Starting phenix.real_space_refine (version: dev) on Thu Dec 22 12:47:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eu0_3955/12_2022/6eu0_3955_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1125": "NH1" <-> "NH2" Residue "A ARG 1160": "NH1" <-> "NH2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A ARG 1265": "NH1" <-> "NH2" Residue "A ARG 1337": "NH1" <-> "NH2" Residue "A ARG 1373": "NH1" <-> "NH2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "B ARG 576": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 874": "NH1" <-> "NH2" Residue "B ARG 1038": "NH1" <-> "NH2" Residue "B ARG 1043": "NH1" <-> "NH2" Residue "B ARG 1056": "NH1" <-> "NH2" Residue "B ARG 1061": "NH1" <-> "NH2" Residue "B ARG 1082": "NH1" <-> "NH2" Residue "B ARG 1142": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "E ARG 7": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 12": "NH1" <-> "NH2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "M ARG 95": "NH1" <-> "NH2" Residue "M ARG 99": "NH1" <-> "NH2" Residue "M TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 199": "NH1" <-> "NH2" Residue "M ARG 208": "NH1" <-> "NH2" Residue "N ARG 292": "NH1" <-> "NH2" Residue "N ARG 303": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "O ARG 291": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O ARG 317": "NH1" <-> "NH2" Residue "O ARG 368": "NH1" <-> "NH2" Residue "O ARG 512": "NH1" <-> "NH2" Residue "O ARG 542": "NH1" <-> "NH2" Residue "O ARG 553": "NH1" <-> "NH2" Residue "O ARG 561": "NH1" <-> "NH2" Residue "O ARG 578": "NH1" <-> "NH2" Residue "P ARG 113": "NH1" <-> "NH2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 262": "NH1" <-> "NH2" Residue "V ARG 307": "NH1" <-> "NH2" Residue "V ARG 311": "NH1" <-> "NH2" Residue "V ARG 318": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "Y ARG 105": "NH1" <-> "NH2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ARG 121": "NH1" <-> "NH2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z ARG 276": "NH1" <-> "NH2" Residue "Z ARG 286": "NH1" <-> "NH2" Residue "Z PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 298": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 48918 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 11119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11119 Classifications: {'peptide': 1421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 1356} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8771 Classifications: {'peptide': 1112} Link IDs: {'PTRANS': 43, 'TRANS': 1068} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1698 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 197} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 313 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4421 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 531} Chain breaks: 1 Chain: "P" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2355 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 287} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "Q" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 589 Classifications: {'peptide': 88} Incomplete info: {'backbone_only': 24} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1038 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1174 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain breaks: 1 Chain: "V" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 1829 Classifications: {'peptide': 273} Incomplete info: {'backbone_only': 107} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 234 Chain: "Y" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "Z" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2705 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 565 SG CYS A 77 89.240 78.682 82.095 1.00 15.62 S ATOM 803 SG CYS A 107 70.622 120.519 94.308 1.00 25.60 S ATOM 826 SG CYS A 110 68.829 122.010 91.555 1.00 24.86 S ATOM 1192 SG CYS A 154 70.379 124.084 94.613 1.00 30.78 S ATOM 1216 SG CYS A 157 66.756 123.509 94.933 1.00 32.12 S ATOM 19552 SG CYS B1107 90.960 91.902 74.367 1.00 23.75 S ATOM 19572 SG CYS B1110 87.525 94.671 72.454 1.00 28.41 S ATOM 29029 SG CYS I 8 75.732 122.593 160.337 1.00 52.02 S ATOM 29157 SG CYS I 26 76.510 125.739 157.214 1.00 62.82 S ATOM 29180 SG CYS I 29 72.878 122.243 157.747 1.00 63.56 S ATOM 29338 SG CYS J 7 141.358 55.387 124.484 1.00 8.95 S ATOM 29641 SG CYS J 45 143.358 59.689 125.920 1.00 10.79 S ATOM 29647 SG CYS J 46 143.946 55.475 126.975 1.00 10.18 S ATOM 30831 SG CYS L 51 98.829 38.407 126.374 1.00 19.89 S ATOM 46256 SG CYS Z 7 104.254 57.406 75.138 1.00 58.99 S ATOM 46397 SG CYS Z 25 106.490 59.854 78.173 1.00 42.65 S ATOM 46417 SG CYS Z 28 108.589 59.174 75.011 1.00 38.35 S Time building chain proxies: 25.56, per 1000 atoms: 0.52 Number of scatterers: 48918 At special positions: 0 Unit cell: (198.22, 173.84, 205.64, 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 7 29.99 S 245 16.00 P 108 15.00 Mg 1 11.99 O 9462 8.00 N 8525 7.00 C 30570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.31 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb=" ZN Z 601 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 7 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 28 " pdb="ZN ZN Z 601 " - pdb=" SG CYS Z 25 " Number of angles added : 6 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11002 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 37.4% alpha, 7.1% beta 34 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 11.78 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.721A pdb=" N GLY A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.980A pdb=" N LYS A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.984A pdb=" N LYS A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.090A pdb=" N ARG A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.757A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 283 through 306 removed outlier: 3.596A pdb=" N SER A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 325 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.795A pdb=" N GLY A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.281A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.881A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 565 removed outlier: 3.632A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 605 through 615 removed outlier: 3.562A pdb=" N