Starting phenix.real_space_refine on Sat Feb 7 05:14:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.map" model { file = "/net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qk2_53217/02_2026/9qk2_53217.cif" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 141 5.16 5 C 18918 2.51 5 N 5164 2.21 5 O 5693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29917 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5012 Classifications: {'peptide': 651} Link IDs: {'PCIS': 3, 'PTRANS': 42, 'TRANS': 605} Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2241 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain: "E" Number of atoms: 4021 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 507, 4013 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 18, 'TRANS': 488} Conformer: "B" Number of residues, atoms: 507, 4013 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 18, 'TRANS': 488} bond proxies already assigned to first conformer: 4084 Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4788 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 26, 'TRANS': 591} Chain breaks: 5 Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 1 Chain: "F" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4976 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 37, 'TRANS': 600} Chain breaks: 1 Chain: "G" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7858 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 939} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.96, per 1000 atoms: 0.20 Number of scatterers: 29917 At special positions: 0 Unit cell: (142.48, 178.88, 206.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 Mg 1 11.99 O 5693 8.00 N 5164 7.00 C 18918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C1471 " - pdb=" SG CYS C1535 " distance=2.03 Simple disulfide: pdb=" SG CYS C1566 " - pdb=" SG CYS B1394 " distance=2.03 Simple disulfide: pdb=" SG CYS C1583 " - pdb=" SG CYS C1588 " distance=2.03 Simple disulfide: pdb=" SG CYS C1590 " - pdb=" SG CYS B 876 " distance=2.03 Simple disulfide: pdb=" SG CYS C1595 " - pdb=" SG CYS C1673 " distance=2.03 Simple disulfide: pdb=" SG CYS C1618 " - pdb=" SG CYS C1742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1718 " - pdb=" SG CYS C1727 " distance=2.03 Simple disulfide: pdb=" SG CYS E 463 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 492 " - pdb=" SG CYS E 508 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 600 " distance=2.02 Simple disulfide: pdb=" SG CYS E 638 " - pdb=" SG CYS E 665 " distance=2.03 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 559 " - pdb=" SG CYS G 816 " distance=2.03 Simple disulfide: pdb=" SG CYS F 627 " - pdb=" SG CYS F 662 " distance=2.03 Simple disulfide: pdb=" SG CYS G 693 " - pdb=" SG CYS G 720 " distance=2.03 Simple disulfide: pdb=" SG CYS G 694 " - pdb=" SG CYS G 727 " distance=2.03 Simple disulfide: pdb=" SG CYS G 707 " - pdb=" SG CYS G 728 " distance=2.03 Simple disulfide: pdb=" SG CYS G 873 " - pdb=" SG CYS G1513 " distance=2.03 Simple disulfide: pdb=" SG CYS G1101 " - pdb=" SG CYS G1158 " distance=2.03 Simple disulfide: pdb=" SG CYS G1358 " - pdb=" SG CYS G1489 " distance=2.03 Simple disulfide: pdb=" SG CYS G1389 " - pdb=" SG CYS G1458 " distance=2.03 Simple disulfide: pdb=" SG CYS G1506 " - pdb=" SG CYS G1511 " distance=2.03 Simple disulfide: pdb=" SG CYS G1518 " - pdb=" SG CYS G1590 " distance=2.03 Simple disulfide: pdb=" SG CYS G1537 " - pdb=" SG CYS G1661 " distance=2.03 Simple disulfide: pdb=" SG CYS G1637 " - pdb=" SG CYS G1646 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A1801 " - " ASN A 226 " " NAG B1801 " - " ASN B 862 " " NAG E 802 " - " ASN E 290 " " NAG E 803 " - " ASN E 467 " " NAG E 804 " - " ASN E 471 " " NAG E 805 " - " ASN E 621 " " NAG F1701 " - " ASN F 85 " " NAG G1701 " - " ASN G 939 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 61 sheets defined 23.0% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.874A pdb=" N LEU A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 315 through 326 Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.603A pdb=" N LEU A 333 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.827A pdb=" N ALA A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 642 through 651 Processing helix chain 'C' and resid 1497 through 1506 removed outlier: 3.839A pdb=" N LEU C1501 " --> pdb=" O LEU C1497 " (cutoff:3.500A) Processing helix chain 'C' and resid 1613 through 1619 Processing helix chain 'C' and resid 1720 through 1740 removed outlier: 3.974A pdb=" N ALA C1725 " --> pdb=" O THR C1721 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA C1726 " --> pdb=" O ARG C1722 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 287 removed outlier: 3.580A pdb=" N SER E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 removed outlier: 4.096A pdb=" N ARG E 314 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 Processing helix chain 'E' and resid 328 through 332 removed outlier: 3.888A pdb=" N HIS E 331 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 384 through 396 removed outlier: 4.139A pdb=" N ALA E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 396 " --> pdb=" O ILE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 419 through 427 Processing helix chain 'E' and resid 441 through 452 removed outlier: 3.752A pdb=" N LEU E 445 " --> pdb=" O ASP E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 removed outlier: 3.608A pdb=" N THR E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 592 Processing helix chain 'E' and resid 599 through 608 removed outlier: 3.812A pdb=" N ASN E 605 " --> pdb=" O ARG E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 645 removed outlier: 3.933A pdb=" N THR E 636 " --> pdb=" O GLY E 632 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER E 637 " --> pdb=" O VAL E 633 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS E 638 " --> pdb=" O GLU E 634 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU E 640 " --> pdb=" O THR E 636 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 641 " --> pdb=" O SER E 637 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL E 642 " --> pdb=" O CYS E 638 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER E 643 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN E 644 " --> pdb=" O GLU E 640 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 645 " --> pdb=" O VAL E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 734 No H-bonds generated for 'chain 'E' and resid 732 through 734' Processing helix chain 'E' and resid 735 through 744 removed outlier: 3.892A pdb=" N GLN E 741 " --> pdb=" O PRO E 737 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS E 742 " --> pdb=" O TRP E 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 955 No H-bonds generated for 'chain 'B' and resid 953 through 955' Processing helix chain 'B' and resid 996 through 1002 removed outlier: 3.545A pdb=" N VAL B1000 " --> pdb=" O SER B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1032 Proline residue: B1020 - end of helix Processing helix chain 'B' and resid 1033 through 1037 Processing helix chain 'B' and resid 1038 through 1056 removed outlier: 3.977A pdb=" N LYS B1042 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B1043 " --> pdb=" O PRO B1039 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1059 No H-bonds generated for 'chain 'B' and resid 1057 through 1059' Processing helix chain 'B' and resid 1075 through 1089 Processing helix chain 'B' and resid 1096 through 1110 removed outlier: 3.763A pdb=" N LEU B1100 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B1102 " --> pdb=" O GLU B1098 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B1103 " --> pdb=" O LYS B1099 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B1110 " --> pdb=" O TRP B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1126 through 1133 removed outlier: 4.048A pdb=" N GLY B1130 " --> pdb=" O SER B1127 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY B1131 " --> pdb=" O MET B1128 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B1132 " --> pdb=" O GLN B1129 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B1133 " --> pdb=" O GLY B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1155 removed outlier: 3.771A pdb=" N ALA B1154 " --> pdb=" O HIS B1150 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B1155 " --> pdb=" O HIS B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1186 Processing helix chain 'B' and resid 1189 through 1203 Processing helix chain 'B' and resid 1206 through 1220 removed outlier: 3.795A pdb=" N MET B1220 " --> pdb=" O ASN B1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1275 Processing helix chain 'B' and resid 1281 through 1294 removed outlier: 3.915A pdb=" N ALA B1285 " --> pdb=" O MET B1281 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1320 Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 303 through 311 removed outlier: 3.762A pdb=" N VAL F 311 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 320 removed outlier: 3.556A pdb=" N ASP F 318 " --> pdb=" O ARG F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 436 Processing helix chain 'F' and resid 483 through 487 