 (mmm) cc_final: 0.8305 (mmm) REVERT: C 1190 ARG cc_start: 0.8814 (tpt170) cc_final: 0.8400 (tpt170) REVERT: C 1270 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8831 (t0) REVERT: C 1363 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8034 (ttm) REVERT: C 1411 MET cc_start: 0.7714 (ttt) cc_final: 0.7341 (tpt) REVERT: C 1780 LYS cc_start: 0.8769 (tppt) cc_final: 0.8269 (tppt) REVERT: C 1791 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7760 (p0) REVERT: C 1906 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6693 (mm-30) REVERT: C 1931 GLU cc_start: 0.7881 (mp0) cc_final: 0.7635 (mp0) REVERT: D 53 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7185 (mtm110) REVERT: D 416 MET cc_start: 0.7610 (tpt) cc_final: 0.7182 (tpt) REVERT: D 973 GLU cc_start: 0.6839 (tt0) cc_final: 0.6580 (tt0) REVERT: D 985 TYR cc_start: 0.8075 (t80) cc_final: 0.7573 (t80) REVERT: D 1064 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7787 (ttt) REVERT: D 1105 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 1264 MET cc_start: 0.8859 (ttm) cc_final: 0.8591 (ttm) REVERT: D 1331 ASP cc_start: 0.8283 (m-30) cc_final: 0.8046 (p0) REVERT: D 1411 MET cc_start: 0.7745 (ttt) cc_final: 0.7332 (tpt) REVERT: D 1633 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 1791 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7618 (p0) REVERT: D 1879 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 1906 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6742 (mm-30) REVERT: D 1986 MET cc_start: 0.8198 (tpp) cc_final: 0.7824 (tpp) REVERT: D 2027 ASP cc_start: 0.8204 (m-30) cc_final: 0.7519 (m-30) REVERT: D 2053 ILE cc_start: 0.8445 (mm) cc_final: 0.8188 (mt) REVERT: D 2145 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7939 (tm-30) outliers start: 160 outliers final: 131 residues processed: 1702 average time/residue: 1.6112 time to fit residues: 4590.1514 Evaluate side-chains 1702 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1563 time to evaluate : 8.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 2130 ASP Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 703 HIS Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 973 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1648 ILE Chi-restraints excluded: chain B residue 1695 LEU Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1997 SER Chi-restraints excluded: chain B residue 2061 SER Chi-restraints excluded: chain B residue 2143 ILE Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1285 HIS Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1777 MET Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 854 GLU Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1648 ILE Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1868 LEU Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 1997 SER Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2143 ILE Chi-restraints excluded: chain D residue 2155 LEU 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: 0.9990 chunk 515 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 549 optimal weight: 9.9990 chunk 588 optimal weight: 0.6980 chunk 426 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 678 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN B2510 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN C1939 GLN ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2472 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1270 ASN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 73644 Z= 0.163 Angle : 0.471 8.377 99580 Z= 0.249 Chirality : 0.034 0.161 11428 Planarity : 0.003 0.072 12652 Dihedral : 4.132 50.638 9916 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.50 % Allowed : 16.89 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 2.73 (0.09), residues: 8876 helix: 2.96 (0.07), residues: 5688 sheet: -0.87 (0.20), residues: 716 loop : -0.17 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D2601 HIS 0.007 0.001 HIS A1790 PHE 0.036 0.001 PHE C1286 TYR 0.016 0.001 TYR A2583 ARG 0.009 0.000 ARG A 388 *********************** 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 1700 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1580 time to evaluate : 8.760 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8164 (mt0) cc_final: 0.7835 (mm110) REVERT: A 100 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 263 VAL cc_start: 0.9006 (m) cc_final: 0.8665 (p) REVERT: A 714 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 816 ASP cc_start: 0.7737 (m-30) cc_final: 0.7316 (m-30) REVERT: A 840 TYR cc_start: 0.7630 (t80) cc_final: 0.7364 (t80) REVERT: A 1087 GLU cc_start: 0.7891 (tt0) cc_final: 0.7639 (tt0) REVERT: A 1474 ASP cc_start: 0.8525 (t0) cc_final: 0.8272 (m-30) REVERT: A 1617 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6188 (tp) REVERT: A 1731 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 1780 LYS cc_start: 0.8593 (tppt) cc_final: 0.8117 (tppt) REVERT: A 2053 ILE cc_start: 0.8415 (mm) cc_final: 0.8147 (mt) REVERT: A 2225 TYR cc_start: 0.7189 (p90) cc_final: 0.6940 (p90) REVERT: A 2370 LEU cc_start: 0.8526 (mm) cc_final: 0.8222 (mt) REVERT: B 53 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7291 (ttp-110) REVERT: B 107 GLU cc_start: 0.8121 (tp30) cc_final: 0.7894 (tp30) REVERT: B 370 ASP cc_start: 0.7571 (m-30) cc_final: 0.7315 (m-30) REVERT: B 399 GLN cc_start: 0.7845 (tt0) cc_final: 0.7643 (tt0) REVERT: B 402 ASN cc_start: 0.8440 (t0) cc_final: 0.8115 (t0) REVERT: B 441 ASP cc_start: 0.7970 (m-30) cc_final: 0.7738 (m-30) REVERT: B 509 MET cc_start: 0.8247 (tpt) cc_final: 0.7953 (mmm) REVERT: B 552 MET cc_start: 0.7990 (ttp) cc_final: 0.7757 (ttp) REVERT: B 816 ASP cc_start: 0.7965 (m-30) cc_final: 0.7502 (m-30) REVERT: B 1105 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 1190 ARG cc_start: 0.8824 (tpt170) cc_final: 0.8281 (tpt170) REVERT: B 1448 MET cc_start: 0.7672 (tmm) cc_final: 0.7334 (tmm) REVERT: B 1594 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8721 (mmtm) REVERT: B 1731 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 1780 LYS cc_start: 0.8653 (tppt) cc_final: 0.8316 (tppt) REVERT: B 1956 GLN cc_start: 0.8236 (mt0) cc_final: 0.8016 (mt0) REVERT: B 2004 MET cc_start: 0.7019 (mtp) cc_final: 0.6808 (mtm) REVERT: B 2046 PRO cc_start: 0.9197 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: C 45 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8472 (tt) REVERT: C 53 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7352 (mtm180) REVERT: C 62 MET cc_start: 0.7059 (tpp) cc_final: 0.6810 (ttm) REVERT: C 107 GLU cc_start: 0.7831 (tp30) cc_final: 0.7521 (tp30) REVERT: C 388 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8249 (mtm-85) REVERT: C 816 ASP cc_start: 0.7490 (m-30) cc_final: 0.7191 (m-30) REVERT: C 1105 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 1120 MET cc_start: 0.8574 (mmm) cc_final: 0.8305 (mmm) REVERT: C 1190 ARG cc_start: 0.8810 (tpt170) cc_final: 0.8435 (tpt170) REVERT: C 1270 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8777 (t0) REVERT: C 1411 MET cc_start: 0.7695 (ttt) cc_final: 0.7315 (tpt) REVERT: C 1780 LYS cc_start: 0.8747 (tppt) cc_final: 0.8238 (tppt) REVERT: C 1791 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7700 (p0) REVERT: C 1906 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6701 (mm-30) REVERT: C 1931 GLU cc_start: 0.7897 (mp0) cc_final: 0.7652 (mp0) REVERT: C 2131 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7057 (mmt-90) REVERT: D 53 ARG cc_start: 0.7488 (mtm110) cc_final: 0.7018 (mtm110) REVERT: D 103 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8139 (tp-100) REVERT: D 416 MET cc_start: 0.7594 (tpt) cc_final: 0.7182 (tpt) REVERT: D 985 TYR cc_start: 0.7992 (t80) cc_final: 0.7465 (t80) REVERT: D 1105 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8045 (mm-30) REVERT: D 1264 MET cc_start: 0.8850 (ttm) cc_final: 0.8583 (ttm) REVERT: D 1331 ASP cc_start: 0.8217 (m-30) cc_final: 0.8002 (p0) REVERT: D 1411 MET cc_start: 0.7723 (ttt) cc_final: 0.7310 (tpt) REVERT: D 1791 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7558 (p0) REVERT: D 1906 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6672 (mm-30) REVERT: D 1986 MET cc_start: 0.8199 (tpp) cc_final: 0.7779 (tpp) REVERT: D 2053 ILE cc_start: 0.8427 (mm) cc_final: 0.8145 (mt) REVERT: D 2145 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7946 (tm-30) outliers start: 120 outliers final: 98 residues processed: 1643 average time/residue: 1.6698 time to fit residues: 4615.3183 Evaluate side-chains 1646 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1543 time to evaluate : 8.