Starting phenix.real_space_refine (version: dev) on Thu Dec 22 14:19:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/12_2022/6c3o_7338_updated.pdb" } resolution = 3.9 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= 0.020 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 "E ARG 16": "NH1" <-> "NH2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 527": "NH1" <-> "NH2" Residue "E ARG 702": "NH1" <-> "NH2" Residue "E ARG 841": "NH1" <-> "NH2" Residue "E ARG 1123": "NH1" <-> "NH2" Residue "E ARG 1221": "NH1" <-> "NH2" Residue "E ARG 1313": "NH1" <-> "NH2" Residue "E ARG 1418": "NH1" <-> "NH2" Residue "E ARG 1436": "NH1" <-> "NH2" Residue "E ARG 1486": "NH1" <-> "NH2" Residue "E ARG 1493": "NH1" <-> "NH2" Residue "E ARG 1497": "NH1" <-> "NH2" Residue "H ARG 16": "NH1" <-> "NH2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 841": "NH1" <-> "NH2" Residue "H ARG 1123": "NH1" <-> "NH2" Residue "H ARG 1221": "NH1" <-> "NH2" Residue "H ARG 1313": "NH1" <-> "NH2" Residue "H ARG 1418": "NH1" <-> "NH2" Residue "H ARG 1436": "NH1" <-> "NH2" Residue "H ARG 1486": "NH1" <-> "NH2" Residue "H ARG 1493": "NH1" <-> "NH2" Residue "H ARG 1497": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 527": "NH1" <-> "NH2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "G ARG 841": "NH1" <-> "NH2" Residue "G ARG 1123": "NH1" <-> "NH2" Residue "G ARG 1221": "NH1" <-> "NH2" Residue "G ARG 1313": "NH1" <-> "NH2" Residue "G ARG 1418": "NH1" <-> "NH2" Residue "G ARG 1436": "NH1" <-> "NH2" Residue "G ARG 1486": "NH1" <-> "NH2" Residue "G ARG 1493": "NH1" <-> "NH2" Residue "G ARG 1497": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F ARG 841": "NH1" <-> "NH2" Residue "F ARG 1123": "NH1" <-> "NH2" Residue "F ARG 1221": "NH1" <-> "NH2" Residue "F ARG 1313": "NH1" <-> "NH2" Residue "F ARG 1418": "NH1" <-> "NH2" Residue "F ARG 1436": "NH1" <-> "NH2" Residue "F ARG 1486": "NH1" <-> "NH2" Residue "F ARG 1493": "NH1" <-> "NH2" Residue "F ARG 1497": "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: 49055 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "H" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "G" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "F" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' K': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 26.56, per 1000 atoms: 0.54 Number of scatterers: 49055 At special positions: 0 Unit cell: (180.7, 180.7, 140.4, 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) K 3 19.00 S 272 16.00 P 32 15.00 Mg 8 11.99 O 8656 8.00 N 8272 7.00 C 31812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.04 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.04 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: 20.98 Conformation dependent library (CDL) restraints added in 7.8 seconds 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 36 sheets defined 58.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.074A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.073A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.075A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 266 through 269 removed outlier: 4.074A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 96 removed outlier: 3.690A pdb=" N ASP E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 127 Processing helix chain 'E' and resid 137 through 159 removed outlier: 3.924A pdb=" N ASP E 159 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 191 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 288 through 314 removed outlier: 6.800A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU E 299 " --> pdb=" O PHE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 327 Processing helix chain 'E' and resid 355 through 401 removed outlier: 3.525A pdb=" N ALA E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 Processing helix chain 'E' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Proline residue: E 436 - end of helix Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 462 through 504 removed outlier: 3.735A pdb=" N ALA E 471 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.891A pdb=" N ARG E 486 " --> pdb=" O GLN E 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 491 " --> pdb=" O THR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 511 Processing helix chain 'E' and resid 515 through 562 removed outlier: 3.508A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) Proline residue: E 551 - end of helix removed outlier: 4.042A pdb=" N HIS E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 615 Proline residue: E 589 - end of helix removed outlier: 3.710A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG E 598 " --> pdb=" O SER E 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 615 " --> pdb=" O SER E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 727 Processing helix chain 'E' and resid 783 through 788 Processing helix chain 'E' and resid 795 through 805 Processing helix chain 'E' and resid 808 through 812 Processing helix chain 'E' and resid 817 through 819 No H-bonds generated for 'chain 'E' and resid 817 through 819' Processing helix chain 'E' and resid 831 through 843 removed outlier: 3.604A pdb=" N ALA E 842 " --> pdb=" O SER E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 877 Processing helix chain 'E' and resid 890 through 892 No H-bonds generated for 'chain 'E' and resid 890 through 892' Processing helix chain 'E' and resid 920 through 929 removed outlier: 5.011A pdb=" N THR E 929 " --> pdb=" O GLU E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1006 Processing helix chain 'E' and resid 1010 through 1035 Processing helix chain 'E' and resid 1062 through 1106 removed outlier: 3.731A pdb=" N LEU E1106 " --> pdb=" O ASN E1102 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1114 Processing helix chain 'E' and resid 1117 through 1125 removed outlier: 3.945A pdb=" N ARG E1123 " --> pdb=" O SER E1119 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE E1124 " --> pdb=" O ILE E1120 " (cutoff:3.500A) Processing helix chain 'E' and resid 1127 through 1159 Proline residue: E1136 - end of helix Processing helix