Processing helix chain 'F' and resid 522 through 526 Processing helix chain 'F' and resid 600 through 606 removed outlier: 3.738A pdb=" N VAL F 604 " --> pdb=" O LYS F 600 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU F 605 " --> pdb=" O GLY F 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 609 No H-bonds generated for 'chain 'F' and resid 607 through 609' Processing helix chain 'F' and resid 612 through 622 Processing helix chain 'F' and resid 634 through 642 Processing helix chain 'G' and resid 675 through 684 removed outlier: 3.633A pdb=" N ARG G 679 " --> pdb=" O LEU G 675 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 699 removed outlier: 4.477A pdb=" N LYS G 692 " --> pdb=" O LYS G 688 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS G 693 " --> pdb=" O GLU G 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY G 697 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET G 698 " --> pdb=" O CYS G 694 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG G 699 " --> pdb=" O GLU G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 711 Processing helix chain 'G' and resid 712 through 714 No H-bonds generated for 'chain 'G' and resid 712 through 714' Processing helix chain 'G' and resid 717 through 742 Processing helix chain 'G' and resid 987 through 996 removed outlier: 3.771A pdb=" N ASP G 996 " --> pdb=" O GLU G 992 " (cutoff:3.500A) Processing helix chain 'G' and resid 999 through 1004 removed outlier: 4.179A pdb=" N ILE G1004 " --> pdb=" O LYS G1001 " (cutoff:3.500A) Processing helix chain 'G' and resid 1012 through 1016 removed outlier: 3.779A pdb=" N ILE G1016 " --> pdb=" O GLN G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1018 through 1032 Processing helix chain 'G' and resid 1033 through 1038 Processing helix chain 'G' and resid 1040 through 1057 removed outlier: 4.367A pdb=" N GLY G1044 " --> pdb=" O GLU G1040 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1060 No H-bonds generated for 'chain 'G' and resid 1058 through 1060' Processing helix chain 'G' and resid 1075 through 1088 removed outlier: 3.528A pdb=" N LEU G1088 " --> pdb=" O LYS G1084 " (cutoff:3.500A) Processing helix chain 'G' and resid 1096 through 1111 removed outlier: 3.648A pdb=" N LEU G1100 " --> pdb=" O ASP G1096 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS G1111 " --> pdb=" O LEU G1107 " (cutoff:3.500A) Processing helix chain 'G' and resid 1139 through 1154 removed outlier: 3.696A pdb=" N GLU G1153 " --> pdb=" O ILE G1149 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G1154 " --> pdb=" O SER G1150 " (cutoff:3.500A) Processing helix chain 'G' and resid 1164 through 1179 Processing helix chain 'G' and resid 1180 through 1183 removed outlier: 3.781A pdb=" N LEU G1183 " --> pdb=" O TYR G1180 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1180 through 1183' Processing helix chain 'G' and resid 1185 through 1200 Processing helix chain 'G' and resid 1204 through 1214 removed outlier: 3.793A pdb=" N ASN G1208 " --> pdb=" O GLY G1204 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA G1214 " --> pdb=" O PHE G1210 " (cutoff:3.500A) Processing helix chain 'G' and resid 1226 through 1243 Processing helix chain 'G' and resid 1248 through 1257 removed outlier: 4.138A pdb=" N VAL G1252 " --> pdb=" O PHE G1248 " (cutoff:3.500A) Processing helix chain 'G' and resid 1268 through 1285 removed outlier: 3.698A pdb=" N THR G1272 " --> pdb=" O SER G1268 " (cutoff:3.500A) Processing helix chain 'G' and resid 1414 through 1424 Processing helix chain 'G' and resid 1509 through 1516 removed outlier: 3.710A pdb=" N ALA G1514 " --> pdb=" O LEU G1510 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU G1515 " --> pdb=" O CYS G1511 " (cutoff:3.500A) Processing helix chain 'G' and resid 1528 through 1537 removed outlier: 4.346A pdb=" N CYS G1537 " --> pdb=" O LEU G1533 " (cutoff:3.500A) Processing helix chain 'G' and resid 1590 through 1595 Processing helix chain 'G' and resid 1634 through 1638 removed outlier: 4.194A pdb=" N GLN G1638 " --> pdb=" O ASP G1635 " (cutoff:3.500A) Processing helix chain 'G' and resid 1639 through 1659 removed outlier: 4.184A pdb=" N LYS G1644 " --> pdb=" O GLU G1640 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN G1645 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN G1647 " --> pdb=" O GLN G1643 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP G1648 " --> pdb=" O LYS G1644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.510A pdb=" N GLN A 42 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.440A pdb=" N VAL A 31 " --> pdb=" O SER A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.610A pdb=" N GLN A 128 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA5, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.640A pdb=" N LYS A 214 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 218 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 241 through 247 removed outlier: 4.098A pdb=" N MET A 262 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 253 removed outlier: 5.556A pdb=" N ILE A 252 " --> pdb=" O VAL A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 295 removed outlier: 3.660A pdb=" N TYR A 281 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 340 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 367 through 368 Processing sheet with id=AB2, first strand: chain 'A' and resid 384 through 389 Processing sheet with id=AB3, first strand: chain 'A' and resid 417 through 424 Processing sheet with id=AB4, first strand: chain 'A' and resid 472 through 476 Processing sheet with id=AB5, first strand: chain 'A' and resid 514 through 522 removed outlier: 5.385A pdb=" N ILE A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 511 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 507 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 514 through 522 removed outlier: 5.385A pdb=" N ILE A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 511 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 517 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 507 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS A 504 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 548 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 586 through 591 Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 782 Processing sheet with id=AB9, first strand: chain 'B' and resid 781 through 782 removed outlier: 3.909A pdb=" N GLY A 602 " --> pdb=" O HIS B 809 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1494 through 1496 Processing sheet with id=AC2, first strand: chain 'C' and resid 1535 through 1536 Processing sheet with id=AC3, first strand: chain 'C' and resid 1514 through 1518 removed outlier: 3.897A pdb=" N HIS C1514 " --> pdb=" O TYR C1525 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER C1553 " --> pdb=" O THR C1489 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1692 through 1693 removed outlier: 4.441A pdb=" N THR C1692 " --> pdb=" O GLN C1700 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN C1666 " --> pdb=" O PRO C1699 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN C1663 " --> pdb=" O ILE C1647 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU C1642 " --> pdb=" O SER C1636 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER C1636 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C1644 " --> pdb=" O GLU C1634 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLU C1634 " --> pdb=" O GLU C1644 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N LYS C1646 " --> pdb=" O LEU C1632 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU C1632 " --> pdb=" O LYS C1646 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR C1648 " --> pdb=" O LYS C1630 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LYS C1630 " --> pdb=" O THR C1648 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C1650 " --> pdb=" O GLN C1628 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN C1628 " --> pdb=" O VAL C1650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 245 through 246 removed outlier: 7.136A pdb=" N ILE E 245 " --> pdb=" O ASP E 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 302 through 306 removed outlier: 6.510A pdb=" N ILE E 295 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N HIS E 252 " --> pdb=" O ARG E 368 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ALA E 370 " --> pdb=" O HIS E 252 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN E 254 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE E 372 " --> pdb=" O ASN E 254 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR E 256 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU E 374 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU E 258 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ASP E 407 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS E 369 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N TYR E 409 " --> pdb=" O HIS E 369 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE E 371 " --> pdb=" O TYR E 409 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE E 411 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 373 " --> pdb=" O ILE E 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 