ILE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 709 Proline residue: A 687 - end of helix removed outlier: 3.876A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 747 removed outlier: 3.602A pdb=" N GLU A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.965A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 810 Processing helix chain 'A' and resid 857 through 889 removed outlier: 4.022A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.633A pdb=" N ASP A 919 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.224A pdb=" N ASP A 940 " --> pdb=" O ASN A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 968 removed outlier: 3.525A pdb=" N ILE A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 removed outlier: 3.754A pdb=" N VAL A 995 " --> pdb=" O ALA A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1027 removed outlier: 3.727A pdb=" N ARG A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1018 " --> pdb=" O GLY A1014 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1081 removed outlier: 3.749A pdb=" N ARG A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1098 Processing helix chain 'A' and resid 1122 through 1131 removed outlier: 3.614A pdb=" N ILE A1126 " --> pdb=" O GLY A1122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A1131 " --> pdb=" O LYS A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1161 removed outlier: 4.291A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.015A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1210 removed outlier: 3.596A pdb=" N ALA A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1265 removed outlier: 3.527A pdb=" N LEU A1263 " --> pdb=" O ARG A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1270 removed outlier: 3.630A pdb=" N ASP A1269 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1320 through 1345 removed outlier: 8.185A pdb=" N ILE A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N GLU A1329 " --> pdb=" O VAL A1325 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA A1330 " --> pdb=" O LEU A1326 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A1331 " --> pdb=" O GLY A1327 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A1339 " --> pdb=" O ILE A1335 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A1345 " --> pdb=" O TYR A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1361 removed outlier: 3.934A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1361 " --> pdb=" O LEU A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1394 through 1402 removed outlier: 3.658A pdb=" N TYR A1402 " --> pdb=" O ASP A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1418 removed outlier: 3.956A pdb=" N LEU A1417 " --> pdb=" O GLU A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1428 removed outlier: 3.798A pdb=" N SER A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A1428 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1455 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.801A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.130A pdb=" N LYS B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.944A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.506A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 4.160A pdb=" N ILE B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 343 through 359 removed outlier: 3.508A pdb=" N ARG B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 379 through 407 removed outlier: 3.927A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.886A pdb=" N LEU B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 439 removed outlier: 3.899A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.790A pdb=" N LEU B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS B 550 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 551' Processing helix chain 'B' and resid 567 through 582 removed outlier: 3.545A pdb=" N PHE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 633 removed outlier: 3.810A pdb=" N GLY B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 662 through 666 removed outlier: 4.029A pdb=" N ASP B 665 " --> pdb=" O TYR B 662 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.807A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 676 through 680' Processing helix chain 'B' and resid 690 through 694 removed outlier: 3.584A pdb=" N HIS B 693 " --> pdb=" O TYR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 955 through 971 removed outlier: 4.188A pdb=" N ILE B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 995 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1066 through 1074 removed outlier: 4.168A pdb=" N VAL B1070 " --> pdb=" O GLU B1066 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 Processing helix chain 'B' and resid 1122 through 1134 removed outlier: 3.654A pdb=" N LYS B1126 " --> pdb=" O PRO B1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.717A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.738A pdb=" N VAL C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.083A pdb=" N ASP C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 4.231A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.613A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.704A pdb=" N LYS D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.948A pdb=" N ARG D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 68 removed outlier: 4.238A pdb=" N ASN D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 4.022A pdb=" N GLU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.788A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.642A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 120 through 124 removed outlier: 4.385A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 124 " --> pdb=" O MET E 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 120 through 124' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.527A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.573A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.947A pdb=" N THR G 27 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 removed outlier: 4.131A pdb=" N LEU G 174 " --> pdb=" O GLU G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'J' and resid 18 through 27 removed outlier: 3.596A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 removed outlier: 4.334A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 