chain 'E' and resid 1161 through 1207 removed outlier: 3.723A pdb=" N LEU E1164 " --> pdb=" O PRO E1161 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU E1168 " --> pdb=" O VAL E1165 " (cutoff:3.500A) Proline residue: E1169 - end of helix removed outlier: 4.020A pdb=" N ARG E1186 " --> pdb=" O VAL E1183 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E1197 " --> pdb=" O THR E1194 " (cutoff:3.500A) Proline residue: E1198 - end of helix Processing helix chain 'E' and resid 1210 through 1216 Processing helix chain 'E' and resid 1219 through 1272 Processing helix chain 'E' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN E1295 " --> pdb=" O SER E1291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP E1296 " --> pdb=" O ASN E1292 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1392 removed outlier: 4.270A pdb=" N PHE E1391 " --> pdb=" O PHE E1387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE E1392 " --> pdb=" O SER E1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1419 Processing helix chain 'E' and resid 1435 through 1439 Processing helix chain 'E' and resid 1447 through 1455 Processing helix chain 'E' and resid 1460 through 1464 Processing helix chain 'E' and resid 1476 through 1478 No H-bonds generated for 'chain 'E' and resid 1476 through 1478' Processing helix chain 'E' and resid 1483 through 1495 Processing helix chain 'E' and resid 1513 through 1526 Processing helix chain 'E' and resid 1542 through 1544 No H-bonds generated for 'chain 'E' and resid 1542 through 1544' Processing helix chain 'E' and resid 1562 through 1568 Processing helix chain 'E' and resid 1572 through 1580 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 25 through 43 removed outlier: 3.681A pdb=" N VAL H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Proline residue: H 35 - end of helix Processing helix chain 'H' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 96 removed outlier: 3.690A pdb=" N ASP H 96 " --> pdb=" O GLY H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 108 through 127 Processing helix chain 'H' and resid 137 through 159 removed outlier: 3.924A pdb=" N ASP H 159 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 191 Processing helix chain 'H' and resid 263 through 276 Processing helix chain 'H' and resid 288 through 314 removed outlier: 6.799A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 327 Processing helix chain 'H' and resid 355 through 401 removed outlier: 3.526A pdb=" N ALA H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR H 425 " --> pdb=" O VAL H 421 " (cutoff:3.500A) Proline residue: H 436 - end of helix Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 462 through 504 removed outlier: 3.735A pdb=" N ALA H 471 " --> pdb=" O ILE H 468 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.892A pdb=" N ARG H 486 " --> pdb=" O GLN H 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR H 491 " --> pdb=" O THR H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 511 Processing helix chain 'H' and resid 515 through 562 removed outlier: 3.509A pdb=" N THR H 525 " --> pdb=" O ARG H 521 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 4.041A pdb=" N HIS H 562 " --> pdb=" O THR H 558 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 615 Proline residue: H 589 - end of helix removed outlier: 3.710A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG H 598 " --> pdb=" O SER H 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER H 615 " --> pdb=" O SER H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 727 Processing helix chain 'H' and resid 783 through 788 Processing helix chain 'H' and resid 795 through 805 Processing helix chain 'H' and resid 808 through 812 Processing helix chain 'H' and resid 817 through 819 No H-bonds generated for 'chain 'H' and resid 817 through 819' Processing helix chain 'H' and resid 831 through 843 removed outlier: 3.605A pdb=" N ALA H 842 " --> pdb=" O SER H 838 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 877 Processing helix chain 'H' and resid 890 through 892 No H-bonds generated for 'chain 'H' and resid 890 through 892' Processing helix chain 'H' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR H 929 " --> pdb=" O GLU H 925 " (cutoff:3.500A) Processing helix chain 'H' and resid 995 through 1006 Processing helix chain 'H' and resid 1010 through 1035 Processing helix chain 'H' and resid 1062 through 1106 removed outlier: 3.732A pdb=" N LEU H1106 " --> pdb=" O ASN H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1114 Processing helix chain 'H' and resid 1117 through 1125 removed outlier: 3.946A pdb=" N ARG H1123 " --> pdb=" O SER H1119 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE H1124 " --> pdb=" O ILE H1120 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1159 Proline residue: H1136 - end of helix Processing helix chain 'H' and resid 1161 through 1207 removed outlier: 3.722A pdb=" N LEU H1164 " --> pdb=" O PRO H1161 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU H1168 " --> pdb=" O VAL H1165 " (cutoff:3.500A) Proline residue: H1169 - end of helix removed outlier: 4.019A pdb=" N ARG H1186 " --> pdb=" O VAL H1183 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU H1197 " --> pdb=" O THR H1194 " (cutoff:3.500A) Proline residue: H1198 - end of helix Processing helix chain 'H' and resid 1210 through 1216 Processing helix chain 'H' and resid 1219 through 1272 Processing helix chain 'H' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN H1295 " --> pdb=" O SER H1291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP H1296 " --> pdb=" O ASN H1292 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1392 removed outlier: 4.269A pdb=" N PHE H1391 " --> pdb=" O PHE H1387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE H1392 " --> pdb=" O SER H1388 " (cutoff:3.500A) Processing helix chain 'H' and resid 1414 through 1419 Processing helix chain 'H' and resid 1435 through 1439 Processing helix chain 'H' and resid 1447 through 1455 Processing helix chain 'H' and resid 1460 through 1464 Processing helix chain 'H' and resid 1476 through 1478 No H-bonds