481 through 485 removed outlier: 3.707A pdb=" N VAL E 482 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS E 492 " --> pdb=" O ILE E 484 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 564 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA E 538 " --> pdb=" O LEU E 564 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS E 566 " --> pdb=" O GLU E 536 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 612 through 618 Processing sheet with id=AC9, first strand: chain 'E' and resid 663 through 664 removed outlier: 3.546A pdb=" N HIS E 729 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE E 730 " --> pdb=" O VAL E 697 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL E 697 " --> pdb=" O ILE E 730 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE E 691 " --> pdb=" O ARG E 687 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG E 687 " --> pdb=" O PHE E 691 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN E 693 " --> pdb=" O LEU E 685 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU E 685 " --> pdb=" O GLN E 693 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E 695 " --> pdb=" O VAL E 683 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 774 through 775 removed outlier: 3.665A pdb=" N VAL B 843 " --> pdb=" O GLN B 932 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 934 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 774 through 775 Processing sheet with id=AD3, first strand: chain 'B' and resid 813 through 814 removed outlier: 3.597A pdb=" N SER B 814 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 833 through 836 Processing sheet with id=AD5, first strand: chain 'B' and resid 849 through 851 removed outlier: 3.852A pdb=" N VAL B 902 " --> pdb=" O CYS B 876 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 938 through 948 removed outlier: 3.720A pdb=" N GLU B1356 " --> pdb=" O VAL B 980 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 957 through 960 removed outlier: 3.823A pdb=" N ILE B1366 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN B1328 " --> pdb=" O GLY B1371 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B1333 " --> pdb=" O LYS B1340 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B1340 " --> pdb=" O SER B1333 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.249A pdb=" N TRP D 32 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D 88 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL D 116 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 83 through 89 removed outlier: 8.474A pdb=" N THR F 41 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 30 " --> pdb=" O THR F 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.965A pdb=" N SER F 70 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP F 61 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL F 68 " --> pdb=" O ASP F 61 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 129 through 134 Processing sheet with id=AE4, first strand: chain 'F' and resid 174 through 181 removed outlier: 3.677A pdb=" N LYS F 176 " --> pdb=" O ILE F 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 232 through 238 removed outlier: 3.630A pdb=" N GLU F 237 " --> pdb=" O THR F 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 243 through 244 removed outlier: 5.587A pdb=" N TYR F 243 " --> pdb=" O VAL F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 289 through 293 removed outlier: 3.562A pdb=" N SER F 323 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL F 326 " --> pdb=" O SER F 344 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER F 344 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA F 328 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU F 342 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 330 " --> pdb=" O GLN F 340 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN F 340 " --> pdb=" O VAL F 330 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU F 332 " --> pdb=" O MET F 338 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET F 338 " --> pdb=" O LEU F 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 354 through 357 Processing sheet with id=AE9, first strand: chain 'F' and resid 363 through 364 Processing sheet with id=AF1, first strand: chain 'F' and resid 370 through 371 Processing sheet with id=AF2, first strand: chain 'F' and resid 455 through 459 removed outlier: 3.538A pdb=" N ARG F 478 " --> pdb=" O TYR F 455 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 499 through 503 removed outlier: 6.660A pdb=" N ILE F 494 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA F 503 " --> pdb=" O TYR F 492 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR F 492 " --> pdb=" O ALA F 503 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 499 through 503 removed outlier: 6.660A pdb=" N ILE F 494 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA F 503 " --> pdb=" O TYR F 492 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR F 492 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR F 489 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N THR F 536 " --> pdb=" O TYR F 489 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 563 through 567 Processing sheet with id=AF6, first strand: chain 'G' and resid 775 through 777 Processing sheet with id=AF7, first strand: chain 'G' and resid 775 through 777 Processing sheet with id=AF8, first strand: chain 'G' and resid 829 through 834 removed outlier: 3.559A pdb=" N SER G 892 " --> pdb=" O ASN G 853 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 838 through 840 removed outlier: 3.644A pdb=" N VAL G 932 " --> pdb=" O VAL G 839 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G 915 " --> pdb=" O ARG G 863 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS G 882 " --> pdb=" O LEU G 866 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 844 through 845 Processing sheet with id=AG2, first strand: chain 'G' and resid 936 through 943 removed outlier: 6.602A pdb=" N VAL G1344 " --> pdb=" O VAL G 942 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 936 through 943 removed outlier: 6.602A pdb=" N VAL G1344 " --> pdb=" O VAL G 942 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 958 through 962 removed outlier: 4.112A pdb=" N THR G1331 " --> pdb=" O GLN G1299 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN G1299 " --> pdb=" O THR G1331 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 1361 through 1369 removed outlier: 3.771A pdb=" N ASN G1382 " --> pdb=" O GLN G1465 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 1431 through 1433 removed outlier: 3.788A pdb=" N LYS G1431 " --> pdb=" O TYR G1447 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 1620 through 1621 removed outlier: 7.004A pdb=" N GLU G1560 " --> pdb=" O VAL G1552 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL G1552 " --> pdb=" O GLU G1560 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE G1562 " --> pdb=" O VAL G1550 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS G1546 " --> pdb=" O GLU G1566 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR G1568 " --> pdb=" O VAL G1544 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL G1544 " --> pdb=" O THR G1568 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS G1570 " --> pdb=" O ASP G1542 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP G1542 " --> pdb=" O LYS G1570 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR G1543 " --> pdb=" O GLY G1606 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N HIS G1601 " --> pdb=" O TRP G1631 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3215 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: 8.16 Time building geometry restraints manager: 3.01 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: 9916 1.34 - 1.46: 6631 1.46 - 1.58: 13756 1.58 - 1.70: 0 1.70 - 1.83: 220 Bond restraints: 30523 Sorted by residual: bond pdb=" CB GLU E 640 " pdb=" CG GLU E 640 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C GLU G1538 " pdb=" N PRO G1539 " ideal model delta sigma weight residual 1.333 1.352 -0.018 1.44e-02 4.82e+03 1.63e+00 bond pdb=" C1 NAG B1801 " pdb=" C2 NAG B1801 " ideal model delta sigma weight residual 1.532 1.558 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" CA ASP F 395 " pdb=" CB ASP F 395 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.57e+00 bond pdb=" CB GLU E 425 " pdb=" CG GLU E 425 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 ... (remaining 30518 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 40924 2.30 - 4.61: 384 4.61 - 6.91: 43 6.91 - 9.21: 5 9.21 - 11.52: 4 Bond angle restraints: 41360 Sorted by residual: angle pdb=" CA GLU E 640 " pdb=" CB GLU E 640 " pdb=" CG GLU E 640 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" C ALA E 709 " pdb=" N ASP E 710 " pdb=" CA ASP E 710 " ideal model delta sigma weight residual 122.45 128.91 -6.46 1.78e+00 3.16e-01 1.32e+01 angle pdb=" N GLY F 630 " pdb=" CA GLY F 630 " pdb=" C GLY F 630 " ideal model delta sigma weight residual 113.18 121.33 -8.15 2.37e+00 1.78e-01 1.18e+01 angle pdb=" CB MET B1411 " pdb=" CG MET B1411 " pdb=" SD MET B1411 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CB