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1491 LEU Chi-restraints excluded: chain A residue 1588 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 973 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1775 LEU Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1868 LEU Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2155 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 785 optimal weight: 10.0000 chunk 827 optimal weight: 2.9990 chunk 754 optimal weight: 2.9990 chunk 804 optimal weight: 1.9990 chunk 484 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 631 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 727 optimal weight: 10.0000 chunk 761 optimal weight: 2.9990 chunk 801 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 474 GLN A 869 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** C 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 HIS C 869 ASN C1939 GLN ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 HIS D 290 HIS D1270 ASN D1939 GLN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 73644 Z= 0.357 Angle : 0.531 9.655 99580 Z= 0.287 Chirality : 0.036 0.172 11428 Planarity : 0.004 0.064 12652 Dihedral : 4.295 49.420 9916 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 1.65 % Allowed : 17.27 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: 2.46 (0.09), residues: 8876 helix: 2.77 (0.07), residues: 5684 sheet: -0.81 (0.21), residues: 684 loop : -0.38 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 219 HIS 0.010 0.001 HIS A 868 PHE 0.023 0.002 PHE D 25 TYR 0.020 0.001 TYR A2583 ARG 0.011 0.000 ARG A1455 *********************** 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 1716 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1584 time to evaluate : 8.637 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8185 (mt0) cc_final: 0.7874 (mm110) REVERT: A 100 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 158 GLU cc_start: 0.7999 (tt0) cc_final: 0.7755 (tm-30) REVERT: A 263 VAL cc_start: 0.9028 (m) cc_final: 0.8696 (p) REVERT: A 352 TYR cc_start: 0.7910 (m-80) cc_final: 0.7647 (m-10) REVERT: A 714 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 763 CYS cc_start: 0.8155 (m) cc_final: 0.7781 (m) REVERT: A 816 ASP cc_start: 0.7826 (m-30) cc_final: 0.7392 (m-30) REVERT: A 840 TYR cc_start: 0.7705 (t80) cc_final: 0.7494 (t80) REVERT: A 1087 GLU cc_start: 0.7961 (tt0) cc_final: 0.7722 (tt0) REVERT: A 1120 MET cc_start: 0.8506 (mmm) cc_final: 0.8180 (mmm) REVERT: A 1411 MET cc_start: 0.7672 (tmt) cc_final: 0.7093 (tpt) REVERT: A 1455 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7732 (ttp80) REVERT: A 1474 ASP cc_start: 0.8555 (t0) cc_final: 0.8294 (m-30) REVERT: A 1617 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6389 (tp) REVERT: A 1731 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7116 (mm-30) REVERT: A 2053 ILE cc_start: 0.8447 (mm) cc_final: 0.8186 (mt) REVERT: A 2225 TYR cc_start: 0.7308 (p90) cc_final: 0.7051 (p90) REVERT: B 53 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7171 (ttp-110) REVERT: B 107 GLU cc_start: 0.8158 (tp30) cc_final: 0.7927 (tp30) REVERT: B 370 ASP cc_start: 0.7590 (m-30) cc_final: 0.7333 (m-30) REVERT: B 402 ASN cc_start: 0.8525 (t0) cc_final: 0.8085 (t0) REVERT: B 441 ASP cc_start: 0.8067 (m-30) cc_final: 0.7824 (m-30) REVERT: B 509 MET cc_start: 0.8267 (tpt) cc_final: 0.7972 (mmm) REVERT: B 552 MET cc_start: 0.8040 (ttp) cc_final: 0.7817 (ttp) REVERT: B 745 TYR cc_start: 0.7563 (m-80) cc_final: 0.7346 (m-80) REVERT: B 816 ASP cc_start: 0.8039 (m-30) cc_final: 0.7560 (m-30) REVERT: B 1056 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (tt) REVERT: B 1105 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 1190 ARG cc_start: 0.8829 (tpt170) cc_final: 0.8283 (tpt170) REVERT: B 1320 MET cc_start: 0.8563 (mmm) cc_final: 0.8262 (mmm) REVERT: B 1448 MET cc_start: 0.7746 (tmm) cc_final: 0.7384 (tmm) REVERT: B 1695 LEU cc_start: 0.6641 (mt) cc_final: 0.6347 (mp) REVERT: B 1731 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 1780 LYS cc_start: 0.8685 (tppt) cc_final: 0.8343 (tppt) REVERT: B 2046 PRO cc_start: 0.9233 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: C 53 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7400 (mtm180) REVERT: C 107 GLU cc_start: 0.7848 (tp30) cc_final: 0.7529 (tp30) REVERT: C 388 ARG cc_start: 0.8642 (mtt90) cc_final: 0.8263 (mtm-85) REVERT: C 1105 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8074 (mm-30) REVERT: C 1120 MET cc_start: 0.8583 (mmm) cc_final: 0.8310 (mmm) REVERT: C 1190 ARG cc_start: 0.8808 (tpt170) cc_final: 0.8429 (tpt170) REVERT: C 1270 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8819 (t0) REVERT: C 1411 MET cc_start: 0.7773 (ttt) cc_final: 0.7389 (tpt) REVERT: C 1614 LEU cc_start: 0.8445 (mm) cc_final: 0.8228 (mm) REVERT: C 1780 LYS cc_start: 0.8784 (tppt) cc_final: 0.8280 (tppt) REVERT: C 1791 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7747 (p0) REVERT: C 1906 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6760 (mm-30) REVERT: C 1931 GLU cc_start: 0.7994 (mp0) cc_final: 0.7772 (mp0) REVERT: C 2131 ARG cc_start: 0.7497 (mmm-85) cc_final: 0.7142 (mmt-90) REVERT: D 53 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7109 (mtm110) REVERT: D 416 MET cc_start: 0.7631 (tpt) cc_final: 0.7192 (tpt) REVERT: D 839 ASP cc_start: 0.7656 (m-30) cc_final: 0.7404 (m-30) REVERT: D 985 TYR cc_start: 0.8116 (t80) cc_final: 0.7635 (t80) REVERT: D 1064 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7807 (ttt) REVERT: D 1105 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8069 (mm-30) REVERT: D 1264 MET cc_start: 0.8876 (ttm) cc_final: 0.8614 (ttm) REVERT: D 1331 ASP cc_start: 0.8246 (m-30) cc_final: 0.8034 (p0) REVERT: D 1633 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 1791 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7620 (p0) REVERT: D 1879 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7538 (mm) REVERT: D 1906 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 1986 MET cc_start: 0.8219 (tpp) cc_final: 0.7812 (tpp) REVERT: D 2053 ILE cc_start: 0.8455 (mm) cc_final: 0.8197 (mt) REVERT: D 2145 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7964 (tm-30) outliers start: 132 outliers final: 113 residues processed: 1661 average time/residue: 1.5916 time to fit residues: 4419.2132 Evaluate side-chains 1676 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1556 time to evaluate : 8.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1491 LEU Chi-restraints excluded: chain A residue 1588 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2130 ASP Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 1997 SER Chi-restraints excluded: chain B residue 2130 ASP Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 290 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1775 LEU Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2130 ASP Chi-restraints excluded: chain C residue 2143 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 786 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1066 ASP Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1868 LEU Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 528 optimal weight: 0.9980 chunk 850 optimal weight: 0.2980 chunk 519 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 chunk 591 optimal weight: 3.9990 chunk 892 optimal weight: 6.9990 chunk 821 optimal weight: 1.9990 chunk 710 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 549 optimal weight: 10.0000 chunk 435 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 869 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 GLN ** B2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN C1939 GLN ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS D1270 ASN D1285 HIS D1939 GLN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 73644 Z= 0.171 Angle : 0.486 8.441 99580 Z= 0.255 Chirality : 0.034 0.148 11428 Planarity : 0.003 0.066 12652 Dihedral : 4.109 48.148 9916 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 17.56 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 2.70 (0.09), residues: 8876 helix: 2.95 (0.07), residues: 5688 sheet: -0.79 (0.21), residues: 656 loop : -0.25 (0.13), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D2601 HIS 0.006 0.001 HIS B1790 PHE 0.020 0.001 PHE B 761 