Starting phenix.real_space_refine on Fri Mar 6 08:59:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aoc_11840/03_2026/7aoc_11840.map" } resolution = 3.84 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 570 atoms to isotropic. 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 Zn 6 6.06 5 S 165 5.16 5 C 18860 2.51 5 N 5136 2.21 5 O 5557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 249 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29724 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 11051 Classifications: {'peptide': 1394} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1327} Chain breaks: 12 Chain: "B" Number of atoms: 9148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9148 Classifications: {'peptide': 1159} Link IDs: {'PTRANS': 59, 'TRANS': 1099} Chain breaks: 3 Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2533 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1663 Classifications: {'peptide': 207} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 195} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1267 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 10, 'TRANS': 149} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "L" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 368 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 483 SG CYS A 63 77.752 60.209 58.365 1.00 93.27 S ATOM 501 SG CYS A 66 74.149 61.180 57.450 1.00 95.46 S ATOM 565 SG CYS A 73 74.149 61.209 59.501 1.00 84.44 S ATOM 809 SG CYS A 103 81.341 18.476 87.647 1.00110.95 S ATOM 1540 SG CYS A 228 80.800 17.695 89.490 1.00102.85 S ATOM 1562 SG CYS A 231 82.126 13.918 87.382 1.00111.41 S ATOM 27663 SG CYS I 10 125.367 43.834 144.167 1.00100.65 S ATOM 27684 SG CYS I 13 126.037 44.283 140.827 1.00102.67 S ATOM 27789 SG CYS I 27 126.217 41.033 141.731 1.00128.76 S ATOM 27812 SG CYS I 30 127.155 42.411 141.870 1.00125.54 S ATOM 28111 SG CYS J 7 75.288 120.630 103.630 1.00 3.36 S ATOM 28134 SG CYS J 10 71.372 121.754 105.969 1.00 3.55 S ATOM 28406 SG CYS J 44 72.291 119.519 107.188 1.00 3.74 S ATOM 28412 SG CYS J 45 74.016 122.212 105.891 1.00 12.41 S ATOM 29399 SG CYS L 24 113.087 106.412 84.682 1.00 33.38 S ATOM 29418 SG CYS L 27 114.114 108.827 84.566 1.00 46.11 S ATOM 29525 SG CYS L 41 114.859 107.058 83.207 1.00 37.24 S ATOM 29551 SG CYS L 44 117.022 108.444 86.275 1.00 45.93 S Time building chain proxies: 6.13, per 1000 atoms: 0.21 Number of scatterers: 29724 At special positions: 0 Unit cell: (151.017, 155.271, 169.097, 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) Zn 6 29.99 S 165 16.00 O 5557 8.00 N 5136 7.00 C 18860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B1089 " - pdb=" SG CYS B1092 " 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 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 918.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 66 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 63 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 103 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 228 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 231 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 27 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 24 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 44 " Number of angles added : 21 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 43 sheets defined 36.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.551A pdb=" N VAL A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.793A pdb=" N VAL A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 195 removed outlier: 3.840A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.706A pdb=" N LYS A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.795A pdb=" N PHE A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 4.407A pdb=" N VAL A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 385 through 411 Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 463 through 469 Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 558 through 568 removed outlier: 3.622A pdb=" N GLN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 634 through 641 removed outlier: 4.135A pdb=" N ASN A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 668 through 672 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 717 Processing helix chain 'A' and resid 717 through 722 removed outlier: 3.914A pdb=" N THR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.337A pdb=" N TRP A 775 " --> pdb=" O PRO A 771 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 776' Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.521A pdb=" N SER A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 840 removed outlier: 3.545A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 865 Processing helix chain 'A' and resid 867 through 878 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 899 through 925 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.727A pdb=" N VAL A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 1004 through 1022 removed outlier: 3.769A pdb=" N PHE A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 removed outlier: 3.524A pdb=" N LYS A1072 " --> pdb=" O ASP A1069 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A1074 " --> pdb=" O THR A1071 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS A1075 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A1076 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1086 removed outlier: 3.738A pdb=" N ASN A1085 " --> pdb=" O PHE A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.690A pdb=" N ILE A1090 " --> pdb=" O TYR A1086 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 removed outlier: 4.436A pdb=" N SER A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA A1101 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.969A pdb=" N SER A1108 " --> pdb=" O SER A1104 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A1112 " --> pdb=" O SER A1108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1138 through 1152 Processing helix chain 'A' and resid 1163 through 1167 Processing helix chain 'A' and resid 1171 through 1186 Processing helix chain 'A' and resid 1194 through 1209 Proline residue: A1205 - end of helix removed outlier: 3.867A pdb=" N MET A1209 " --> pdb=" O PRO A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1256 through 1268 Processing helix chain 'A' and resid 1271 through 1274 Processing helix chain 'A' and resid 1305 through 1312 removed outlier: 3.898A pdb=" N GLU A1312 " --> pdb=" O GLU A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1345 removed outlier: 4.178A pdb=" N GLN A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1516 Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1568 through 1577 removed outlier: 3.506A pdb=" N ILE A1572 " --> pdb=" O ASP A1568 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY A1577 " --> pdb=" O LEU A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1593 Processing helix chain 'A' and resid 1601 through 1613 removed outlier: 3.902A pdb=" N LEU A1605 " --> pdb=" O ASP A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 Processing helix chain 'A' and resid 1631 through 1639 removed outlier: 3.534A pdb=" N LYS A1635 " --> pdb=" O SER A1631 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A1636 " --> pdb=" O PRO A1632 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU A1639 " --> pdb=" O LYS A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 3.581A pdb=" N PHE A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1666 removed outlier: 3.503A pdb=" N VAL A1666 " --> pdb=" O SER A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1676 Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.205A pdb=" N GLN B 26 " --> pdb=" O PHE B 22 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.032A pdb=" N GLY B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.825A pdb=" N ALA B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.843A pdb=" N ASN B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 205 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 4.153A pdb=" N LEU B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.540A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.668A pdb=" N GLY B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 361 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 409 removed outlier: 4.022A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.768A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 468 through 478 removed outlier: 3.595A pdb=" N MET B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.772A pdb=" N ALA B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.856A pdb=" N ASN B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.736A pdb=" N MET B 688 " --> pdb=" O ILE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 removed outlier: 3.681A pdb=" N ASN B 700 " --> pdb=" O GLN B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.880A pdb=" N HIS B 749 " --> pdb=" O GLY B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 935 through 939 Processing helix chain 'B' and resid 944 through 961 removed outlier: 3.619A pdb=" N PHE B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 959 " --> pdb=" O LYS B 955 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 989 Processing helix chain 'B' and resid 1022 through 1026 removed outlier: 4.197A pdb=" N SER B1026 " --> pdb=" O HIS B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1069 through 1079 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 66 through 79 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 181 through 186 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.682A pdb=" N PHE C 226 " --> pdb=" O HIS C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.669A pdb=" N PHE C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.731A pdb=" N LYS C 282 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.534A pdb=" N ASN C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.935A pdb=" N ILE D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.525A pdb=" N ARG E 10 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 removed outlier: 3.660A pdb=" N PHE E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 97 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'F' and resid 76 through 93 removed outlier: 4.033A pdb=" N ALA F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 removed outlier: 3.763A pdb=" N GLN F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 24 through 37 removed outlier: 4.379A pdb=" N ALA G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 71 removed outlier: 4.307A pdb=" N LYS H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.516A pdb=" N GLN I 38 " --> pdb=" O PRO I 35 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I 39 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA I 40 " --> pdb=" O GLU I 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 40' Processing helix chain 'I' and resid 57 through 61 Processing helix chain 'J' and resid 21 through 26 removed outlier: 3.666A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 37 removed outlier: 3.871A pdb=" N LEU J 35 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 56 removed outlier: 3.565A pdb=" N GLY K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS K 56 " --> pdb=" O TYR K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 113 removed outlier: 3.765A pdb=" N VAL K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 113 " --> pdb=" O PHE K 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1654 through 1655 removed outlier: 3.941A pdb=" N ASP A1655 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 14 " --> pdb=" O ASP A1655 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 13 " --> pdb=" O GLU B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 87 removed outlier: 