GLU E 640 " pdb=" CG GLU E 640 " pdb=" CD GLU E 640 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.70e+00 3.46e-01 1.10e+01 ... (remaining 41355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16241 17.98 - 35.96: 1825 35.96 - 53.94: 461 53.94 - 71.92: 123 71.92 - 89.90: 31 Dihedral angle restraints: 18681 sinusoidal: 7688 harmonic: 10993 Sorted by residual: dihedral pdb=" CB CYS F 627 " pdb=" SG CYS F 627 " pdb=" SG CYS F 662 " pdb=" CB CYS F 662 " ideal model delta sinusoidal sigma weight residual -86.00 -170.59 84.59 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS G 873 " pdb=" SG CYS G 873 " pdb=" SG CYS G1513 " pdb=" CB CYS G1513 " ideal model delta sinusoidal sigma weight residual -86.00 -2.87 -83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS C1718 " pdb=" SG CYS C1718 " pdb=" SG CYS C1727 " pdb=" CB CYS C1727 " ideal model delta sinusoidal sigma weight residual 93.00 159.89 -66.89 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 18678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3273 0.039 - 0.077: 939 0.077 - 0.116: 396 0.116 - 0.154: 59 0.154 - 0.193: 3 Chirality restraints: 4670 Sorted by residual: chirality pdb=" C2 NAG B1801 " pdb=" C1 NAG B1801 " pdb=" C3 NAG B1801 " pdb=" N2 NAG B1801 " both_signs ideal model delta sigma weight residual False -2.49 -2.30 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA GLU E 490 " pdb=" N GLU E 490 " pdb=" C GLU E 490 " pdb=" CB GLU E 490 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C1 NAG F1701 " pdb=" ND2 ASN F 85 " pdb=" C2 NAG F1701 " pdb=" O5 NAG F1701 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 4667 not shown) Planarity restraints: 5363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 395 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASP F 395 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP F 395 " -0.016 2.00e-02 2.50e+03 pdb=" N THR F 396 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 722 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO E 723 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 723 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 723 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 425 " -0.008 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" CD GLU E 425 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU E 425 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU E 425 " -0.011 2.00e-02 2.50e+03 ... (remaining 5360 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 534 2.68 - 3.23: 27087 3.23 - 3.79: 43260 3.79 - 4.34: 57930 4.34 - 4.90: 100073 Nonbonded interactions: 228884 Sorted by model distance: nonbonded pdb=" OE1 GLU F 45 " pdb=" OH TYR F 534 " model vdw 2.123 3.040 nonbonded pdb=" OG SER G1555 " pdb=" O PHE G1558 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 270 " pdb=" OE2 GLU A 346 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR E 337 " pdb="MG MG E 801 " model vdw 2.139 2.170 nonbonded pdb=" OG SER E 264 " pdb="MG MG E 801 " model vdw 2.151 2.170 ... (remaining 228879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.29 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 27.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.003 0.041 30560 Z= 0.128 Angle : 0.575 11.516 41442 Z= 0.289 Chirality : 0.043 0.193 4670 Planarity : 0.004 0.049 5355 Dihedral : 16.414 89.901 11500 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.06 % Allowed : 19.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3760 helix: 1.68 (0.20), residues: 716 sheet: 0.33 (0.15), residues: 1238 loop : -0.96 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.018 0.001 TYR F 385 PHE 0.022 0.001 PHE B1360 TRP 0.013 0.001 TRP B1077 HIS 0.012 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00296 (30523) covalent geometry : angle 0.56667 (41360) SS BOND : bond 0.00206 ( 29) SS BOND : angle 1.06137 ( 58) hydrogen bonds : bond 0.16660 ( 1140) hydrogen bonds : angle 6.94397 ( 3215) link_NAG-ASN : bond 0.00571 ( 8) link_NAG-ASN : angle 3.90142 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 332 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8398 (t) cc_final: 0.7993 (m) REVERT: A 307 ASN cc_start: 0.8309 (t0) cc_final: 0.7772 (t0) REVERT: E 392 ILE cc_start: 0.8465 (mm) cc_final: 0.7991 (mt) REVERT: E 429 LYS cc_start: 0.7665 (mppt) cc_final: 0.7252 (mmmt) REVERT: E 514 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.7787 (p0) REVERT: E 735 MET cc_start: 0.7798 (mmm) cc_final: 0.7392 (mtp) REVERT: B 764 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5955 (mp0) REVERT: B 1049 ILE cc_start: 0.5400 (OUTLIER) cc_final: 0.5013 (tp) REVERT: B 1281 MET cc_start: 0.3213 (tpp) cc_final: 0.2956 (tpt) REVERT: B 1317 ILE cc_start: 0.7880 (tt) cc_final: 0.7626 (tt) REVERT: B 1369 LYS cc_start: 0.7313 (ttpp) cc_final: 0.6898 (ptpp) REVERT: D 30 MET cc_start: 0.7751 (mpp) cc_final: 0.7424 (mpp) REVERT: D 97 ARG cc_start: 0.8221 (ptp-110) cc_final: 0.7858 (ptp90) REVERT: F 83 MET cc_start: 0.7810 (tpt) cc_final: 0.7298 (tpt) REVERT: F 258 ARG cc_start: 0.7719 (ptp-110) cc_final: 0.7241 (mtt-85) REVERT: F 280 GLN cc_start: 0.7196 (mp10) cc_final: 0.6733 (pt0) REVERT: G 973 ASP cc_start: 0.6106 (t0) cc_final: 0.5631 (t0) REVERT: G 1627 TRP cc_start: 0.6666 (t-100) cc_final: 0.6197 (t-100) outliers start: 35 outliers final: 24 residues processed: 355 average time/residue: 0.1943 time to fit residues: 111.0239 Evaluate side-chains 349 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain C residue 1666 ASN Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 1362 ASP Chi-restraints excluded: chain G residue 1397 ASP Chi-restraints excluded: chain G residue 1557 ASP Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1475 ASN C1706 ASN G 844 GLN G 856 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.171170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142914 restraints weight = 37875.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142824 restraints weight = 71185.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143705 restraints weight = 65991.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143472 restraints weight = 45425.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144052 restraints weight = 40488.580| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30560 Z= 0.110 Angle : 0.534 9.834 41442 Z= 0.273 Chirality : 0.043 0.200 4670 Planarity : 0.004 0.042 5355 Dihedral : 5.268 59.572 4320 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.34 % Allowed : 18.62 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3760 helix: 1.58 (0.19), residues: 748 sheet: 0.35 (0.15), residues: 1221 loop : -1.01 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 748 TYR 0.013 0.001 TYR F 385 PHE 0.020 0.001 PHE G1438 TRP 0.013 0.001 TRP E 699 HIS 0.006 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00249 (30523) covalent geometry : angle 0.52558 (41360) SS BOND : bond 0.00230 ( 29) SS BOND : angle 0.97462 ( 58) hydrogen bonds : bond 0.03429 ( 1140) hydrogen bonds : angle 5.21625 ( 3215) link_NAG-ASN : bond 0.00557 ( 8) link_NAG-ASN : angle 3.80952 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 355 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 120 SER cc_start: 0.8374 (t) cc_final: 0.7906 (m) REVERT: A 307 ASN cc_start: 0.8229 (t0) cc_final: 0.7721 (t0) REVERT: E 392 ILE cc_start: 0.8438 (mm) cc_final: 0.7965 (mt) REVERT: E 429 LYS cc_start: 0.7683 (mppt) cc_final: 0.7269 (mmmt) REVERT: E 631 MET cc_start: 0.5418 (mmm) cc_final: 0.5166 (mmm) REVERT: B 764 GLU cc_start: 0.6556 (mm-30) cc_final: 0.5871 (mp0) REVERT: B 790 ASP cc_start: 0.8179 (t0) cc_final: 0.7851 (t0) REVERT: B 1049 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5275 (tp) REVERT: B 1317 ILE cc_start: 0.8022 (tt) cc_final: 0.7747 (tt) REVERT: B 1369 LYS cc_start: 0.7359 (ttpp) cc_final: 0.7061 (ptpp) REVERT: F 186 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8539 (tt) REVERT: F 254 THR cc_start: 0.8882 (m) cc_final: 0.8522 (p) REVERT: F 280 GLN cc_start: 0.7106 (mp10) cc_final: 0.6747 (pt0) REVERT: F 501 LEU cc_start: 0.8840 (tp) cc_final: 0.8620 (tp) REVERT: G 881 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5760 (ptt90) REVERT: G 973 ASP cc_start: 0.6286 (t0) cc_final: 0.5720 (t0) REVERT: G 1627 TRP cc_start: 0.6650 (t-100) cc_final: 0.6248 (t-100) outliers start: 77 outliers final: 45 residues processed: 408 average time/residue: 0.1725 time to fit residues: 116.2070 Evaluate side-chains 377 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1511 TYR Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1362 ASP Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 23 optimal weight: 3.9990 chunk 339 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 350 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 252 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1475 ASN C1521 HIS C1628 GLN E 380 ASN E 515 HIS D 13 GLN F 398 GLN F 442 GLN G 760 ASN G1014 ASN G1061 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.162475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.133144 restraints weight = 48266.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132886 restraints weight = 121475.