generated for 'chain 'H' and resid 1476 through 1478' Processing helix chain 'H' and resid 1483 through 1495 Processing helix chain 'H' and resid 1513 through 1526 Processing helix chain 'H' and resid 1542 through 1544 No H-bonds generated for 'chain 'H' and resid 1542 through 1544' Processing helix chain 'H' and resid 1562 through 1568 Processing helix chain 'H' and resid 1572 through 1580 Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'G' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Proline residue: G 35 - end of helix Processing helix chain 'G' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 96 removed outlier: 3.691A pdb=" N ASP G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 108 through 127 Processing helix chain 'G' and resid 137 through 159 removed outlier: 3.923A pdb=" N ASP G 159 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 191 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 288 through 314 removed outlier: 6.799A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU G 299 " --> pdb=" O PHE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 355 through 401 removed outlier: 3.524A pdb=" N ALA G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 408 Processing helix chain 'G' and resid 414 through 454 removed outlier: 4.272A pdb=" N THR G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Proline residue: G 436 - end of helix Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 462 through 504 removed outlier: 3.736A pdb=" N ALA G 471 " --> pdb=" O ILE G 468 " (cutoff:3.500A) Proline residue: G 472 - end of helix removed outlier: 3.890A pdb=" N ARG G 486 " --> pdb=" O GLN G 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR G 491 " --> pdb=" O THR G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 511 Processing helix chain 'G' and resid 515 through 562 removed outlier: 3.507A pdb=" N THR G 525 " --> pdb=" O ARG G 521 " (cutoff:3.500A) Proline residue: G 551 - end of helix removed outlier: 4.041A pdb=" N HIS G 562 " --> pdb=" O THR G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 615 Proline residue: G 589 - end of helix removed outlier: 3.710A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG G 598 " --> pdb=" O SER G 594 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER G 615 " --> pdb=" O SER G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 727 Processing helix chain 'G' and resid 783 through 788 Processing helix chain 'G' and resid 795 through 805 Processing helix chain 'G' and resid 808 through 812 Processing helix chain 'G' and resid 817 through 819 No H-bonds generated for 'chain 'G' and resid 817 through 819' Processing helix chain 'G' and resid 831 through 843 removed outlier: 3.605A pdb=" N ALA G 842 " --> pdb=" O SER G 838 " (cutoff:3.500A) Processing helix chain 'G' and resid 861 through 877 Processing helix chain 'G' and resid 890 through 892 No H-bonds generated for 'chain 'G' and resid 890 through 892' Processing helix chain 'G' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR G 929 " --> pdb=" O GLU G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 995 through 1006 Processing helix chain 'G' and resid 1010 through 1035 Processing helix chain 'G' and resid 1062 through 1106 removed outlier: 3.733A pdb=" N LEU G1106 " --> pdb=" O ASN G1102 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1114 Processing helix chain 'G' and resid 1117 through 1125 removed outlier: 3.945A pdb=" N ARG G1123 " --> pdb=" O SER G1119 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE G1124 " --> pdb=" O ILE G1120 " (cutoff:3.500A) Processing helix chain 'G' and resid 1127 through 1159 Proline residue: G1136 - end of helix Processing helix chain 'G' and resid 1161 through 1207 removed outlier: 3.723A pdb=" N LEU G1164 " --> pdb=" O PRO G1161 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU G1168 " --> pdb=" O VAL G1165 " (cutoff:3.500A) Proline residue: G1169 - end of helix removed outlier: 4.022A pdb=" N ARG G1186 " --> pdb=" O VAL G1183 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU G1197 " --> pdb=" O THR G1194 " (cutoff:3.500A) Proline residue: G1198 - end of helix Processing helix chain 'G' and resid 1210 through 1216 Processing helix chain 'G' and resid 1219 through 1272 Processing helix chain 'G' and resid 1278 through 1318 removed outlier: 4.854A pdb=" N ASN G1295 " --> pdb=" O SER G1291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP G1296 " --> pdb=" O ASN G1292 " (cutoff:3.500A) Processing helix chain 'G' and resid 1384 through 1392 removed outlier: 4.270A pdb=" N PHE G1391 " --> pdb=" O PHE G1387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE G1392 " --> pdb=" O SER G1388 " (cutoff:3.500A) Processing helix chain 'G' and resid 1414 through 1419 Processing helix chain 'G' and resid 1435 through 1439 Processing helix chain 'G' and resid 1447 through 1455 Processing helix chain 'G' and resid 1460 through 1464 Processing helix chain 'G' and resid 1476 through 1478 No H-bonds generated for 'chain 'G' and resid 1476 through 1478' Processing helix chain 'G' and resid 1483 through 1495 Processing helix chain 'G' and resid 1513 through 1526 Processing helix chain 'G' and resid 1542 through 1544 No H-bonds generated for 'chain 'G' and resid 1542 through 1544' Processing helix chain 'G' and resid 1562 through 1568 Processing helix chain 'G' and resid 1572 through 1580 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Proline residue: F 35 - end of helix Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 96 removed outlier: 3.689A pdb=" N ASP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 108 through 127 Processing helix chain 'F' and resid 137 through 159 removed outlier: 3.923A pdb=" N ASP F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 191 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 288 through 314 removed outlier: 6.800A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 327 Processing helix chain 'F' and resid 355 through 401 removed outlier: 3.525A pdb=" N ALA F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) Proline residue: F 436 - end of