11.160A pdb=" N LEU A 82 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ALA A 366 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 10.823A pdb=" N ILE A 84 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ASN A 364 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 86 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 482 through 483 removed outlier: 3.595A pdb=" N PHE B1056 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 494 removed outlier: 3.764A pdb=" N ILE A 630 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE A 503 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 619 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 490 " --> pdb=" O MET A 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 518 removed outlier: 6.668A pdb=" N LYS A 592 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 544 " --> pdb=" O LYS A 592 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 594 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 764 through 767 removed outlier: 7.158A pdb=" N ASP A 787 " --> pdb=" O LEU A 791 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 961 through 962 removed outlier: 3.905A pdb=" N ILE A 995 " --> pdb=" O GLY A 961 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1044 through 1045 Processing sheet with id=AA9, first strand: chain 'A' and resid 1524 through 1529 removed outlier: 4.886A pdb=" N ARG A1526 " --> pdb=" O GLU A1545 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A1250 " --> pdb=" O ASN A1562 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A1562 " --> pdb=" O ARG A1250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1479 through 1482 removed outlier: 6.516A pdb=" N ALA A1298 " --> pdb=" O VAL A1281 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A1281 " --> pdb=" O ALA A1298 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG A1300 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A1279 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP A1302 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL I 44 " --> pdb=" O GLU A1283 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1678 through 1679 Processing sheet with id=AB3, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.733A pdb=" N ARG B 78 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS B 120 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL B 82 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 118 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE B 84 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG B 116 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B 115 " --> pdb=" O MET B 139 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 139 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 117 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.607A pdb=" N VAL B 175 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 375 through 378 removed outlier: 3.580A pdb=" N LEU B 185 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.280A pdb=" N TYR B 211 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR B 226 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 242 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 250 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 526 through 528 removed outlier: 3.564A pdb=" N VAL B 635 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 633 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 571 removed outlier: 5.553A pdb=" N ILE B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 563 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 569 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 560 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 627 " --> pdb=" O CYS B 560 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 562 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 610 " --> pdb=" O PHE B 628 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 725 through 729 removed outlier: 4.029A pdb=" N GLN B 885 " --> pdb=" O LEU B 874 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 870 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL B 871 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 737 through 738 Processing sheet with id=AC4, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR B1012 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 932 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 902 through 903 removed outlier: 3.653A pdb=" N GLN B1019 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 809 through 810 removed outlier: 3.615A pdb=" N VAL B 845 " --> pdb=" O GLU B 858 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 923 through 924 Processing sheet with id=AC8, first strand: chain 'B' and resid 1085 through 1089 Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1099 Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.742A pdb=" N VAL C 59 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 53 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 300 " --> pdb=" O HIS C 241 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 241 " --> pdb=" O GLN C 300 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 237 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ASP C 306 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N ARG C 235 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N TYR C 308 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N SER C 233 " --> pdb=" O TYR C 308 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N PHE C 310 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR C 231 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N VAL C 312 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 229 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 175 through 176 removed outlier: 6.894A pdb=" N GLU C 208 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 94 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP C 210 