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133794 restraints weight = 52294.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133478 restraints weight = 46779.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133738 restraints weight = 43321.957| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 30560 Z= 0.323 Angle : 0.730 10.772 41442 Z= 0.372 Chirality : 0.050 0.243 4670 Planarity : 0.005 0.049 5355 Dihedral : 5.995 59.351 4301 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.69 % Allowed : 18.50 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3760 helix: 0.82 (0.19), residues: 751 sheet: -0.01 (0.15), residues: 1243 loop : -1.39 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 601 TYR 0.037 0.002 TYR F 446 PHE 0.031 0.003 PHE G1438 TRP 0.017 0.002 TRP E 699 HIS 0.011 0.002 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00816 (30523) covalent geometry : angle 0.72221 (41360) SS BOND : bond 0.00555 ( 29) SS BOND : angle 1.47798 ( 58) hydrogen bonds : bond 0.04678 ( 1140) hydrogen bonds : angle 5.58017 ( 3215) link_NAG-ASN : bond 0.00646 ( 8) link_NAG-ASN : angle 4.13740 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 325 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7772 (p0) cc_final: 0.7491 (p0) REVERT: A 104 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.3848 (ttp-170) REVERT: A 120 SER cc_start: 0.8429 (t) cc_final: 0.8027 (m) REVERT: A 137 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7340 (mtt-85) REVERT: A 307 ASN cc_start: 0.8270 (t0) cc_final: 0.7696 (t0) REVERT: A 365 SER cc_start: 0.9025 (t) cc_final: 0.8805 (p) REVERT: C 1686 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7205 (ttp) REVERT: E 309 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6174 (mt) REVERT: E 392 ILE cc_start: 0.8549 (mm) cc_final: 0.8230 (mt) REVERT: E 429 LYS cc_start: 0.7704 (mppt) cc_final: 0.7254 (mmmt) REVERT: E 631 MET cc_start: 0.6091 (mmm) cc_final: 0.5761 (mmm) REVERT: E 721 LYS cc_start: 0.7252 (tptm) cc_final: 0.6294 (mmtt) REVERT: B 764 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7198 (mm-30) REVERT: B 956 ARG cc_start: 0.6950 (mmm160) cc_final: 0.6719 (mmm160) REVERT: B 1369 LYS cc_start: 0.7623 (ttpp) cc_final: 0.7407 (ptpt) REVERT: F 81 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6668 (m-40) REVERT: F 186 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8580 (tt) REVERT: F 343 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7203 (tpt90) REVERT: F 501 LEU cc_start: 0.8903 (tp) cc_final: 0.8679 (tp) REVERT: G 851 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8060 (mt) REVERT: G 973 ASP cc_start: 0.6367 (t0) cc_final: 0.5810 (t0) outliers start: 154 outliers final: 111 residues processed: 445 average time/residue: 0.1652 time to fit residues: 121.2541 Evaluate side-chains 431 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 314 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1475 ASN Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1511 TYR Chi-restraints excluded: chain C residue 1556 LEU Chi-restraints excluded: chain C residue 1568 VAL Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1686 MET Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 496 LEU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1273 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1342 HIS Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 303 SER Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 451 ASN Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 570 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1213 THR Chi-restraints excluded: chain G residue 1253 VAL Chi-restraints excluded: chain G residue 1362 ASP Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1626 THR Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 252 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 277 optimal weight: 0.4980 chunk 347 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 chunk 315 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 397 ASN E 515 HIS B1176 ASN F 442 GLN G1061 GLN G1242 GLN G1556 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.147330 restraints weight = 42487.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139962 restraints weight = 95002.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136769 restraints weight = 52406.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.136271 restraints weight = 46755.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.136895 restraints weight = 36569.531| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30560 Z= 0.122 Angle : 0.551 10.262 41442 Z= 0.282 Chirality : 0.043 0.216 4670 Planarity : 0.004 0.041 5355 Dihedral : 5.479 59.279 4301 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.44 % Allowed : 20.38 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3760 helix: 1.19 (0.19), residues: 750 sheet: 0.04 (0.15), residues: 1233 loop : -1.27 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 740 TYR 0.015 0.001 TYR B 946 PHE 0.024 0.001 PHE G1438 TRP 0.016 0.001 TRP E 699 HIS 0.007 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00288 (30523) covalent geometry : angle 0.54274 (41360) SS BOND : bond 0.00256 ( 29) SS BOND : angle 0.99968 ( 58) hydrogen bonds : bond 0.03329 ( 1140) hydrogen bonds : angle 5.10835 ( 3215) link_NAG-ASN : bond 0.00552 ( 8) link_NAG-ASN : angle 3.75562 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 334 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 120 SER cc_start: 0.8270 (t) cc_final: 0.7839 (m) REVERT: A 307 ASN cc_start: 0.8153 (t0) cc_final: 0.7657 (t0) REVERT: A 365 SER cc_start: 0.8982 (t) cc_final: 0.8741 (p) REVERT: C 1730 LEU cc_start: 0.8155 (mt) cc_final: 0.7769 (mt) REVERT: E 381 MET cc_start: 0.7415 (ptm) cc_final: 0.7040 (ppp) REVERT: E 392 ILE cc_start: 0.8525 (mm) cc_final: 0.8171 (mt) REVERT: E 429 LYS cc_start: 0.7729 (mppt) cc_final: 0.7235 (mmmt) REVERT: E 458 LEU cc_start: 0.8124 (tp) cc_final: 0.7871 (tp) REVERT: E 631 MET cc_start: 0.5939 (mmm) cc_final: 0.5680 (mmm) REVERT: E 721 LYS cc_start: 0.7283 (tptm) cc_final: 0.6169 (mmtt) REVERT: E 735 MET cc_start: 0.8000 (mmm) cc_final: 0.7692 (mtp) REVERT: B 764 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 1049 ILE cc_start: 0.5313 (OUTLIER) cc_final: 0.4788 (tp) REVERT: B 1369 LYS cc_start: 0.7378 (ttpp) cc_final: 0.7091 (ptpt) REVERT: D 30 MET cc_start: 0.7859 (mpp) cc_final: 0.7389 (mpp) REVERT: F 81 ASN cc_start: 0.7235 (m110) cc_final: 0.6600 (m-40) REVERT: F 186 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8710 (tt) REVERT: F 254 THR cc_start: 0.8908 (m) cc_final: 0.8566 (p) REVERT: F 280 GLN cc_start: 0.7087 (mp10) cc_final: 0.6852 (pt0) REVERT: F 343 ARG cc_start: 0.7669 (tpt90) cc_final: 0.7123 (tpt90) REVERT: F 501 LEU cc_start: 0.8886 (tp) cc_final: 0.8673 (tp) REVERT: G 851 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7966 (mt) REVERT: G 973 ASP cc_start: 0.6265 (t0) cc_final: 0.5668 (t0) REVERT: G 1470 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7040 (mm-30) REVERT: G 1627 TRP cc_start: 0.6763 (t-100) cc_final: 0.6211 (t-100) REVERT: G 1636 GLU cc_start: 0.5154 (OUTLIER) cc_final: 0.4950 (mp0) outliers start: 113 outliers final: 76 residues processed: 422 average time/residue: 0.1825 time to fit residues: 127.0399 Evaluate side-chains 393 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1475 ASN Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 605 ASN Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 705 PHE Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1362 ASP Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1636 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 200 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 307 optimal weight: 0.0030 chunk 239 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN C1475 ASN E 515 HIS F 442 GLN ** G1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.164338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.144031 restraints weight = 41637.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.143253 restraints weight = 102604.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141432 restraints weight = 61512.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140336 restraints weight = 52339.