helix Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 462 through 504 removed outlier: 3.736A pdb=" N ALA F 471 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.891A pdb=" N ARG F 486 " --> pdb=" O GLN F 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 491 " --> pdb=" O THR F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 511 Processing helix chain 'F' and resid 515 through 562 removed outlier: 3.507A pdb=" N THR F 525 " --> pdb=" O ARG F 521 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 4.042A pdb=" N HIS F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 615 Proline residue: F 589 - end of helix removed outlier: 3.710A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG F 598 " --> pdb=" O SER F 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER F 615 " --> pdb=" O SER F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 727 Processing helix chain 'F' and resid 783 through 788 Processing helix chain 'F' and resid 795 through 805 Processing helix chain 'F' and resid 808 through 812 Processing helix chain 'F' and resid 817 through 819 No H-bonds generated for 'chain 'F' and resid 817 through 819' Processing helix chain 'F' and resid 831 through 843 removed outlier: 3.604A pdb=" N ALA F 842 " --> pdb=" O SER F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 877 Processing helix chain 'F' and resid 890 through 892 No H-bonds generated for 'chain 'F' and resid 890 through 892' Processing helix chain 'F' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR F 929 " --> pdb=" O GLU F 925 " (cutoff:3.500A) Processing helix chain 'F' and resid 995 through 1006 Processing helix chain 'F' and resid 1010 through 1035 Processing helix chain 'F' and resid 1062 through 1106 removed outlier: 3.731A pdb=" N LEU F1106 " --> pdb=" O ASN F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1114 Processing helix chain 'F' and resid 1117 through 1125 removed outlier: 3.944A pdb=" N ARG F1123 " --> pdb=" O SER F1119 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE F1124 " --> pdb=" O ILE F1120 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1159 Proline residue: F1136 - end of helix Processing helix chain 'F' and resid 1161 through 1207 removed outlier: 3.722A pdb=" N LEU F1164 " --> pdb=" O PRO F1161 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU F1168 " --> pdb=" O VAL F1165 " (cutoff:3.500A) Proline residue: F1169 - end of helix removed outlier: 4.020A pdb=" N ARG F1186 " --> pdb=" O VAL F1183 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU F1197 " --> pdb=" O THR F1194 " (cutoff:3.500A) Proline residue: F1198 - end of helix Processing helix chain 'F' and resid 1210 through 1216 Processing helix chain 'F' and resid 1219 through 1272 Processing helix chain 'F' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN F1295 " --> pdb=" O SER F1291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP F1296 " --> pdb=" O ASN F1292 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1392 removed outlier: 4.269A pdb=" N PHE F1391 " --> pdb=" O PHE F1387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE F1392 " --> pdb=" O SER F1388 " (cutoff:3.500A) Processing helix chain 'F' and resid 1414 through 1419 Processing helix chain 'F' and resid 1435 through 1439 Processing helix chain 'F' and resid 1447 through 1455 Processing helix chain 'F' and resid 1460 through 1464 Processing helix chain 'F' and resid 1476 through 1478 No H-bonds generated for 'chain 'F' and resid 1476 through 1478' Processing helix chain 'F' and resid 1483 through 1495 Processing helix chain 'F' and resid 1513 through 1526 Processing helix chain 'F' and resid 1542 through 1544 No H-bonds generated for 'chain 'F' and resid 1542 through 1544' Processing helix chain 'F' and resid 1562 through 1568 Processing helix chain 'F' and resid 1572 through 1580 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.092A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= F, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'C' and resid 188 through 192 Processing sheet with id= H, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.091A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= K, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'B' and resid 188 through 192 Processing sheet with id= M, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.092A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.091A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= U, first strand: chain 'E' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA E 736 " --> pdb=" O MET E 682 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET E 682 " --> pdb=" O ALA E 736 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 699 " --> pdb=" O GLY E 683 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 906 through 910 removed outlier: 7.091A pdb=" N ALA E 901 " --> pdb=" O GLN E 908 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU E 910 " --> pdb=" O ILE E 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 899 " --> pdb=" O GLU E 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL E 883 " --> pdb=" O THR E 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE E 711 " --> pdb=" O VAL E 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU E 885 " --> pdb=" O ILE E 711 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLY E 713 " --> pdb=" O LEU E 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 886 " --> pdb=" O LEU E 852 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1366 through 1368 Processing sheet with id= X, first strand: chain 'E' and resid 1548 through 1550 removed outlier: 6.480A pdb=" N GLY E1375 " --> pdb=" O ILE E1549 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E1534 " --> pdb=" O ILE E1374 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 736 through 738 removed outlier: 3.992A pdb=" N ALA H 736 " --> pdb=" O MET H 682 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET H 682 " --> pdb=" O ALA H 736 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE H 699 " --> pdb=" O GLY H 683 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 906 through 910 removed outlier: 