TYR 0.017 0.001 TYR A2583 ARG 0.008 0.000 ARG A 388 ********************** 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 1675 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1570 time to evaluate : 8.672 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLN cc_start: 0.8154 (mt0) cc_final: 0.7852 (mm110) REVERT: A 100 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 158 GLU cc_start: 0.7952 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 263 VAL cc_start: 0.8999 (m) cc_final: 0.8672 (p) REVERT: A 714 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7317 (mt-10) REVERT: A 816 ASP cc_start: 0.7705 (m-30) cc_final: 0.7229 (m-30) REVERT: A 1087 GLU cc_start: 0.7892 (tt0) cc_final: 0.7633 (tt0) REVERT: A 1120 MET cc_start: 0.8497 (mmm) cc_final: 0.8171 (mmm) REVERT: A 1411 MET cc_start: 0.7661 (tmt) cc_final: 0.7048 (tpt) REVERT: A 1474 ASP cc_start: 0.8526 (t0) cc_final: 0.8279 (m-30) REVERT: A 1617 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6227 (tp) REVERT: A 1671 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7685 (mm-40) REVERT: A 1731 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7072 (mm-30) REVERT: A 2053 ILE cc_start: 0.8392 (mm) cc_final: 0.8115 (mt) REVERT: A 2225 TYR cc_start: 0.7202 (p90) cc_final: 0.6968 (p90) REVERT: A 2370 LEU cc_start: 0.8530 (mm) cc_final: 0.8218 (mt) REVERT: B 53 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7294 (ttp-110) REVERT: B 107 GLU cc_start: 0.8120 (tp30) cc_final: 0.7897 (tp30) REVERT: B 352 TYR cc_start: 0.7696 (m-10) cc_final: 0.7107 (m-10) REVERT: B 370 ASP cc_start: 0.7569 (m-30) cc_final: 0.7320 (m-30) REVERT: B 402 ASN cc_start: 0.8491 (t0) cc_final: 0.7962 (t0) REVERT: B 419 THR cc_start: 0.7209 (p) cc_final: 0.6892 (t) REVERT: B 441 ASP cc_start: 0.7988 (m-30) cc_final: 0.7754 (m-30) REVERT: B 509 MET cc_start: 0.8228 (tpt) cc_final: 0.7902 (mmm) REVERT: B 552 MET cc_start: 0.8000 (ttp) cc_final: 0.7782 (ttp) REVERT: B 637 LEU cc_start: 0.9304 (tp) cc_final: 0.9096 (tp) REVERT: B 745 TYR cc_start: 0.7458 (m-80) cc_final: 0.7223 (m-80) REVERT: B 816 ASP cc_start: 0.7965 (m-30) cc_final: 0.7456 (m-30) REVERT: B 1056 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7049 (tt) REVERT: B 1105 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8001 (mm-30) REVERT: B 1190 ARG cc_start: 0.8812 (tpt170) cc_final: 0.8277 (tpt170) REVERT: B 1320 MET cc_start: 0.8517 (mmm) cc_final: 0.8241 (mmm) REVERT: B 1594 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8747 (mmtm) REVERT: B 1695 LEU cc_start: 0.6631 (mt) cc_final: 0.6276 (mp) REVERT: B 1731 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7133 (mm-30) REVERT: B 1780 LYS cc_start: 0.8660 (tppt) cc_final: 0.8318 (tppt) REVERT: B 2004 MET cc_start: 0.7032 (mtp) cc_final: 0.6811 (mtm) REVERT: B 2046 PRO cc_start: 0.9186 (Cg_exo) cc_final: 0.8950 (Cg_endo) REVERT: B 2466 MET cc_start: 0.7748 (ttp) cc_final: 0.7448 (ttp) REVERT: C 45 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (tt) REVERT: C 53 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7346 (mtm180) REVERT: C 107 GLU cc_start: 0.7806 (tp30) cc_final: 0.7498 (tp30) REVERT: C 388 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8286 (mtm-85) REVERT: C 562 HIS cc_start: 0.7473 (m-70) cc_final: 0.7183 (m-70) REVERT: C 1105 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8057 (mm-30) REVERT: C 1120 MET cc_start: 0.8586 (mmm) cc_final: 0.8310 (mmm) REVERT: C 1190 ARG cc_start: 0.8808 (tpt170) cc_final: 0.8488 (tpt170) REVERT: C 1270 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8772 (t0) REVERT: C 1411 MET cc_start: 0.7768 (ttt) cc_final: 0.7374 (tpt) REVERT: C 1780 LYS cc_start: 0.8751 (tppt) cc_final: 0.8226 (tppt) REVERT: C 1791 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7688 (p0) REVERT: C 1906 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6691 (mm-30) REVERT: C 1931 GLU cc_start: 0.8009 (mp0) cc_final: 0.7760 (mp0) REVERT: C 2131 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7122 (mmt-90) REVERT: C 2144 CYS cc_start: 0.8461 (m) cc_final: 0.7977 (m) REVERT: D 53 ARG cc_start: 0.7521 (mtm110) cc_final: 0.7034 (mtm110) REVERT: D 416 MET cc_start: 0.7615 (tpt) cc_final: 0.7160 (tpt) REVERT: D 985 TYR