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140773 restraints weight = 44513.266| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30560 Z= 0.223 Angle : 0.630 10.656 41442 Z= 0.320 Chirality : 0.046 0.219 4670 Planarity : 0.004 0.043 5355 Dihedral : 5.655 57.460 4298 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.78 % Allowed : 19.68 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3760 helix: 0.97 (0.19), residues: 749 sheet: -0.03 (0.15), residues: 1234 loop : -1.39 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 601 TYR 0.026 0.002 TYR F 446 PHE 0.028 0.002 PHE G1438 TRP 0.013 0.001 TRP E 699 HIS 0.006 0.001 HIS B1342 Details of bonding type rmsd covalent geometry : bond 0.00557 (30523) covalent geometry : angle 0.62142 (41360) SS BOND : bond 0.00330 ( 29) SS BOND : angle 1.26818 ( 58) hydrogen bonds : bond 0.03843 ( 1140) hydrogen bonds : angle 5.23003 ( 3215) link_NAG-ASN : bond 0.00576 ( 8) link_NAG-ASN : angle 3.87214 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 321 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 120 SER cc_start: 0.8282 (t) cc_final: 0.7887 (m) REVERT: A 137 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7274 (mtt-85) REVERT: A 289 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: A 307 ASN cc_start: 0.8186 (t0) cc_final: 0.7684 (t0) REVERT: A 365 SER cc_start: 0.8992 (t) cc_final: 0.8757 (p) REVERT: C 1684 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7827 (tp) REVERT: E 392 ILE cc_start: 0.8399 (mm) cc_final: 0.8024 (mt) REVERT: E 429 LYS cc_start: 0.7654 (mppt) cc_final: 0.7289 (mmmt) REVERT: B 764 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 1049 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5397 (tp) REVERT: D 30 MET cc_start: 0.7940 (mpp) cc_final: 0.7490 (mpp) REVERT: F 81 ASN cc_start: 0.7143 (m110) cc_final: 0.6613 (m-40) REVERT: F 186 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8704 (tt) REVERT: F 343 ARG cc_start: 0.7752 (tpt90) cc_final: 0.7268 (tpt90) REVERT: F 501 LEU cc_start: 0.8914 (tp) cc_final: 0.8684 (tp) REVERT: G 851 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8009 (mt) REVERT: G 973 ASP cc_start: 0.6247 (t0) cc_final: 0.5747 (t0) REVERT: G 1470 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7010 (mm-30) outliers start: 157 outliers final: 116 residues processed: 446 average time/residue: 0.1856 time to fit residues: 137.4320 Evaluate side-chains 427 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 306 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1568 VAL Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 360 GLU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 973 ASP Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1342 HIS Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 451 ASN Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1013 GLN Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1144 THR Chi-restraints excluded: chain G residue 1213 THR Chi-restraints excluded: chain G residue 1362 ASP Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 266 optimal weight: 0.8980 chunk 226 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1475 ASN E 515 HIS F 442 GLN G 883 GLN G1242 GLN G1556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.168030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.147177 restraints weight = 38039.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146766 restraints weight = 86283.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145965 restraints weight = 80118.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.144781 restraints weight = 58466.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145324 restraints weight = 48513.278| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30560 Z= 0.117 Angle : 0.546 10.008 41442 Z= 0.278 Chirality : 0.043 0.214 4670 Planarity : 0.004 0.044 5355 Dihedral : 5.339 55.929 4298 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.89 % Allowed : 20.90 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3760 helix: 1.31 (0.19), residues: 744 sheet: 0.05 (0.15), residues: 1221 loop : -1.25 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 601 TYR 0.013 0.001 TYR B 946 PHE 0.023 0.001 PHE A 134 TRP 0.014 0.001 TRP E 699 HIS 0.007 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00279 (30523) covalent geometry : angle 0.53902 (41360) SS BOND : bond 0.00236 ( 29) SS BOND : angle 0.94050 ( 58) hydrogen bonds : bond 0.03100 ( 1140) hydrogen bonds : angle 4.93234 ( 3215) link_NAG-ASN : bond 0.00552 ( 8) link_NAG-ASN : angle 3.53956 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 331 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8227 (t) cc_final: 0.7872 (m) REVERT: A 289 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: A 307 ASN cc_start: 0.8086 (t0) cc_final: 0.7576 (t0) REVERT: A 365 SER cc_start: 0.8968 (t) cc_final: 0.8706 (p) REVERT: C 1684 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7782 (tp) REVERT: E 392 ILE cc_start: 0.8363 (mm) cc_final: 0.7929 (mt) REVERT: E 429 LYS cc_start: 0.7628 (mppt) cc_final: 0.7275 (mmmt) REVERT: E 631 MET cc_start: 0.5630 (mmm) cc_final: 0.5357 (mmm) REVERT: E 735 MET cc_start: 0.7980 (mmm) cc_final: 0.7708 (mtp) REVERT: B 764 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 832 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 845 ARG cc_start: 0.7422 (ptm160) cc_final: 0.7093 (ptm160) REVERT: B 1049 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5507 (tp) REVERT: F 81 ASN cc_start: 0.7062 (m110) cc_final: 0.6550 (m-40) REVERT: F 186 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8703 (tt) REVERT: F 254 THR cc_start: 0.8912 (m) cc_final: 0.8626 (p) REVERT: F 343 ARG cc_start: 0.7613 (tpt90) cc_final: 0.7119 (tpt90) REVERT: F 501 LEU cc_start: 0.8819 (tp) cc_final: 0.8602 (tp) REVERT: G 851 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7976 (mt) REVERT: G 973 ASP cc_start: 0.6223 (t0) cc_final: 0.5708 (t0) REVERT: G 1342 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8477 (tp) REVERT: G 1470 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6912 (mm-30) REVERT: G 1603 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7123 (tt) outliers start: 128 outliers final: 99 residues processed: 429 average time/residue: 0.1858 time to fit residues: 132.7133 Evaluate side-chains 423 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 316 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 467 ASN Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1342 HIS Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 570 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 705 PHE Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 993 ASP Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1242 GLN Chi-restraints excluded: chain G residue 1324 THR Chi-restraints excluded: chain G residue 1342 LEU Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1603 LEU Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 252 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 361 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 371 optimal weight: 9.9990 chunk 323 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1475 ASN F 512 GLN G1556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.139044 restraints weight = 39636.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138372 restraints weight = 71742.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.139313 restraints weight = 63339.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140095 restraints weight = 35617.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142060 restraints weight = 29356.515| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30560 Z= 0.122 Angle : 0.546 9.984 41442 Z= 0.277 Chirality : 0.043 0.212 4670 Planarity : 0.004 0.043 5355 Dihedral : 5.262 55.735 4296 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.11 % Allowed : 21.08 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 3760 helix: 1.32 (0.19), residues: 743 sheet: 0.13 (0.15), residues: 1225 loop : -1.21 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 519 TYR 0.015 0.001 TYR F 446 PHE 0.023 0.001 PHE G1438 TRP 0.011 0.001 TRP E 699 HIS 0.007 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00291 (30523) covalent geometry : angle 0.53925 (41360) SS BOND : bond 0.00215 ( 29) SS BOND : angle 0.91356 ( 58) hydrogen bonds : bond 0.03084 ( 1140) hydrogen bonds : angle 4.85453 ( 3215) link_NAG-ASN : bond 0.00526 ( 8) link_NAG-ASN : angle 3.52341 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 326 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8273 (t) cc_final: 0.7874 (m) REVERT: A 289 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: A 307 ASN cc_start: 0.8092 (t0) cc_final: 0.7576 (t0) REVERT: A 365 SER cc_start: 0.9038 (t) cc_final: 0.8749 (p) REVERT: C 1646 LYS cc_start: 0.7978 (ptmm) cc_final: 0.7668 (ptmm) REVERT: C 1684 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7760 (tp) REVERT: E 381 MET cc_start: 0.7194 (ptm) cc_final: 0.6799 (ptt) REVERT: E 429 LYS cc_start: 0.7733 (mppt) cc_final: 0.7286 (mmmt) REVERT: E 735 MET cc_start: 0.8060 (mmm) cc_final: 0.7725 (mtp) REVERT: B 764 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6108 (mm-30) REVERT: B 832 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 845 ARG cc_start: 0.7525 (ptm160) cc_final: 0.7161 (ptm160) REVERT: B 1049 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5152 (tp) REVERT: D 30 MET cc_start: 0.7697 (mpp) cc_final: 0.7427 (mpp) REVERT: F 186 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8698 (tt) REVERT: F 254 THR cc_start: 0.8939 (m) cc_final: 0.8679 (p) REVERT: F 266 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: F 295 ASP cc_start: 0.6898 (t0) cc_final: 0.6594 (t0) REVERT: F 343 ARG cc_start: 0.7629 (tpt90) cc_final: 0.7097 (tpt90) REVERT: F 501 LEU cc_start: 0.8880 (tp) cc_final: 0.8648 (tp) REVERT: G 675 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7689 (tt) REVERT: G 851 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7948 (mt) REVERT: G 973 ASP cc_start: 0.6283 (t0) cc_final: 