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 216 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE C 86 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 168 through 170 removed outlier: 6.664A pdb=" N VAL C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.714A pdb=" N GLN C 274 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.905A pdb=" N TYR E 73 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY E 102 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 149 removed outlier: 4.231A pdb=" N LYS E 147 " --> pdb=" O VAL E 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 9 through 17 removed outlier: 3.954A pdb=" N ARG G 55 " --> pdb=" O ARG G 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 9 through 17 Processing sheet with id=AD9, first strand: chain 'G' and resid 40 through 41 removed outlier: 3.781A pdb=" N GLY G 46 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 109 through 114 removed outlier: 6.179A pdb=" N LEU G 104 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE G 93 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL G 153 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 123 through 124 Processing sheet with id=AE3, first strand: chain 'H' and resid 15 through 17 removed outlier: 6.021A pdb=" N LEU H 101 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU H 100 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG H 82 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL H 80 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AE5, first strand: chain 'I' and resid 25 through 26 removed outlier: 4.682A pdb=" N THR I 25 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR I 34 " --> pdb=" O THR I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 24 removed outlier: 3.595A pdb=" N ILE K 23 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.666A pdb=" N GLN K 80 " --> pdb=" O GLU K 61 " (cutoff:3.500A) 1108 hydrogen bonds defined for protein. 3078 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: 6.77 Time building geometry restraints manager: 3.23 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: 9716 1.34 - 1.46: 5308 1.46 - 1.58: 15026 1.58 - 1.70: 0 1.70 - 1.81: 266 Bond restraints: 30316 Sorted by residual: bond pdb=" CA ASN B 147 " pdb=" C ASN B 147 " ideal model delta sigma weight residual 1.522 1.471 0.051 1.37e-02 5.33e+03 1.40e+01 bond pdb=" CA ASN B 680 " pdb=" C ASN B 680 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.69e+00 bond pdb=" C GLN A 735 " pdb=" N ARG A 736 " ideal model delta sigma weight residual 1.325 1.289 0.036 1.25e-02 6.40e+03 8.22e+00 bond pdb=" C GLN E 169 " pdb=" N LEU E 170 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.45e-02 4.76e+03 7.09e+00 bond pdb=" N SER A1067 " pdb=" CA SER A1067 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 ... (remaining 30311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 40454 3.08 - 6.16: 466 6.16 - 9.24: 37 9.24 - 12.32: 2 12.32 - 15.40: 1 Bond angle restraints: 40960 Sorted by residual: angle pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" C ASP E 24 " ideal model delta sigma weight residual 110.80 126.20 -15.40 2.13e+00 2.20e-01 5.23e+01 angle pdb=" C GLY E 49 " pdb=" N ARG E 50 " pdb=" CA ARG E 50 " ideal model delta sigma weight residual 121.70 132.26 -10.56 1.80e+00 3.09e-01 3.44e+01 angle pdb=" N ASP A1066 " pdb=" CA ASP A1066 " pdb=" C ASP A1066 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.85e+01 angle pdb=" C ASP H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta sigma weight residual 121.70 130.90 -9.20 1.80e+00 3.09e-01 2.61e+01 angle pdb=" N SER G 99 " pdb=" CA SER G 99 " pdb=" C SER G 99 " ideal model delta sigma weight residual 114.62 108.94 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 40955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.39: 17425 26.39 - 52.79: 944 52.79 - 79.18: 61 79.18 - 105.57: 13 105.57 - 131.96: 1 Dihedral angle restraints: 18444 sinusoidal: 7554 harmonic: 10890 Sorted by residual: dihedral pdb=" CA HIS E 23 " pdb=" C HIS E 23 " pdb=" N ASP E 24 " pdb=" CA ASP E 24 " ideal model delta harmonic sigma weight residual -180.00 -48.04 -131.96 0 5.00e+00 4.00e-02 6.97e+02 dihedral pdb=" CA ILE A 84 " pdb=" C ILE A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta harmonic sigma weight residual 180.00 -122.13 -57.87 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLU A1065 " pdb=" C GLU A1065 " pdb=" N ASP A1066 " pdb=" CA ASP A1066 " ideal model delta harmonic sigma weight residual -180.00 -138.67 -41.33 0 5.00e+00 4.00e-02 6.83e+01 ... (remaining 18441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3620 0.059 - 0.117: 861 0.117 - 0.176: 86 0.176 - 0.234: 6 0.234 - 0.292: 4 Chirality restraints: 4577 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE I 8 " pdb=" CA ILE I 8 " pdb=" CG1 ILE I 8 " pdb=" CG2 ILE I 8 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB VAL E 137 " pdb=" CA VAL E 137 " pdb=" CG1 VAL E 137 " pdb=" CG2 VAL E 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4574 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.056 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO A 85 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 786 " 0.025 2.00e-02 2.50e+03 2.17e-02 8.25e+00 pdb=" CG PHE A 786 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 786 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 786 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 786 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 786 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 786 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 895 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 896 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 896 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 896 " 0.037 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 233 2.52 - 3.12: 23683 3.12 - 3.71: 44440 3.71 - 4.31: 