72 through 82 removed outlier: 4.246A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.628A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 removed outlier: 3.845A pdb=" N LYS M 100 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 136 removed outlier: 3.683A pdb=" N LYS M 135 " --> pdb=" O ASN M 132 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA M 136 " --> pdb=" O LYS M 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 132 through 136' Processing helix chain 'M' and resid 188 through 198 Processing helix chain 'M' and resid 205 through 209 Processing helix chain 'M' and resid 231 through 236 Processing helix chain 'M' and resid 252 through 266 removed outlier: 3.786A pdb=" N ASP M 257 " --> pdb=" O GLU M 253 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR M 258 " --> pdb=" O GLN M 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE M 259 " --> pdb=" O PHE M 255 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU M 262 " --> pdb=" O THR M 258 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA M 263 " --> pdb=" O ILE M 259 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 295 removed outlier: 3.715A pdb=" N LYS N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 57 removed outlier: 3.793A pdb=" N ALA O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 72 removed outlier: 3.953A pdb=" N ALA O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 83 removed outlier: 3.905A pdb=" N LEU O 79 " --> pdb=" O SER O 75 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL O 80 " --> pdb=" O VAL O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 99 removed outlier: 3.959A pdb=" N THR O 93 " --> pdb=" O ASP O 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 138 removed outlier: 6.305A pdb=" N GLY O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 144 removed outlier: 4.069A pdb=" N GLN O 143 " --> pdb=" O GLU O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 165 removed outlier: 3.916A pdb=" N ALA O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN O 162 " --> pdb=" O GLU O 158 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL O 163 " --> pdb=" O ILE O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 175 Processing helix chain 'O' and resid 176 through 178 No H-bonds generated for 'chain 'O' and resid 176 through 178' Processing helix chain 'O' and resid 181 through 197 removed outlier: 4.337A pdb=" N TYR O 185 " --> pdb=" O ASP O 181 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR O 186 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.750A pdb=" N ASN O 225 " --> pdb=" O LYS O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 255 Processing helix chain 'O' and resid 285 through 303 Processing helix chain 'O' and resid 306 through 320 removed outlier: 4.562A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU O 318 " --> pdb=" O ILE O 314 " (cutoff:3.500A) Processing helix chain 'O' and resid 339 through 356 removed outlier: 3.839A pdb=" N LYS O 343 " --> pdb=" O LEU O 339 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN O 346 " --> pdb=" O ALA O 342 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 367 Processing helix chain 'O' and resid 451 through 463 removed outlier: 3.505A pdb=" N SER O 455 " --> pdb=" O SER O 451 " (cutoff:3.500A) Processing helix chain 'O' and resid 483 through 500 removed outlier: 4.022A pdb=" N LEU O 500 " --> pdb=" O ILE O 496 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 514 Processing helix chain 'O' and resid 519 through 524 removed outlier: 3.720A pdb=" N ASN O 523 " --> pdb=" O LYS O 520 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 542 Processing helix chain 'O' and resid 569 through 598 removed outlier: 3.710A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 610 removed outlier: 3.892A pdb=" N LEU O 603 " --> pdb=" O ASN O 599 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 606 " --> pdb=" O LEU O 602 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP O 609 " --> pdb=" O LYS O 605 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP O 610 " --> pdb=" O ALA O 606 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 651 removed outlier: 3.559A pdb=" N ASN O 625 " --> pdb=" O PRO O 621 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG O 643 " --> pdb=" O ALA O 639 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 24 Processing helix chain 'P' and resid 29 through 40 removed outlier: 3.911A pdb=" N GLN P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N MET P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 54 Processing helix chain 'P' and resid 89 through 99 removed outlier: 3.936A pdb=" N ALA P 99 " --> pdb=" O SER P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 removed outlier: 3.605A pdb=" N ILE P 110 " --> pdb=" O TRP P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 116 No H-bonds generated for 'chain 'P' and resid 114 through 116' Processing helix chain 'P' and resid 118 through 130 Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 203 through 209 removed outlier: 3.999A pdb=" N PHE P 207 " --> pdb=" O LYS P 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR P 208 " --> pdb=" O LYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 228 removed outlier: 3.792A pdb=" N ALA P 228 " --> pdb=" O PHE P 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 250 removed outlier: 3.619A pdb=" N ASP P 250 " --> pdb=" O VAL P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 273 Processing helix chain 'Q' and resid 48 through 67 removed outlier: 3.529A pdb=" N ARG Q 52 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 Processing helix chain 'Q' and resid 86 through 91 Processing helix chain 'Q' and resid 101 through 116 Processing helix chain 'V' and resid 293 through 317 removed outlier: 4.304A pdb=" N ALA V 299 " --> pdb=" O LYS V 295 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS V 300 " --> pdb=" O SER V 296 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS V 301 " --> pdb=" O LYS V 297 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA V 302 " --> pdb=" O MET V 298 " (cutoff:3.500A) Processing helix chain 'V' and resid 322 through 346 removed outlier: 3.610A pdb=" N LEU V 346 " --> pdb=" O GLU V 342 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 421 through 435 Processing helix