0.5701 (t0) REVERT: G 1014 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7812 (t0) REVERT: G 1342 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8347 (tp) REVERT: G 1470 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6827 (mm-30) REVERT: G 1603 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6876 (tt) outliers start: 135 outliers final: 111 residues processed: 434 average time/residue: 0.1875 time to fit residues: 135.5386 Evaluate side-chains 432 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 310 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1673 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 467 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1342 HIS Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 570 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 675 LEU Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 864 VAL Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 993 ASP Chi-restraints excluded: chain G residue 1014 ASN Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1144 THR Chi-restraints excluded: chain G residue 1324 THR Chi-restraints excluded: chain G residue 1342 LEU Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1603 LEU Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 271 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1475 ASN F 442 GLN G1556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.163601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.134542 restraints weight = 55312.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.134655 restraints weight = 106607.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134415 restraints weight = 50137.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134462 restraints weight = 65485.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134490 restraints weight = 44949.192| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30560 Z= 0.253 Angle : 0.664 10.593 41442 Z= 0.338 Chirality : 0.047 0.222 4670 Planarity : 0.005 0.046 5355 Dihedral : 5.751 58.083 4296 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.87 % Allowed : 21.05 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.14), residues: 3760 helix: 0.97 (0.19), residues: 742 sheet: -0.07 (0.15), residues: 1231 loop : -1.41 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 740 TYR 0.028 0.002 TYR F 446 PHE 0.031 0.002 PHE G1438 TRP 0.014 0.002 TRP E 699 HIS 0.006 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00635 (30523) covalent geometry : angle 0.65696 (41360) SS BOND : bond 0.00360 ( 29) SS BOND : angle 1.26928 ( 58) hydrogen bonds : bond 0.03962 ( 1140) hydrogen bonds : angle 5.20579 ( 3215) link_NAG-ASN : bond 0.00578 ( 8) link_NAG-ASN : angle 3.78467 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 304 time to evaluate : 1.128 Fit side-chains REVERT: A 79 GLU cc_start: 0.7387 (pm20) cc_final: 0.7181 (mp0) REVERT: A 120 SER cc_start: 0.8343 (t) cc_final: 0.7887 (m) REVERT: A 137 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7280 (mtt-85) REVERT: A 289 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: A 307 ASN cc_start: 0.8188 (t0) cc_final: 0.7681 (t0) REVERT: A 365 SER cc_start: 0.9088 (t) cc_final: 0.8872 (p) REVERT: C 1483 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7502 (pmm) REVERT: C 1684 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7721 (tp) REVERT: E 429 LYS cc_start: 0.7724 (mppt) cc_final: 0.7244 (mmmt) REVERT: E 721 LYS cc_start: 0.7188 (tptm) cc_final: 0.6182 (mmtt) REVERT: B 764 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6964 (mm-30) REVERT: B 1049 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.4920 (tp) REVERT: D 53 MET cc_start: 0.5429 (mtt) cc_final: 0.5222 (mtt) REVERT: D 79 MET cc_start: 0.6146 (mpp) cc_final: 0.4695 (mtp) REVERT: F 186 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (tt) REVERT: F 266 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: F 343 ARG cc_start: 0.7824 (tpt90) cc_final: 0.7257 (tpt90) REVERT: F 501 LEU cc_start: 0.8906 (tp) cc_final: 0.8700 (tp) REVERT: G 851 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7968 (mt) REVERT: G 973 ASP cc_start: 0.6389 (t0) cc_final: 0.5900 (t0) REVERT: G 1342 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8366 (tp) REVERT: G 1470 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7118 (mm-30) REVERT: G 1603 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6950 (tt) REVERT: G 1617 ASN cc_start: 0.3561 (OUTLIER) cc_final: 0.3086 (m-40) outliers start: 160 outliers final: 127 residues processed: 436 average time/residue: 0.1723 time to fit residues: 125.5427 Evaluate side-chains 434 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 297 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1483 MET Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1595 CYS Chi-restraints excluded: chain C residue 1673 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain C residue 1709 ILE Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1273 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1342 HIS Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 570 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 790 LEU Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 864 VAL Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 911 GLU Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1144 THR Chi-restraints excluded: chain G residue 1321 SER Chi-restraints excluded: chain G residue 1324 THR Chi-restraints excluded: chain G residue 1342 LEU Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1603 LEU Chi-restraints excluded: chain G residue 1617 ASN Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 171 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 188 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 212 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1561 ASN F 512 GLN G 760 ASN G1556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.166142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145701 restraints weight = 48206.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.141250 restraints weight = 115493.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.137085 restraints weight = 55086.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137261 restraints weight = 43205.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137706 restraints weight = 28853.624| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30560 Z= 0.152 Angle : 0.583 10.084 41442 Z= 0.296 Chirality : 0.044 0.223 4670 Planarity : 0.004 0.044 5355 Dihedral : 5.538 59.776 4296 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.38 % Allowed : 21.42 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.14), residues: 3760 helix: 1.12 (0.19), residues: 742 sheet: -0.07 (0.15), residues: 1246 loop : -1.34 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 740 TYR 0.018 0.001 TYR F 446 PHE 0.027 0.002 PHE G1438 TRP 0.014 0.001 TRP E 699 HIS 0.007 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00373 (30523) covalent geometry : angle 0.57656 (41360) SS BOND : bond 0.00259 ( 29) SS BOND : angle 0.99646 ( 58) hydrogen bonds : bond 0.03362 ( 1140) hydrogen bonds : angle 5.02433 ( 3215) link_NAG-ASN : bond 0.00524 ( 8) link_NAG-ASN : angle 3.54146 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 305 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8339 (t) cc_final: 0.7929 (m) REVERT: A 137 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7225 (mtt-85) REVERT: A 289 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: A 307 ASN cc_start: 0.8128 (t0) cc_final: 0.7573 (t0) REVERT: A 365 SER cc_start: 0.9027 (t) cc_final: 0.8789 (p) REVERT: C 1684 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7720 (tp) REVERT: E 381 MET cc_start: 0.7298 (ptm) cc_final: 0.6897 (ptt) REVERT: E 429 LYS cc_start: 0.7720 (mppt) cc_final: 0.7244 (mmmt) REVERT: E 735 MET cc_start: 0.8057 (mmm) cc_final: 0.7769 (mtp) REVERT: B 764 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 1049 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5100 (tp) REVERT: D 29 TYR cc_start: 0.5395 (p90) cc_final: 0.4917 (p90) REVERT: D 79 MET cc_start: 0.6009 (mpp) cc_final: 0.4589 (mtp) REVERT: D 95 ASP cc_start: 0.6930 (p0) cc_final: 0.5594 (p0) REVERT: F 186 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8710 (tt) REVERT: F 254 THR cc_start: 0.8957 (m) cc_final: 0.8623 (p) REVERT: F 266 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: F 343 ARG cc_start: 0.7653 (tpt90) cc_final: 0.7151 (tpt90) REVERT: F 501 LEU cc_start: 0.8831 (tp) cc_final: 0.8607 (tp) REVERT: F 661 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6583 (mt0) REVERT: G 851 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7984 (mt) REVERT: G 973 ASP cc_start: 0.6313 (t0) cc_final: 0.5832 (t0) REVERT: G 1342 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8383 (tp) REVERT: G 1470 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6998 (mm-30) REVERT: G 1603 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6871 (tt) REVERT: G 1604 MET cc_start: 0.6927 (mpp) cc_final: 0.6677 (mpp) outliers start: 144 outliers final: 118 residues processed: 427 average time/residue: 0.1818 time to fit residues: 129.1475 Evaluate side-chains 425 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 298 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1673 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 467 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 866 SER Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 507 VAL Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 564 VAL Chi-restraints excluded: chain F residue 570 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain F residue 661 GLN Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 864 VAL Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 926 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1144 THR Chi-restraints excluded: chain G residue 1324 THR Chi-restraints excluded: chain G residue 1342 LEU Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1603 LEU Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 263 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 182 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 332 optimal weight: 0.