61939 4.31 - 4.90: 104375 Nonbonded interactions: 234670 Sorted by model distance: nonbonded pdb=" OG SER B1097 " pdb=" OG SER B1117 " model vdw 1.929 3.040 nonbonded pdb=" OH TYR A 19 " pdb="ZN ZN B1301 " model vdw 1.993 2.230 nonbonded pdb=" OG SER B1117 " pdb="ZN ZN B1301 " model vdw 2.032 2.230 nonbonded pdb=" SG CYS A 103 " pdb=" CB CYS A 106 " model vdw 2.039 3.800 nonbonded pdb=" CB CYS A 106 " pdb="ZN ZN A1702 " model vdw 2.074 2.630 ... (remaining 234665 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.480 Find NCS groups from input model: 0.140 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.008 0.446 30336 Z= 0.347 Angle : 1.212 66.240 40983 Z= 0.527 Chirality : 0.049 0.292 4577 Planarity : 0.005 0.085 5268 Dihedral : 15.048 131.965 11415 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.20 % Favored : 88.53 % Rotamer: Outliers : 0.33 % Allowed : 11.60 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.37 % 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: -4.08 (0.12), residues: 3688 helix: -2.06 (0.12), residues: 1205 sheet: -2.88 (0.19), residues: 536 loop : -3.14 (0.12), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 595 TYR 0.032 0.002 TYR A 19 PHE 0.050 0.002 PHE A 786 TRP 0.026 0.002 TRP E 15 HIS 0.009 0.002 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00745 (30316) covalent geometry : angle 0.87782 (40960) SS BOND : bond 0.00051 ( 1) SS BOND : angle 2.06667 ( 2) hydrogen bonds : bond 0.14922 ( 1088) hydrogen bonds : angle 7.31833 ( 3078) metal coordination : bond 0.13490 ( 19) metal coordination : angle 36.91709 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 636 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.4865 (tp30) cc_final: 0.4280 (pt0) REVERT: A 358 ASP cc_start: 0.7492 (m-30) cc_final: 0.7169 (p0) REVERT: A 479 MET cc_start: 0.7657 (mtt) cc_final: 0.7303 (mtp) REVERT: A 634 TYR cc_start: 0.8253 (m-80) cc_final: 0.7928 (m-80) REVERT: A 941 MET cc_start: 0.8839 (mtm) cc_final: 0.8626 (mtp) REVERT: A 966 GLU cc_start: 0.7338 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1131 SER cc_start: 0.8520 (m) cc_final: 0.8284 (m) REVERT: A 1280 ARG cc_start: 0.7258 (ptp90) cc_final: 0.7041 (mtm110) REVERT: A 1337 LYS cc_start: 0.7017 (tptt) cc_final: 0.6649 (mttt) REVERT: A 1501 GLU cc_start: 0.6984 (mp0) cc_final: 0.6115 (tp30) REVERT: A 1530 LYS cc_start: 0.6104 (mttt) cc_final: 0.5816 (tmtt) REVERT: A 1557 ASN cc_start: 0.7234 (m110) cc_final: 0.7014 (p0) REVERT: A 1559 ILE cc_start: 0.8450 (tt) cc_final: 0.8241 (tp) REVERT: A 1601 ASP cc_start: 0.8613 (p0) cc_final: 0.8381 (p0) REVERT: A 1627 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 1 MET cc_start: 0.3032 (tpt) cc_final: 0.2036 (tpt) REVERT: B 44 LEU cc_start: 0.8887 (tp) cc_final: 0.8371 (tt) REVERT: B 190 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.7993 (mmm-85) REVERT: B 424 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6721 (mmt90) REVERT: B 653 GLU cc_start: 0.8015 (mp0) cc_final: 0.7670 (mt-10) REVERT: B 705 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 861 HIS cc_start: 0.7010 (m170) cc_final: 0.6736 (m90) REVERT: B 943 MET cc_start: 0.9116 (mmt) cc_final: 0.8512 (mmt) REVERT: B 970 ILE cc_start: 0.9034 (mt) cc_final: 0.8828 (mt) REVERT: B 1024 MET cc_start: 0.5786 (ppp) cc_final: 0.5090 (tpt) REVERT: B 1168 LYS cc_start: 0.7461 (mtpt) cc_final: 0.7236 (mtpt) REVERT: C 100 ASP cc_start: 0.8257 (t0) cc_final: 0.8003 (t0) REVERT: C 313 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6916 (tm-30) REVERT: E 40 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7301 (mm110) REVERT: E 166 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7171 (mmm160) REVERT: E 181 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7631 (mtp180) REVERT: G 75 ARG cc_start: 0.6458 (ttm170) cc_final: 0.6151 (ptm160) REVERT: H 35 ASP cc_start: 0.6151 (p0) cc_final: 0.5913 (p0) REVERT: J 48 MET cc_start: 0.8730 (mmm) cc_final: 0.8359 (tpp) REVERT: K 40 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8259 (tp-100) REVERT: L 49 MET cc_start: 0.8328 (mmm) cc_final: 0.7822 (mtm) outliers start: 11 outliers final: 2 residues processed: 643 average time/residue: 0.2103 time to fit residues: 206.9858 Evaluate side-chains 457 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 HIS A 60 ASN A 67 HIS A 79 HIS A 94 GLN A 108 HIS A 232 GLN A 257 GLN A 364 ASN A 439 HIS A 501 ASN A 533 ASN A 543 HIS A 599 ASN ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 655 GLN A 735 GLN A 952 ASN A 963 GLN ** A1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 126 ASN ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 233 ASN B 300 GLN B 374 HIS B 386 GLN B 530 HIS B 640 HIS ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 HIS B 887 HIS B1038 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1067 HIS B1145 ASN C 182 GLN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS C 300 GLN C 307 HIS D 51 ASN E 19 HIS E 20 GLN E 65 ASN E 98 ASN E 99 HIS E 131 GLN ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN G 167 GLN H 37 ASN H 118 HIS I 41 ASN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146584 restraints weight = 39095.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144344 restraints weight = 69890.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142134 restraints weight = 77653.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141450 restraints weight = 70387.