cc_start: 0.8032 (t80) cc_final: 0.7607 (t80) REVERT: D 1105 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 1264 MET cc_start: 0.8857 (ttm) cc_final: 0.8597 (ttm) REVERT: D 1791 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7546 (p0) REVERT: D 1882 GLU cc_start: 0.7808 (tt0) cc_final: 0.7554 (tt0) REVERT: D 1906 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6666 (mm-30) REVERT: D 1986 MET cc_start: 0.8181 (tpp) cc_final: 0.7761 (tpp) REVERT: D 2053 ILE cc_start: 0.8431 (mm) cc_final: 0.8142 (mt) REVERT: D 2145 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7889 (tm-30) outliers start: 105 outliers final: 93 residues processed: 1629 average time/residue: 1.5943 time to fit residues: 4360.9437 Evaluate side-chains 1644 residues out of total 8176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1545 time to evaluate : 8.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1363 MET Chi-restraints excluded: chain A residue 1491 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1617 LEU Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 2155 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 443 ASP Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain B residue 854 GLU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1271 ASN Chi-restraints excluded: chain B residue 1322 MET Chi-restraints excluded: chain B residue 1363 MET Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1791 ASP Chi-restraints excluded: chain B residue 2464 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 1270 ASN Chi-restraints excluded: chain C residue 1271 ASN Chi-restraints excluded: chain C residue 1363 MET Chi-restraints excluded: chain C residue 1775 LEU Chi-restraints excluded: chain C residue 1791 ASP Chi-restraints excluded: chain C residue 1868 LEU Chi-restraints excluded: chain C residue 1900 ASN Chi-restraints excluded: chain C residue 2029 ILE Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 511 GLU Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 833 THR Chi-restraints excluded: chain D residue 879 SER Chi-restraints excluded: chain D residue 885 THR Chi-restraints excluded: chain D residue 1064 MET Chi-restraints excluded: chain D residue 1271 ASN Chi-restraints excluded: chain D residue 1363 MET Chi-restraints excluded: chain D residue 1648 ILE Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1868 LEU Chi-restraints excluded: chain D residue 1879 LEU Chi-restraints excluded: chain D residue 2130 ASP Chi-restraints excluded: chain D residue 2155 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 896 random chunks: chunk 564 optimal weight: 20.0000 chunk 757 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 655 optimal weight: 0.0370 chunk 104 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 711 optimal weight: 0.0770 chunk 297 optimal weight: 0.9980 chunk 731 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS A 869 ASN ** A1102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1939 GLN ** B2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2510 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 ASN C1939 GLN ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS D1270 ASN ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2210 ASN ** D2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134920 restraints weight = 323774.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136792 restraints weight = 183847.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136869 restraints weight = 150530.591| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 73644 Z= 0.155 Angle : 0.481 8.870 99580 Z= 0.251 Chirality : 0.034 0.173 11428 Planarity : 0.003 0.066 12652 Dihedral : 3.996 47.194 9916 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 17.83 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: 2.85 (0.09), residues: 8876 helix: 3.06 (0.07), residues: 5684 sheet: -0.81 (0.21), residues: 664 loop : -0.15 (0.13), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D2601 HIS 0.007 0.000 HIS A1790 PHE 0.019 0.001 PHE B 761 TYR 0.018 0.001 TYR C 71 ARG 0.011 0.000 ARG A 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57590.94 seconds wall clock time: 983 minutes 1.66 seconds (58981.66 seconds total)