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 442 GLN F 512 GLN G 983 GLN G1556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.168098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152263 restraints weight = 52751.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.144313 restraints weight = 114599.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141352 restraints weight = 60905.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.140425 restraints weight = 41637.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140564 restraints weight = 30581.144| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30560 Z= 0.117 Angle : 0.554 10.251 41442 Z= 0.281 Chirality : 0.043 0.215 4670 Planarity : 0.004 0.044 5355 Dihedral : 5.336 55.917 4293 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.71 % Allowed : 22.09 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3760 helix: 1.30 (0.19), residues: 742 sheet: 0.06 (0.15), residues: 1222 loop : -1.28 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 740 TYR 0.013 0.001 TYR F 446 PHE 0.025 0.001 PHE G1037 TRP 0.012 0.001 TRP G1605 HIS 0.007 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00279 (30523) covalent geometry : angle 0.54707 (41360) SS BOND : bond 0.00208 ( 29) SS BOND : angle 0.88815 ( 58) hydrogen bonds : bond 0.03066 ( 1140) hydrogen bonds : angle 4.86538 ( 3215) link_NAG-ASN : bond 0.00509 ( 8) link_NAG-ASN : angle 3.39651 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 312 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 SER cc_start: 0.8282 (t) cc_final: 0.7888 (m) REVERT: A 289 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: A 307 ASN cc_start: 0.8098 (t0) cc_final: 0.7531 (t0) REVERT: A 365 SER cc_start: 0.9008 (t) cc_final: 0.8737 (p) REVERT: C 1684 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (tp) REVERT: E 429 LYS cc_start: 0.7659 (mppt) cc_final: 0.7241 (mmmt) REVERT: E 735 MET cc_start: 0.8029 (mmm) cc_final: 0.7784 (mtp) REVERT: B 764 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6376 (mp0) REVERT: B 1049 ILE cc_start: 0.5677 (OUTLIER) cc_final: 0.5211 (tp) REVERT: D 79 MET cc_start: 0.5865 (mpp) cc_final: 0.4608 (mtp) REVERT: F 186 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8702 (tt) REVERT: F 254 THR cc_start: 0.8995 (m) cc_final: 0.8726 (p) REVERT: F 266 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: F 343 ARG cc_start: 0.7667 (tpt90) cc_final: 0.7145 (tpt90) REVERT: F 501 LEU cc_start: 0.8832 (tp) cc_final: 0.8613 (tp) REVERT: F 661 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6520 (mt0) REVERT: G 851 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8005 (mt) REVERT: G 973 ASP cc_start: 0.6258 (t0) cc_final: 0.5783 (t0) REVERT: G 1342 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (tp) REVERT: G 1470 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6930 (mm-30) REVERT: G 1603 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6924 (tt) outliers start: 122 outliers final: 108 residues processed: 416 average time/residue: 0.1864 time to fit residues: 128.3258 Evaluate side-chains 423 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 306 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 267 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 360 TRP Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain C residue 1469 THR Chi-restraints excluded: chain C residue 1485 ILE Chi-restraints excluded: chain C residue 1513 SER Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1555 THR Chi-restraints excluded: chain C residue 1583 CYS Chi-restraints excluded: chain C residue 1673 CYS Chi-restraints excluded: chain C residue 1684 LEU Chi-restraints excluded: chain E residue 252 HIS Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 467 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 602 ASP Chi-restraints excluded: chain E residue 603 HIS Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 649 PHE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 769 GLU Chi-restraints excluded: chain B residue 802 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 843 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 902 VAL Chi-restraints excluded: chain B residue 919 PHE Chi-restraints excluded: chain B residue 980 VAL Chi-restraints excluded: chain B residue 1049 ILE Chi-restraints excluded: chain B residue 1085 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1321 THR Chi-restraints excluded: chain B residue 1322 THR Chi-restraints excluded: chain B residue 1364 SER Chi-restraints excluded: chain B residue 1368 VAL Chi-restraints excluded: chain B residue 1386 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 266 GLU Chi-restraints excluded: chain F residue 333 HIS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 410 SER Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 431 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 509 GLU Chi-restraints excluded: chain F residue 512 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 538 ILE Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 596 VAL Chi-restraints excluded: chain F residue 609 ASN Chi-restraints excluded: chain F residue 627 CYS Chi-restraints excluded: chain F residue 661 GLN Chi-restraints excluded: chain G residue 673 VAL Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 720 CYS Chi-restraints excluded: chain G residue 744 LEU Chi-restraints excluded: chain G residue 761 ILE Chi-restraints excluded: chain G residue 775 VAL Chi-restraints excluded: chain G residue 831 ILE Chi-restraints excluded: chain G residue 851 LEU Chi-restraints excluded: chain G residue 864 VAL Chi-restraints excluded: chain G residue 881 ARG Chi-restraints excluded: chain G residue 971 VAL Chi-restraints excluded: chain G residue 1046 LEU Chi-restraints excluded: chain G residue 1144 THR Chi-restraints excluded: chain G residue 1324 THR Chi-restraints excluded: chain G residue 1342 LEU Chi-restraints excluded: chain G residue 1365 VAL Chi-restraints excluded: chain G residue 1390 THR Chi-restraints excluded: chain G residue 1511 CYS Chi-restraints excluded: chain G residue 1518 CYS Chi-restraints excluded: chain G residue 1528 THR Chi-restraints excluded: chain G residue 1562 ILE Chi-restraints excluded: chain G residue 1568 THR Chi-restraints excluded: chain G residue 1603 LEU Chi-restraints excluded: chain G residue 1656 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 187 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 chunk 341 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 chunk 215 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1151 HIS F 442 GLN F 512 GLN G1014 ASN G1556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153001 restraints weight = 52801.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.144212 restraints weight = 111447.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141374 restraints weight = 61537.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140992 restraints weight = 35802.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140959 restraints weight = 29659.679| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30560 Z= 0.119 Angle : 0.558 10.161 41442 Z= 0.282 Chirality : 0.043 0.290 4670 Planarity : 0.004 0.043 5355 Dihedral : 5.310 58.498 4293 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.83 % Allowed : 22.15 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3760 helix: 1.34 (0.19), residues: 741 sheet: 0.12 (0.15), residues: 1216 loop : -1.25 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 740 TYR 0.014 0.001 TYR F 446 PHE 0.026 0.001 PHE G1037 TRP 0.012 0.001 TRP G1605 HIS 0.007 0.001 HIS C1495 Details of bonding type rmsd covalent geometry : bond 0.00285 (30523) covalent geometry : angle 0.55154 (41360) SS BOND : bond 0.00209 ( 29) SS BOND : angle 0.87546 ( 58) hydrogen bonds : bond 0.03038 ( 1140) hydrogen bonds : angle 4.81601 ( 3215) link_NAG-ASN : bond 0.00500 ( 8) link_NAG-ASN : angle 3.36871 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5728.23 seconds wall clock time: 99 minutes 35.90 seconds (5975.90 seconds total)