7.091A pdb=" N ALA H 901 " --> pdb=" O GLN H 908 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU H 910 " --> pdb=" O ILE H 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE H 899 " --> pdb=" O GLU H 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL H 883 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE H 711 " --> pdb=" O VAL H 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU H 885 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLY H 713 " --> pdb=" O LEU H 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 886 " --> pdb=" O LEU H 852 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 1366 through 1368 Processing sheet with id= AB, first strand: chain 'H' and resid 1548 through 1550 removed outlier: 6.479A pdb=" N GLY H1375 " --> pdb=" O ILE H1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR H1534 " --> pdb=" O ILE H1374 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA G 736 " --> pdb=" O MET G 682 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET G 682 " --> pdb=" O ALA G 736 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE G 699 " --> pdb=" O GLY G 683 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 906 through 910 removed outlier: 7.092A pdb=" N ALA G 901 " --> pdb=" O GLN G 908 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU G 910 " --> pdb=" O ILE G 899 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE G 899 " --> pdb=" O GLU G 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL G 883 " --> pdb=" O THR G 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE G 711 " --> pdb=" O VAL G 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU G 885 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N GLY G 713 " --> pdb=" O LEU G 885 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 886 " --> pdb=" O LEU G 852 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1366 through 1368 Processing sheet with id= AF, first strand: chain 'G' and resid 1548 through 1550 removed outlier: 6.479A pdb=" N GLY G1375 " --> pdb=" O ILE G1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR G1534 " --> pdb=" O ILE G1374 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA F 736 " --> pdb=" O MET F 682 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET F 682 " --> pdb=" O ALA F 736 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE F 699 " --> pdb=" O GLY F 683 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 906 through 910 removed outlier: 7.092A pdb=" N ALA F 901 " --> pdb=" O GLN F 908 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU F 910 " --> pdb=" O ILE F 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 899 " --> pdb=" O GLU F 910 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 883 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE F 711 " --> pdb=" O VAL F 883 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU F 885 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLY F 713 " --> pdb=" O LEU F 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 886 " --> pdb=" O LEU F 852 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 1366 through 1368 Processing sheet with id= AJ, first strand: chain 'F' and resid 1548 through 1550 removed outlier: 6.480A pdb=" N GLY F1375 " --> pdb=" O ILE F1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F1534 " --> pdb=" O ILE F1374 " (cutoff:3.500A) 2984 hydrogen bonds defined for protein. 7968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.51 Time building geometry restraints manager: 22.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15468 1.34 - 1.46: 9400 1.46 - 1.57: 24712 1.57 - 1.69: 52 1.69 - 1.81: 424 Bond restraints: 50056 Sorted by residual: bond pdb=" C4 ATP F2004 " pdb=" C5 ATP F2004 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP E2004 " pdb=" C5 ATP E2004 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 ... (remaining 50051 not shown) Histogram of bond angle deviations from ideal: 98.52 - 106.03: 1017 106.03 - 113.55: 30013 113.55 - 121.06: 24559 121.06 - 128.57: 12255 128.57 - 136.08: 436 Bond angle restraints: 68280 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 118.98 20.89 1.00e+00 1.00e+00 4.36e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 116.17 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.46 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.73 20.14 1.00e+00 1.00e+00 4.06e+02 ... (remaining 68275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 28708 24.82 - 49.63: 613 49.63 - 74.45: 52 74.45 - 99.26: 19 99.26 - 124.08: 4 Dihedral angle restraints: 29396 sinusoidal: 10600 harmonic: 18796 Sorted by residual: dihedral pdb=" O1B ADP E2001 " pdb=" O3A ADP E2001 " pdb=" PB ADP E2001 " pdb=" PA ADP E2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.08 -124.08 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.06 -124.06 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O1B ADP H2001 " pdb=" O3A ADP H2001 " pdb=" PB ADP H2001 " pdb=" PA ADP H2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.03 -124.03 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 29393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5432 0.040 - 0.081: 2204 0.081 - 0.121: 607 0.121 - 0.162: 102 0.162 - 0.202: 11 Chirality restraints: 8356 Sorted by residual: chirality pdb=" CB THR E1081 " pdb=" CA THR E1081 " pdb=" OG1 THR E1081 " pdb=" CG2 THR E1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR F1081 " pdb=" CA THR F1081 " pdb=" OG1 THR F1081 " pdb=" CG2 THR F1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR H1081 " pdb=" CA THR H1081 " pdb=" OG1 THR H1081 " pdb=" CG2 THR H1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 8353 not shown) Planarity restraints: 8388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 577 " -0.026 2.00e-02 2.50e+03 1.90e-02 6.30e+00 pdb=" CG PHE H 577 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE H 577 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 577 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 577 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 577 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 577 