chain 'V' and resid 438 through 446 Processing helix chain 'V' and resid 450 through 465 removed outlier: 3.852A pdb=" N VAL V 454 " --> pdb=" O SER V 450 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS V 464 " --> pdb=" O ASN V 460 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG V 465 " --> pdb=" O GLU V 461 " (cutoff:3.500A) Processing helix chain 'V' and resid 466 through 476 removed outlier: 4.041A pdb=" N LYS V 476 " --> pdb=" O ALA V 472 " (cutoff:3.500A) Processing helix chain 'V' and resid 480 through 489 Processing helix chain 'V' and resid 496 through 541 removed outlier: 3.713A pdb=" N LYS V 541 " --> pdb=" O ASN V 537 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 89 removed outlier: 3.556A pdb=" N ALA Y 89 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 147 removed outlier: 3.923A pdb=" N ALA Y 140 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG Y 141 " --> pdb=" O ARG Y 137 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE Y 142 " --> pdb=" O LYS Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 178 Processing helix chain 'Y' and resid 219 through 229 removed outlier: 3.570A pdb=" N ALA Y 229 " --> pdb=" O GLN Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 237 removed outlier: 3.619A pdb=" N PHE Y 237 " --> pdb=" O VAL Y 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 95 Processing helix chain 'Z' and resid 97 through 114 removed outlier: 3.784A pdb=" N THR Z 101 " --> pdb=" O PRO Z 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP Z 102 " --> pdb=" O GLU Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 122 through 137 removed outlier: 4.068A pdb=" N GLU Z 137 " --> pdb=" O ALA Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 148 removed outlier: 4.020A pdb=" N PHE Z 146 " --> pdb=" O MET Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 152 removed outlier: 3.866A pdb=" N VAL Z 152 " --> pdb=" O ARG Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 149 through 152' Processing helix chain 'Z' and resid 153 through 162 removed outlier: 3.599A pdb=" N ILE Z 157 " --> pdb=" O SER Z 153 " (cutoff:3.500A) Processing helix chain 'Z' and resid 179 through 186 removed outlier: 3.533A pdb=" N GLN Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Z 186 " --> pdb=" O ILE Z 182 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 3.851A pdb=" N ASP Z 201 " --> pdb=" O LYS Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 removed outlier: 5.206A pdb=" N ALA Z 231 " --> pdb=" O CYS Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 240 through 248 removed outlier: 3.898A pdb=" N ILE Z 244 " --> pdb=" O THR Z 240 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL Z 245 " --> pdb=" O HIS Z 241 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL Z 247 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 266 removed outlier: 3.940A pdb=" N LEU Z 255 " --> pdb=" O ALA Z 251 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Z 256 " --> pdb=" O GLU Z 252 " (cutoff:3.500A) Processing helix chain 'Z' and resid 269 through 274 removed outlier: 4.568A pdb=" N GLN Z 273 " --> pdb=" O LYS Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 296 removed outlier: 3.843A pdb=" N VAL Z 291 " --> pdb=" O PRO Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 455 removed outlier: 4.040A pdb=" N LEU Z 452 " --> pdb=" O THR Z 448 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL Z 455 " --> pdb=" O TYR Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 480 through 491 Processing helix chain 'Z' and resid 492 through 509 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.594A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B1062 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 373 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.591A pdb=" N GLY A 377 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.677A pdb=" N VAL A 462 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 625 through 629 removed outlier: 6.845A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AA9, first strand: chain 'A' and resid 1281 through 1282 removed outlier: 3.647A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 3.502A pdb=" N GLN A1174 " --> pdb=" O GLN A1185 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1224 through 1225 removed outlier: 3.543A pdb=" N ILE A1225 " --> pdb=" O ARG A1229 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A1229 " --> pdb=" O ILE A1225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1431 through 1432 removed outlier: 3.619A pdb=" N LYS A1432 " --> pdb=" O GLY G 57 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY G 57 " --> pdb=" O LYS A1432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 95 through 100 removed outlier: 6.791A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AB6, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.739A pdb=" N ARG B 376 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 199 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 561 through 564 removed outlier: 3.793A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 613 through 614 Processing sheet with id=AB9, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.539A pdb=" N LEU B 899 " --> pdb=" O GLN B 883 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.539A pdb=" N LEU B 899 " --> pdb=" O GLN B 883 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 753 through 758 Processing sheet with id=AC3, first strand: chain 'B' and resid 753 through 758 Processing sheet with id=AC4, first strand: chain 'B' and resid 770 through 774 removed outlier: 7.688A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 841 through 843 removed outlier: 4.494A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 871 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 1093 through 1094 Processing sheet with id=AC7, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AC8, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.631A pdb=" N SER C 46 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 77 through 86 removed outlier: 5.121A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 106 through 107 removed outlier: 3.768A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AD3, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD4, first strand: chain 'E' and resid 80 through 82 removed outlier: 