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.141092 restraints weight = 62272.321| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30336 Z= 0.153 Angle : 0.759 26.329 40983 Z= 0.366 Chirality : 0.045 0.250 4577 Planarity : 0.005 0.085 5268 Dihedral : 6.161 60.787 4074 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 3.18 % Allowed : 16.00 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.37 % 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: -2.88 (0.13), residues: 3688 helix: -0.69 (0.14), residues: 1240 sheet: -2.47 (0.20), residues: 549 loop : -2.62 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 54 TYR 0.039 0.002 TYR H 120 PHE 0.039 0.002 PHE A1638 TRP 0.018 0.001 TRP A1553 HIS 0.013 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00344 (30316) covalent geometry : angle 0.69690 (40960) SS BOND : bond 0.00252 ( 1) SS BOND : angle 1.73708 ( 2) hydrogen bonds : bond 0.04448 ( 1088) hydrogen bonds : angle 5.61523 ( 3078) metal coordination : bond 0.01818 ( 19) metal coordination : angle 13.29226 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 527 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 TYR cc_start: 0.8316 (m-80) cc_final: 0.8050 (m-80) REVERT: A 1053 ASP cc_start: 0.8317 (t0) cc_final: 0.7994 (t0) REVERT: A 1184 GLN cc_start: 0.8954 (tt0) cc_final: 0.8276 (tt0) REVERT: A 1234 ILE cc_start: 0.9322 (tp) cc_final: 0.9003 (tt) REVERT: A 1557 ASN cc_start: 0.7073 (m110) cc_final: 0.6833 (p0) REVERT: A 1626 ILE cc_start: 0.8161 (mt) cc_final: 0.7720 (tt) REVERT: A 1680 PHE cc_start: 0.8148 (m-10) cc_final: 0.7827 (m-10) REVERT: B 1 MET cc_start: 0.2783 (tpt) cc_final: 0.1597 (tpt) REVERT: B 80 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: B 134 MET cc_start: 0.8299 (mtm) cc_final: 0.7960 (mtp) REVERT: B 152 GLU cc_start: 0.8087 (tt0) cc_final: 0.7811 (tt0) REVERT: B 240 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7975 (ttt180) REVERT: B 254 MET cc_start: 0.8585 (tpp) cc_final: 0.8322 (ttm) REVERT: B 943 MET cc_start: 0.8815 (mmt) cc_final: 0.8369 (mmt) REVERT: B 1024 MET cc_start: 0.6009 (ppp) cc_final: 0.5027 (tpt) REVERT: B 1038 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8256 (t-170) REVERT: B 1168 LYS cc_start: 0.6845 (mtpt) cc_final: 0.6293 (mtpt) REVERT: B 1169 MET cc_start: 0.8281 (pmm) cc_final: 0.7863 (ptp) REVERT: C 179 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7766 (mm110) REVERT: E 129 THR cc_start: 0.5270 (OUTLIER) cc_final: 0.4809 (p) REVERT: E 137 VAL cc_start: 0.6418 (OUTLIER) cc_final: 0.6217 (m) REVERT: E 166 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7171 (mmm160) REVERT: E 193 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8376 (mt) REVERT: H 35 ASP cc_start: 0.5372 (p0) cc_final: 0.4984 (p0) REVERT: J 35 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7890 (pp) REVERT: J 48 MET cc_start: 0.8606 (mmm) cc_final: 0.8239 (tpp) REVERT: J 65 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7277 (pp) REVERT: L 31 ASN cc_start: 0.6096 (OUTLIER) cc_final: 0.5069 (t160) outliers start: 105 outliers final: 59 residues processed: 597 average time/residue: 0.1952 time to fit residues: 185.9174 Evaluate side-chains 513 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 446 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1615 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 31 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 6 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 442 ASN A 536 HIS ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 672 GLN A 952 ASN A1075 HIS A1476 ASN A1519 HIS A1587 HIS ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 374 HIS ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.157482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140847 restraints weight = 39635.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138745 restraints weight = 73344.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137043 restraints weight = 83727.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.136499 restraints weight = 71349.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136500 restraints weight = 64505.681| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 30336 Z= 0.280 Angle : 0.807 22.237 40983 Z= 0.404 Chirality : 0.048 0.321 4577 Planarity : 0.006 0.086 5268 Dihedral : 6.350 55.659 4074 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.52 % Favored : 89.40 % Rotamer: Outliers : 4.88 % Allowed : 18.99 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.65 (0.13), residues: 3688 helix: -0.45 (0.14), residues: 1255 sheet: -2.34 (0.20), residues: 549 loop : -2.53 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 125 TYR 0.045 0.002 TYR H 120 PHE 0.038 0.002 PHE A 786 TRP 0.019 0.002 TRP A1489 HIS 0.012 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00667 (30316) covalent geometry : angle 0.77345 (40960) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.39863 ( 2) hydrogen bonds : bond 0.04882 ( 1088) hydrogen bonds : angle 5.65000 ( 3078) metal coordination : bond 0.01511 ( 19) metal coordination : angle 10.14258 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 458 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: A 1155 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7404 (mmtp) REVERT: A 1184 GLN cc_start: 0.8940 (tt0) cc_final: 0.8411 (tt0) REVERT: A 1557 ASN cc_start: 0.7176 (m110) cc_final: 0.6820 (m110) REVERT: A 1626 ILE cc_start: 0.8246 (mt) cc_final: 0.7949 (tt) REVERT: B 1 MET cc_start: 0.3638 (tpt) cc_final: 0.2316 (tpt) REVERT: B 80 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: B 152 GLU cc_start: 0.8188 (tt0) cc_final: 0.7949 (tt0) REVERT: B 254 MET cc_start: 0.8439 (tpp) cc_final: 0.8155 (ttm) REVERT: B 688 MET cc_start: 0.7880 (mtm) cc_final: 0.7676 (mtm) REVERT: B 943 MET cc_start: 0.9024 (mmt) cc_final: 0.8377 (mmt) REVERT: B 1024 MET cc_start: 0.6163 (ppp) cc_final: 0.5058 (tpt) REVERT: B 1116 ARG cc_start: 0.8282 (mtp85) cc_final: 0.7872 (mtp85) REVERT: C 100 ASP cc_start: 0.8511 (t0) cc_final: 0.8308 (m-30) REVERT: C 179 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8337 (mm-40) REVERT: E 166 ARG cc_start: 0.7575 (mtt180) cc_final: 0.7155 (mmm160) REVERT: H 35 ASP cc_start: 0.5402 (p0) cc_final: 0.5123 (p0) REVERT: J 35 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8119 (pp) REVERT: J 48 MET cc_start: 0.8690 (mmm) cc_final: 0.8484 (tpp) REVERT: J 65 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7234 (pp) REVERT: K 36 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8246 (p) outliers start: 161 outliers final: 105 residues processed: 579 average time/residue: 0.1778 time to fit residues: 169.3633 Evaluate side-chains 537 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 427 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1525 THR Chi-restraints excluded: chain A residue 1528 PHE Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 198 optimal weight: 10.0000 chunk 339 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151771 restraints weight = 40246.