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 577 " 0.026 2.00e-02 2.50e+03 1.89e-02 6.22e+00 pdb=" CG PHE F 577 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 577 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 577 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 577 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 577 " 0.026 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE G 577 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 577 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 577 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 577 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 577 " 0.009 2.00e-02 2.50e+03 ... (remaining 8385 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.36: 199 2.36 - 3.05: 35669 3.05 - 3.75: 90499 3.75 - 4.44: 136701 4.44 - 5.14: 218563 Nonbonded interactions: 481631 Sorted by model distance: nonbonded pdb=" ND1 HIS H 888 " pdb=" OD1 ASP H1512 " model vdw 1.661 2.520 nonbonded pdb=" ND1 HIS F 888 " pdb=" OD1 ASP F1512 " model vdw 1.661 2.520 nonbonded pdb=" ND1 HIS G 888 " pdb=" OD1 ASP G1512 " model vdw 1.662 2.520 nonbonded pdb=" ND1 HIS E 888 " pdb=" OD1 ASP E1512 " model vdw 1.662 2.520 nonbonded pdb=" O1B ADP G2001 " pdb="MG MG G2003 " model vdw 1.893 2.170 ... (remaining 481626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 359 or resid 501)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 K 3 8.98 5 P 32 5.49 5 Mg 8 5.21 5 S 272 5.16 5 C 31812 2.51 5 N 8272 2.21 5 O 8656 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: 1.830 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: 10.620 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.400 Process input model: 127.070 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 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 : 0.006 0.078 50056 Z= 0.403 Angle : 0.920 20.887 68280 Z= 0.590 Chirality : 0.046 0.202 8356 Planarity : 0.004 0.056 8388 Dihedral : 10.429 124.080 17156 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.09), residues: 6384 helix: -1.31 (0.07), residues: 3864 sheet: -2.49 (0.20), residues: 592 loop : -3.11 (0.12), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1649 time to evaluate : 6.016 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: 16 outliers final: 7 residues processed: 1660 average time/residue: 0.5687 time to fit residues: 1580.2109 Evaluate side-chains 1106 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1099 time to evaluate : 5.244 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4103 time to fit residues: 12.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 4.9990 chunk 488 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 329 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 504 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 375 optimal weight: 0.7980 chunk 584 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 186 HIS A 193 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 335 ASN C 46 HIS C 186 HIS C 277 HIS C 335 ASN B 186 HIS B 193 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS B 335 ASN D 41 ASN D 57 GLN D 186 HIS D 193 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN E 36 HIS E 126 ASN E 188 ASN E 374 GLN E 416 GLN E 419 ASN E 427 GLN E 498 GLN E 714 GLN E 821 GLN E 845 GLN E1019 GLN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1223 GLN E1233 ASN E1272 HIS E1483 GLN H 36 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN H 416 GLN H 419 ASN H 437 ASN H 707 GLN H 714 GLN H 821 GLN H1122 ASN H1233 ASN H1272 HIS H1292 ASN ** H1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1363 HIS G 32 ASN G 36 HIS G 126 ASN G 188 ASN G 374 GLN G 416 GLN G 427 GLN G 714 GLN G 821 GLN ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 GLN G1272 HIS F 36 HIS F 416 GLN F 419 ASN F 426 ASN F 437 ASN F 498 GLN F 821 GLN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN F1272 HIS F1295 ASN F1347 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 50056 Z= 0.227 Angle : 0.694 11.223 68280 Z= 0.349 Chirality : 0.044 0.200 8356 Planarity : 0.005 0.062 8388 Dihedral : 6.665 116.777 6900 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.10), residues: 6384 helix: 0.20 (0.08), residues: 3896 sheet: -1.81 (0.21), residues: 552 loop : -2.56 (0.12), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1180 time to evaluate : 5.127 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 outliers start: 171 outliers final: 96 residues processed: 1270 average time/residue: 0.5719 time to fit residues: 1232.0815 Evaluate side-chains 1140 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1044 time to evaluate : 5.044 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.4517 time to fit residues: 89.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 0.2980 chunk 181 optimal weight: 7.9990 chunk 486 optimal weight: 0.8980 chunk 398 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 585 optimal weight: 0.8980 chunk 632 optimal weight: 0.9980 chunk 521 optimal weight: 1.9990 chunk 580 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 470 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 46 HIS B 57 GLN D 46 HIS D 57 GLN E 103 HIS E 707 GLN E 845 GLN E1097 HIS ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1347 GLN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1234 ASN ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 103 HIS G 419 ASN ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 HIS G1019 GLN ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1295 ASN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN F 547 ASN ** F 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1019 GLN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1234 ASN ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1347 GLN F1401 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 50056 Z= 0.229 Angle : 0.669 13.491 68280 Z= 0.332 Chirality : 0.044 0.280 8356 Planarity : 0.005 0.062 8388 Dihedral : 6.385 111.904 6900 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 6384 helix: 0.66 (0.08), residues: 3924 sheet: -1.29 (0.21), residues: 