6.578A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AD6, first strand: chain 'F' and resid 133 through 135 Processing sheet with id=AD7, first strand: chain 'G' and resid 5 through 13 removed outlier: 3.796A pdb=" N SER G 66 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 75 " --> pdb=" O THR G 47 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 84 through 88 removed outlier: 3.946A pdb=" N VAL G 85 " --> pdb=" O PHE G 148 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 128 through 129 removed outlier: 4.620A pdb=" N TRP G 128 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 140 " --> pdb=" O TRP G 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 38 through 43 removed outlier: 8.182A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN H 11 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 57 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.874A pdb=" N GLU H 105 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET H 123 " --> pdb=" O TYR H 116 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 23 through 24 removed outlier: 3.708A pdb=" N LEU I 24 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE I 33 " --> pdb=" O LEU I 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 60 through 66 removed outlier: 3.554A pdb=" N ALA K 61 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE K 105 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY K 90 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 88 through 89 removed outlier: 3.754A pdb=" N VAL N 394 " --> pdb=" O PHE M 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 109 through 111 removed outlier: 3.628A pdb=" N GLU M 120 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 158 through 159 Processing sheet with id=AE8, first strand: chain 'O' and resid 104 through 108 removed outlier: 3.930A pdb=" N LYS O 105 " --> pdb=" O TYR O 121 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 549 through 550 removed outlier: 3.748A pdb=" N LEU O 565 " --> pdb=" O GLN O 549 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 66 through 75 removed outlier: 4.686A pdb=" N LEU Y 67 " --> pdb=" O VAL Y 161 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL Y 161 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN Y 69 " --> pdb=" O ASN Y 159 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASN Y 159 " --> pdb=" O ASN Y 69 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL Y 71 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE Y 157 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR Y 73 " --> pdb=" O PHE Y 155 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE Y 155 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE Y 160 " --> pdb=" O GLY Y 216 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY Y 216 " --> pdb=" O ILE Y 160 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 193 through 197 removed outlier: 3.536A pdb=" N ILE Y 202 " --> pdb=" O MET Y 197 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 13 through 14 removed outlier: 3.589A pdb=" N VAL Z 24 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) 1465 hydrogen bonds defined for protein. 4212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 19.02 Time building geometry restraints manager: 19.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13106 1.33 - 1.46: 9600 1.46 - 1.58: 26678 1.58 - 1.70: 212 1.70 - 1.82: 399 Bond restraints: 49995 Sorted by residual: bond pdb=" C ASP M 221 " pdb=" N PRO M 222 " ideal model delta sigma weight residual 1.334 1.409 -0.075 2.34e-02 1.83e+03 1.02e+01 bond pdb=" C LEU A1267 " pdb=" N PRO A1268 " ideal model delta sigma weight residual 1.339 1.436 -0.097 3.40e-02 8.65e+02 8.09e+00 bond pdb=" C4' DC S 30 " pdb=" O4' DC S 30 " ideal model delta sigma weight residual 1.450 1.399 0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C PHE B 949 " pdb=" N PRO B 950 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.70e+00 bond pdb=" C GLN P 154 " pdb=" N PRO P 155 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.36e+00 ... (remaining 49990 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.47: 1158 104.47 - 112.03: 22783 112.03 - 119.58: 19122 119.58 - 127.13: 24092 127.13 - 134.69: 721 Bond angle restraints: 67876 Sorted by residual: angle pdb=" N PRO B 817 " pdb=" CA PRO B 817 " pdb=" C PRO B 817 " ideal model delta sigma weight residual 111.33 119.80 -8.47 1.43e+00 4.89e-01 3.51e+01 angle pdb=" C GLY O 305 " pdb=" N SER O 306 " pdb=" CA SER O 306 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C SER B 585 " pdb=" N GLU B 586 " pdb=" CA GLU B 586 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C LYS A 2 " pdb=" N GLU A 3 " pdb=" CA GLU A 3 " ideal model delta sigma weight residual 122.46 130.12 -7.66 1.41e+00 5.03e-01 2.95e+01 angle pdb=" O3' DA S 32 " pdb=" C3' DA S 32 " pdb=" C2' DA S 32 " ideal model delta sigma weight residual 111.50 103.36 8.14 1.50e+00 4.44e-01 2.95e+01 ... (remaining 67871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 29432 35.98 - 71.96: 681 71.96 - 107.93: 29 107.93 - 143.91: 2 143.91 - 179.89: 4 Dihedral angle restraints: 30148 sinusoidal: 13033 harmonic: 17115 Sorted by residual: dihedral pdb=" CA PHE P 300 " pdb=" C PHE P 300 " pdb=" N PRO P 301 " pdb=" CA PRO P 301 " ideal model delta harmonic sigma weight residual 180.00 115.73 64.27 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA PHE M 130 " pdb=" C PHE M 130 " pdb=" N TYR M 131 " pdb=" CA TYR M 131 " ideal model delta harmonic sigma weight residual -180.00 -130.39 -49.61 0 5.00e+00 4.00e-02 9.84e+01 dihedral pdb=" CA PRO A 600 " pdb=" C PRO A 600 " pdb=" N TYR A 601 " pdb=" CA TYR A 601 " ideal model delta harmonic sigma weight residual -180.00 -135.78 -44.22 0 5.00e+00 4.00e-02 7.82e+01 ... (remaining 30145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 6334 0.075 - 0.151: 1086 0.151 - 0.226: 138 0.226 - 0.301: 20 0.301 - 0.376: 2 Chirality restraints: 7580 Sorted by residual: chirality pdb=" CG LEU D 28 " pdb=" CB LEU D 28 " pdb=" CD1 LEU D 28 " pdb=" CD2 LEU D 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE Q 79 " pdb=" CA ILE Q 79 " pdb=" CG1 ILE Q 79 " pdb=" CG2 ILE Q 79 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 234 " pdb=" CA ILE A 234 " pdb=" CG1 ILE A 234 " pdb=" CG2 ILE A 234 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 