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.139721 restraints weight = 73374.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.138581 restraints weight = 61667.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.137667 restraints weight = 53226.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137486 restraints weight = 47091.878| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30336 Z= 0.151 Angle : 0.707 20.895 40983 Z= 0.349 Chirality : 0.044 0.216 4577 Planarity : 0.005 0.086 5268 Dihedral : 6.011 55.573 4074 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.51 % Favored : 91.46 % Rotamer: Outliers : 4.73 % Allowed : 20.45 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.11 % Twisted Proline : 0.57 % Twisted General : 0.34 % 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: -2.26 (0.13), residues: 3688 helix: -0.05 (0.14), residues: 1248 sheet: -2.16 (0.21), residues: 528 loop : -2.36 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 13 TYR 0.040 0.001 TYR H 120 PHE 0.025 0.001 PHE A1638 TRP 0.011 0.001 TRP B 916 HIS 0.016 0.001 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00349 (30316) covalent geometry : angle 0.66943 (40960) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.15643 ( 2) hydrogen bonds : bond 0.04023 ( 1088) hydrogen bonds : angle 5.26436 ( 3078) metal coordination : bond 0.01304 ( 19) metal coordination : angle 10.08775 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 464 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 860 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: A 909 MET cc_start: 0.8047 (mmm) cc_final: 0.7545 (mmt) REVERT: A 1155 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7352 (mmtp) REVERT: A 1184 GLN cc_start: 0.8915 (tt0) cc_final: 0.8335 (tt0) REVERT: A 1557 ASN cc_start: 0.7249 (m110) cc_final: 0.6783 (p0) REVERT: A 1626 ILE cc_start: 0.8199 (mt) cc_final: 0.7904 (tt) REVERT: B 1 MET cc_start: 0.3082 (tpt) cc_final: 0.1581 (tpt) REVERT: B 152 GLU cc_start: 0.8121 (tt0) cc_final: 0.7841 (tt0) REVERT: B 240 ARG cc_start: 0.8168 (ttt180) cc_final: 0.7934 (ttt180) REVERT: B 254 MET cc_start: 0.8558 (tpp) cc_final: 0.8340 (ttm) REVERT: B 264 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 289 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7941 (mp) REVERT: B 943 MET cc_start: 0.8967 (mmt) cc_final: 0.8327 (mmt) REVERT: B 1024 MET cc_start: 0.6215 (ppp) cc_final: 0.4932 (tpt) REVERT: C 179 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8292 (mm-40) REVERT: G 108 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6412 (pt) REVERT: J 35 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7905 (pp) REVERT: J 65 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7270 (pp) REVERT: K 36 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8265 (p) REVERT: L 23 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8807 (mp) REVERT: L 53 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8150 (ttt-90) outliers start: 156 outliers final: 97 residues processed: 574 average time/residue: 0.1741 time to fit residues: 164.5846 Evaluate side-chains 530 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 425 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 897 ILE Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 329 optimal weight: 6.9990 chunk 351 optimal weight: 0.0570 chunk 148 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 330 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 364 ASN A 546 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154658 restraints weight = 40190.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152092 restraints weight = 73271.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150332 restraints weight = 87890.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149408 restraints weight = 77750.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.147961 restraints weight = 72638.515| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30336 Z= 0.131 Angle : 0.675 19.757 40983 Z= 0.333 Chirality : 0.043 0.248 4577 Planarity : 0.005 0.088 5268 Dihedral : 5.751 54.357 4074 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.60 % Favored : 91.38 % Rotamer: Outliers : 4.48 % Allowed : 21.78 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.25 % 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: -1.96 (0.13), residues: 3688 helix: 0.22 (0.15), residues: 1245 sheet: -2.02 (0.22), residues: 531 loop : -2.17 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 13 TYR 0.037 0.001 TYR H 120 PHE 0.020 0.001 PHE A1638 TRP 0.010 0.001 TRP C 37 HIS 0.007 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00302 (30316) covalent geometry : angle 0.64301 (40960) SS BOND : bond 0.01194 ( 1) SS BOND : angle 1.92284 ( 2) hydrogen bonds : bond 0.03728 ( 1088) hydrogen bonds : angle 5.03615 ( 3078) metal coordination : bond 0.01014 ( 19) metal coordination : angle 9.13824 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 469 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.7639 (mmm) cc_final: 0.7407 (mmt) REVERT: A 617 MET cc_start: 0.9140 (mtm) cc_final: 0.8926 (mtt) REVERT: A 691 VAL cc_start: 0.9235 (OUTLIER) cc_final: 0.8945 (t) REVERT: A 860 