532 loop : -2.38 (0.12), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1184 time to evaluate : 5.603 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 outliers start: 157 outliers final: 61 residues processed: 1275 average time/residue: 0.5679 time to fit residues: 1241.4585 Evaluate side-chains 1108 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1047 time to evaluate : 5.650 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4427 time to fit residues: 59.1897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 1.9990 chunk 440 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 393 optimal weight: 0.5980 chunk 587 optimal weight: 0.1980 chunk 622 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 557 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 57 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN D 57 GLN E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 426 ASN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 895 HIS ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1295 ASN G 103 HIS ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 GLN G1233 ASN F 188 ASN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 ASN F 845 GLN F 891 GLN F1097 HIS ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 50056 Z= 0.246 Angle : 0.685 12.711 68280 Z= 0.339 Chirality : 0.044 0.377 8356 Planarity : 0.005 0.081 8388 Dihedral : 6.302 108.375 6900 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 6384 helix: 0.93 (0.08), residues: 3888 sheet: -0.95 (0.21), residues: 552 loop : -2.05 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1170 time to evaluate : 5.454 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: 165 outliers final: 93 residues processed: 1257 average time/residue: 0.5666 time to fit residues: 1215.6205 Evaluate side-chains 1146 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1053 time to evaluate : 5.566 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.4366 time to fit residues: 84.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 463 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 531 optimal weight: 4.9990 chunk 430 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 317 optimal weight: 0.4980 chunk 558 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN B 299 GLN D 57 GLN E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 427 GLN E 437 ASN ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS H 289 GLN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN H 416 GLN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 821 GLN H 833 GLN H1019 GLN H1233 ASN ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1485 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 821 GLN F1122 ASN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 50056 Z= 0.404 Angle : 0.769 14.194 68280 Z= 0.385 Chirality : 0.048 0.523 8356 Planarity : 0.006 0.069 8388 Dihedral : 6.617 112.392 6900 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 6384 helix: 0.69 (0.08), residues: 3900 sheet: -1.03 (0.21), residues: 572 loop : -2.05 (0.13), residues: 1912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1415 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1224 time to evaluate : 5.202 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 outliers start: 191 outliers final: 98 residues processed: 1340 average time/residue: 0.5668 time to fit residues: 1292.8656 Evaluate side-chains 1202 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1104 time to evaluate : 5.953 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.4239 time to fit residues: 86.5114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 0.6980 chunk 560 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 365 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 623 optimal weight: 2.9990 chunk 517 optimal weight: 0.8980 chunk 288 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 206 optimal weight: 0.2980 chunk 327 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN B 57 GLN D 57 GLN E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 437 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS H 289 GLN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 ASN H 474 GLN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1122 ASN ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 GLN G 474 GLN ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1097 HIS ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1122 ASN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1347 GLN F1401 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 50056 Z= 0.203 Angle : 0.682 11.286 68280 Z= 0.334 Chirality : 0.044 0.361 8356 Planarity : 0.005 0.067 8388 Dihedral : 6.321 109.181 6900 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 6384 helix: 1.06 (0.08), residues: 3888 sheet: -0.92 (0.21), residues: 552 loop : -1.92 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1149 time to evaluate : 5.414 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 outliers start: 118 outliers final: 60 residues processed: 1210 average time/residue: 0.5617 time to fit residues: 1160.8937 Evaluate side-chains 1128 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1068 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4381 time to fit residues: 56.8413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 chunk 455 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 524 optimal weight: 3.9990 chunk 347 optimal weight: 0.7980 chunk 620 optimal weight: 3.9990 chunk 388 optimal weight: 0.7980 chunk 378 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 437 ASN E 498 GLN E 895 HIS H 103 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1122 ASN ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 GLN ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 821 GLN ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1295 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 50056 Z= 0.331 Angle : 0.734 13.095 68280 Z= 0.363 Chirality : 0.046 0.300 8356 Planarity : 0.005 0.066 8388 Dihedral : 6.352 110.547 6900 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 6384 helix: 0.88 (0.08), residues: 3924 sheet: -0.89 (0.21), residues: 552 loop : -2.00 (0.13), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1137 time to evaluate : 5.510 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: 135 outliers final: 90 residues processed: 1201 average time/residue: 0.5668 time to fit residues: 1162.7570 Evaluate side-chains 1172 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1082 time to evaluate : 5.616 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.4370 time to fit residues: 81.8693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 394 optimal weight: 6.9990 chunk 422 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 487 optimal weight: 3.