7577 not shown) Planarity restraints: 8407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU Z 506 " 0.026 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C GLU Z 506 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU Z 506 " 0.031 2.00e-02 2.50e+03 pdb=" N ALA Z 507 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 130 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C PHE M 130 " 0.083 2.00e-02 2.50e+03 pdb=" O PHE M 130 " -0.032 2.00e-02 2.50e+03 pdb=" N TYR M 131 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE P 300 " 0.071 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO P 301 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO P 301 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO P 301 " 0.059 5.00e-02 4.00e+02 ... (remaining 8404 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 197 2.48 - 3.09: 30456 3.09 - 3.69: 73818 3.69 - 4.30: 101116 4.30 - 4.90: 162804 Nonbonded interactions: 368391 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MG MG A2002 " model vdw 1.879 2.170 nonbonded pdb=" NZ LYS O 289 " pdb=" O PRO O 324 " model vdw 2.099 2.520 nonbonded pdb=" NH2 ARG B 576 " pdb=" OE1 GLU B 647 " model vdw 2.115 2.520 nonbonded pdb=" NZ LYS E 161 " pdb=" O GLY E 193 " model vdw 2.116 2.520 nonbonded pdb=" O ALA M 263 " pdb=" NZ LYS M 266 " model vdw 2.121 2.520 ... (remaining 368386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 245 5.16 5 C 30570 2.51 5 N 8525 2.21 5 O 9462 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.900 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: 0.030 Extract box with map and model: 10.400 Check model and map are aligned: 0.720 Convert atoms to be neutral: 0.400 Process input model: 129.450 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.005 0.097 49995 Z= 0.293 Angle : 1.075 15.478 67876 Z= 0.570 Chirality : 0.058 0.376 7580 Planarity : 0.007 0.110 8407 Dihedral : 14.267 179.888 19146 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.38 % Favored : 84.28 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 2.81 % Twisted General : 0.32 % 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: -5.25 (0.08), residues: 5885 helix: -3.02 (0.08), residues: 2067 sheet: -3.17 (0.23), residues: 394 loop : -4.04 (0.08), residues: 3424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1751 time to evaluate : 5.913 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 outliers start: 27 outliers final: 3 residues processed: 1769 average time/residue: 0.6977 time to fit residues: 2007.3142 Evaluate side-chains 874 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 871 time to evaluate : 6.035 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4574 time to fit residues: 10.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 504 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 251 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 241 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 348 optimal weight: 3.9990 chunk 542 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN A 161 ASN A 229 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 328 ASN A 333 ASN A 355 GLN A 427 HIS A 533 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1118 ASN A1180 ASN A1284 ASN A1317 ASN A1354 HIS A1453 ASN B 42 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS B 286 ASN B 362 ASN B 382 GLN ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 427 ASN B 519 HIS B 574 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN B 859 ASN B 861 ASN ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 HIS B 928 GLN B 936 GLN B 947 HIS B 970 ASN B1077 GLN C 3 ASN C 65 ASN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 69 ASN E 5 ASN E 63 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 28 HIS G 31 ASN G 173 GLN H 11 GLN H 35 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 167 GLN M 254 GLN N 289 HIS ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN O 207 HIS ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 469 ASN ** O 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 631 ASN P 19 HIS P 117 HIS P 119 HIS ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 305 HIS Q 60 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 319 GLN V 391 ASN ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 444 GLN ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 179 HIS Z 18 ASN Z 82 ASN Z 123 GLN Z 207 GLN Z 249 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 49995 Z= 0.346 Angle : 0.839 10.905 67876 Z= 0.433 Chirality : 0.049 0.369 7580 Planarity : 0.006 0.089 8407 Dihedral : 14.873 177.150 7507 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.41 % Favored : 84.37 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.80 % Twisted General : 0.26 % 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: -4.09 (0.09), residues: 5885 helix: -1.43 (0.10), residues: 2096 sheet: -2.78 (0.23), residues: 417 loop : -3.76 (0.09), residues: 3372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 944 time to evaluate : 5.323 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 outliers start: 265 outliers final: 150 residues processed: 1122 average time/residue: 0.5947 time to fit residues: 1113.5884 Evaluate side-chains 911 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 761 time to evaluate : 6.514 Switching outliers to nearest non-outliers outliers start: 150 outliers final: 0 residues processed: 150 average time/residue: 0.4505 time to fit residues: 133.