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E1122 ASN ** E1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 103 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1019 GLN ** H1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1347 GLN ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 427 GLN ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1347 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 50056 Z= 0.252 Angle : 0.706 12.245 68280 Z= 0.346 Chirality : 0.044 0.282 8356 Planarity : 0.005 0.066 8388 Dihedral : 6.264 108.601 6900 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 6384 helix: 1.01 (0.08), residues: 3916 sheet: -0.99 (0.22), residues: 496 loop : -1.97 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1123 time to evaluate : 5.938 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: 96 outliers final: 45 residues processed: 1173 average time/residue: 0.5689 time to fit residues: 1141.0274 Evaluate side-chains 1126 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1081 time to evaluate : 5.434 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5077 time to fit residues: 49.4427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 8.9990 chunk 594 optimal weight: 5.9990 chunk 542 optimal weight: 1.9990 chunk 578 optimal weight: 2.9990 chunk 348 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 454 optimal weight: 0.0770 chunk 177 optimal weight: 2.9990 chunk 522 optimal weight: 0.9990 chunk 547 optimal weight: 0.9980 chunk 576 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E1122 ASN E1244 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1426 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 50056 Z= 0.251 Angle : 0.715 13.663 68280 Z= 0.351 Chirality : 0.044 0.270 8356 Planarity : 0.005 0.065 8388 Dihedral : 6.222 108.758 6900 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.10), residues: 6384 helix: 1.03 (0.08), residues: 3920 sheet: -0.94 (0.22), residues: 496 loop : -1.97 (0.13), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1122 time to evaluate : 5.932 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 outliers start: 59 outliers final: 31 residues processed: 1149 average time/residue: 0.5911 time to fit residues: 1161.6262 Evaluate side-chains 1113 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1082 time to evaluate : 5.701 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4530 time to fit residues: 35.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 0.0470 chunk 611 optimal weight: 0.8980 chunk 373 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 chunk 425 optimal weight: 0.8980 chunk 641 optimal weight: 0.0470 chunk 590 optimal weight: 0.7980 chunk 510 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 394 optimal weight: 7.9990 chunk 313 optimal weight: 0.4980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN B 299 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1426 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 GLN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 819 GLN H1019 GLN H1233 ASN H1295 ASN G 289 GLN ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 50056 Z= 0.196 Angle : 0.703 12.970 68280 Z= 0.340 Chirality : 0.043 0.409 8356 Planarity : 0.005 0.065 8388 Dihedral : 6.100 107.542 6900 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6384 helix: 1.22 (0.08), residues: 3908 sheet: -0.97 (0.23), residues: 444 loop : -1.85 (0.13), residues: 2032 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1100 time to evaluate : 5.626 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 outliers start: 35 outliers final: 18 residues processed: 1113 average time/residue: 0.5743 time to fit residues: 1091.3901 Evaluate side-chains 1069 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1051 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4765 time to fit residues: 23.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 1.9990 chunk 544 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 471 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 511 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 525 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN B 186 HIS ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 103 HIS ** E1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1347 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1019 GLN H1295 ASN H1401 HIS ** G 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 HIS ** G1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 846 HIS ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.204002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.200747 restraints weight = 50073.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.200881 restraints weight = 55710.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.201076 restraints weight = 43995.169| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 50056 Z= 0.226 Angle : 0.710 14.387 68280 Z= 0.345 Chirality : 0.044 0.347 8356 Planarity : 0.005 0.064 8388 Dihedral : 6.067 107.696 6900 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 6384 helix: 1.23 (0.08), residues: 3900 sheet: -0.69 (0.22), residues: 500 loop : -1.83 (0.13), residues: 1984 =============================================================================== Job complete usr+sys time: 16379.03 seconds wall clock time: 290 minutes 45.07 seconds (17445.07 seconds total)