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 301 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 451 optimal weight: 4.9990 chunk 369 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 543 optimal weight: 40.0000 chunk 586 optimal weight: 3.9990 chunk 483 optimal weight: 2.9990 chunk 538 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 540 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1284 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 65 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 173 GLN H 133 ASN I 9 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 GLN ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 584 ASN P 197 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 260 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 49995 Z= 0.307 Angle : 0.788 12.682 67876 Z= 0.404 Chirality : 0.047 0.522 7580 Planarity : 0.005 0.085 8407 Dihedral : 14.775 171.527 7507 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.94 % Favored : 83.82 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.80 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.10), residues: 5885 helix: -0.81 (0.11), residues: 2097 sheet: -2.45 (0.24), residues: 407 loop : -3.59 (0.09), residues: 3381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 863 time to evaluate : 5.905 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 outliers start: 187 outliers final: 79 residues processed: 992 average time/residue: 0.5761 time to fit residues: 967.3117 Evaluate side-chains 805 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 726 time to evaluate : 5.762 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 0 residues processed: 79 average time/residue: 0.4485 time to fit residues: 74.9684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 536 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 364 optimal weight: 6.9990 chunk 545 optimal weight: 50.0000 chunk 577 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 516 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 GLN ** A1346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 425 HIS ** B 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN C 99 HIS C 207 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 117 HIS N 289 HIS ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN P 53 GLN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 6 ASN Z 35 ASN Z 207 GLN Z 461 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.106 49995 Z= 0.448 Angle : 0.899 13.570 67876 Z= 0.462 Chirality : 0.051 0.391 7580 Planarity : 0.006 0.083 8407 Dihedral : 15.017 166.251 7507 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 17.88 % Favored : 81.89 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.80 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.10), residues: 5885 helix: -0.76 (0.11), residues: 2089 sheet: -2.69 (0.22), residues: 474 loop : -3.61 (0.09), residues: 3322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 787 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 269 outliers final: 127 residues processed: 981 average time/residue: 0.5960 time to fit residues: 984.3720 Evaluate side-chains 802 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 675 time to evaluate : 5.430 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 0 residues processed: 127 average time/residue: 0.4611 time to fit residues: 119.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 480 optimal weight: 1.9990 chunk 327 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 429 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 492 optimal weight: 3.9990 chunk 398 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 517 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 589 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1346 HIS B 80 ASN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 GLN ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 ASN C 65 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 257 ASN O 310 GLN ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN Q 60 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 184 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 49995 Z= 0.223 Angle : 0.763 14.064 67876 Z= 0.387 Chirality : 0.046 0.237 7580 Planarity : 0.005 0.080 8407 Dihedral : 14.694 164.309 7507 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.11 % Favored : 84.67 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.10), residues: 5885 helix: -0.36 (0.11), residues: 2092 sheet: -2.39 (0.24), residues: 429 loop : -3.51 (0.10), residues: 3364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 815 time to evaluate : 5.473 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 outliers start: 137 outliers final: 51 residues processed: 915 average time/residue: 0.5842 time to fit residues: 907.2071 Evaluate side-chains 745 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 694 time to evaluate : 5.711 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4494 time to fit residues: 50.6168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 194 optimal weight: 0.3980 chunk 519 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 338 optimal weight: 0.0670 chunk 142 optimal weight: 0.9990 chunk 577 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 303 optimal weight: 8.9990 overall best weight: 1.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 GLN ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN M 254 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 652 GLN P 59 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 49995 Z= 0.235 Angle : 0.757 13.146 67876 Z= 0.383 Chirality : 0.046 0.326 7580 Planarity : 0.005 0.080 8407 Dihedral : 14.580 162.447 7507 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.50 % Favored : 83.30 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.11), residues: 5885 helix: -0.19 (0.12), residues: 2105 sheet: -2.24 (0.24), residues: 431 loop : -3.49 (0.10), residues: 3349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 765 time to evaluate : 6.343 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 outliers start: 117 outliers final: 56 residues processed: 845 average time/residue: 0.5942 time to fit residues: 854.5633 Evaluate side-chains 749 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 693 time to evaluate : 5.550 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4527 time to fit residues: 55.2645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 556 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 421 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 486 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 575 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 350 optimal weight: 0.6980 chunk 265 optimal weight: 0.2980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 595 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS O 579 GLN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 332 GLN ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 49995 Z= 0.288 Angle : 0.785 12.658 67876 Z= 0.399 Chirality : 0.047 0.258 7580 Planarity : 0.005 0.079 8407 Dihedral : 14.619 158.458 7507 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 17.11 % Favored : 82.68 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.11), residues: 5885 helix: -0.16 (0.12), residues: 2107 sheet: -2.21 (0.23), residues: 461 loop : -3.50 (0.10), residues: 3317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 716 time to evaluate : 5.793 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 outliers start: 126 outliers final: 57 residues processed: 798 average time/residue: 0.5983 time to fit residues: 811.0952 Evaluate side-chains 732 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 675 time to evaluate : 6.007 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4625 time to fit residues: 57.6600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 355 optimal weight: 7.9990 chunk 229 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 365 optimal weight: 8.9990 chunk 392 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 452 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 595 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 837 GLN ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS O 579 GLN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 49995 Z= 0.258 Angle : 0.770 12.678 67876 Z= 0.391 Chirality : 0.046 0.307 7580 Planarity : 0.005 0.079 8407 Dihedral : 14.615 155.842 7507 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.58 % Favored : 83.21 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.11), residues: 5885 helix: -0.05 (0.12), residues: 2110 sheet: -2.32 (0.22), residues: 485 loop : -3.48 (0.10), residues: 3290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 725 time to evaluate : 5.819 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 outliers start: 88 outliers final: 37 residues processed: 778 average time/residue: 0.5995 time to fit residues: 795.0731 Evaluate side-chains 717 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 680 time to evaluate : 5.719 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.4510 time to fit residues: 39.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 523 optimal weight: 9.9990 chunk 551 optimal weight: 20.0000 chunk 502 optimal weight: 0.4980 chunk 536 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 421 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 484 optimal weight: 6.9990 chunk 507 optimal weight: 0.9990 chunk 534 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS G 32 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 584 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 49995 Z= 0.278 Angle : 0.798 15.572 67876 Z= 0.403 Chirality : 0.047 0.270 7580 Planarity : 0.005 0.078 8407 Dihedral : 14.659 155.948 7507 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.52 % Favored : 82.26 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.21 % 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 (0.11), residues: 5885 helix: -0.03 (0.12), residues: 2092 sheet: -2.30 (0.23), residues: 463 loop : -3.44 (0.10), residues: 3330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 699 time to evaluate : 5.812 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 outliers start: 59 outliers final: 33 residues processed: 735 average time/residue: 0.6097 time to fit residues: 768.2433 Evaluate side-chains 700 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 667 time to evaluate : 5.880 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4698 time to fit residues: 37.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 352 optimal weight: 8.9990 chunk 567 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 594 optimal weight: 6.9990 chunk 547 optimal weight: 8.9990 chunk 473 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS ** O 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 579 GLN O 584 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 49995 Z= 0.259 Angle : 0.785 15.667 67876 Z= 0.396 Chirality : 0.047 0.263 7580 Planarity : 0.005 0.078 8407 Dihedral : 14.636 156.069 7507 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.04 % Favored : 82.79 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.21 % 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: -2.93 (0.11), residues: 5885 helix: 0.03 (0.12), residues: 2101 sheet: -2.25 (0.23), residues: 464 loop : -3.44 (0.10), residues: 3320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11770 Ramachandran restraints generated. 5885 Oldfield, 0 Emsley, 5885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 709 time to evaluate : 6.372 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 outliers start: 45 outliers final: 18 residues processed: 733 average time/residue: 0.6189 time to fit residues: 771.8384 Evaluate side-chains 688 residues out of total 5259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 670 time to evaluate : 5.963 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4750 time to fit residues: 24.3044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 597 random chunks: chunk 376 optimal weight: 3.9990 chunk 504 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 436 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 487 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 HIS O 579 GLN O 584 ASN ** Q 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.147216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125807 restraints weight = 102426.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.125619 restraints weight = 121262.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126277 restraints weight = 104053.785| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 49995 Z= 0.292 Angle : 0.808 15.582 67876 Z= 0.409 Chirality : 0.048 0.374 7580 Planarity : 0.005 0.078 8407 Dihedral : 14.686 156.050 7507 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.79 % Favored : 81.99 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.80 % Cis-general : 0.05 % Twisted Proline : 0.40 % Twisted General : 0.21 % 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: -2.97 (0.11), residues: 5885 helix: -0.00 (0.12), residues: 2094 sheet: -2.29 (0.23), residues: 477 loop : -3.46 (0.10), residues: 3314 =============================================================================== Job complete usr+sys time: 14406.72 seconds wall clock time: 257 minutes 33.28 seconds (15453.28 seconds total)