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: A 909 MET cc_start: 0.7892 (mmm) cc_final: 0.7289 (mmt) REVERT: A 1053 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: A 1155 LYS cc_start: 0.7547 (mmmt) cc_final: 0.7269 (mmtp) REVERT: A 1182 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7525 (ttt180) REVERT: A 1184 GLN cc_start: 0.8897 (tt0) cc_final: 0.8368 (tt0) REVERT: A 1557 ASN cc_start: 0.7090 (m110) cc_final: 0.6761 (p0) REVERT: A 1626 ILE cc_start: 0.8261 (mt) cc_final: 0.7943 (tt) REVERT: B 1 MET cc_start: 0.3019 (tpt) cc_final: 0.1730 (tpt) REVERT: B 80 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: B 254 MET cc_start: 0.8398 (tpp) cc_final: 0.8157 (ttm) REVERT: B 264 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7942 (t0) REVERT: B 289 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7179 (mp) REVERT: B 626 TYR cc_start: 0.8822 (m-80) cc_final: 0.8552 (m-80) REVERT: B 705 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7371 (tp-100) REVERT: B 714 PRO cc_start: 0.9192 (Cg_endo) cc_final: 0.8911 (Cg_exo) REVERT: B 747 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 943 MET cc_start: 0.8868 (mmt) cc_final: 0.8293 (mmt) REVERT: B 1024 MET cc_start: 0.6277 (ppp) cc_final: 0.4980 (tpt) REVERT: B 1169 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8013 (ptp) REVERT: C 80 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7277 (mp0) REVERT: C 129 GLN cc_start: 0.7870 (pm20) cc_final: 0.7652 (pm20) REVERT: C 179 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8141 (mm110) REVERT: C 221 GLN cc_start: 0.8038 (pt0) cc_final: 0.7805 (pt0) REVERT: J 35 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7837 (pp) REVERT: J 65 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7246 (pp) REVERT: K 36 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8267 (p) REVERT: L 23 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8679 (mp) outliers start: 148 outliers final: 97 residues processed: 576 average time/residue: 0.1806 time to fit residues: 170.9795 Evaluate side-chains 553 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 443 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1182 ARG Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1480 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 23 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 306 optimal weight: 6.9990 chunk 351 optimal weight: 0.5980 chunk 171 optimal weight: 8.9990 chunk 148 optimal weight: 0.0970 chunk 174 optimal weight: 8.9990 chunk 245 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 364 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN ** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 709 GLN ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151814 restraints weight = 40205.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139496 restraints weight = 74982.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137959 restraints weight = 58654.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.136749 restraints weight = 69650.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137166 restraints weight = 51080.702| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30336 Z= 0.173 Angle : 0.697 20.347 40983 Z= 0.346 Chirality : 0.044 0.207 4577 Planarity : 0.005 0.087 5268 Dihedral : 5.770 53.953 4074 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.44 % Favored : 90.54 % Rotamer: Outliers : 5.30 % Allowed : 21.84 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.90 (0.13), residues: 3688 helix: 0.26 (0.15), residues: 1253 sheet: -1.95 (0.21), residues: 545 loop : -2.15 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 13 TYR 0.038 0.002 TYR H 120 PHE 0.024 0.001 PHE A 786 TRP 0.011 0.001 TRP E 15 HIS 0.009 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00409 (30316) covalent geometry : angle 0.66580 (40960) SS BOND : bond 0.00275 ( 1) SS BOND : angle 2.01106 ( 2) hydrogen bonds : bond 0.03895 ( 1088) hydrogen bonds : angle 5.04134 ( 3078) metal coordination : bond 0.00939 ( 19) metal coordination : angle 9.10894 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 464 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: A 334 ARG cc_start: 0.6817 (ttm110) cc_final: 0.6518 (ptm160) REVERT: A 602 MET cc_start: 0.7837 (mmt) cc_final: 0.7604 (mmt) REVERT: A 662 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: A 691 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8830 (t) REVERT: A 860 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: A 909 MET cc_start: 0.7986 (mmm) cc_final: 0.7347 (mmt) REVERT: A 1053 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8619 (m-30) REVERT: A 1155 LYS cc_start: 0.7616 (mmmt) cc_final: 0.7334 (mmtp) REVERT: A 1184 GLN cc_start: 0.8898 (tt0) cc_final: 0.8387 (tt0) REVERT: A 1557 ASN cc_start: 0.7395 (m110) cc_final: 0.6950 (p0) REVERT: A 1626 ILE cc_start: 0.8331 (mt) cc_final: 0.8040 (tt) REVERT: B 1 MET cc_start: 0.3336 (tpt) cc_final: 0.1854 (tpt) REVERT: B 80 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: B 249 LEU cc_start: 0.8259 (mm) cc_final: 0.7987 (mm) REVERT: B 264 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 289 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7535 (mp) REVERT: B 346 PHE cc_start: 0.9079 (t80) cc_final: 0.8775 (t80) REVERT: B 626 TYR cc_start: 0.8880 (m-80) cc_final: 0.8603 (m-80) REVERT: B 688 MET cc_start: 0.8051 (mtm) cc_final: 0.7829 (mpp) REVERT: B 705 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7382 (tp-100) REVERT: B 747 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8955 (mm) REVERT: B 943 MET cc_start: 0.8990 (mmt) cc_final: 0.8304 (mmt) REVERT: B 1024 MET cc_start: 0.6384 (ppp) cc_final: 0.5031 (tpt) REVERT: B 1169 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8115 (ptp) REVERT: C 80 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7444 (mp0) REVERT: C 129 GLN cc_start: 0.7988 (pm20) cc_final: 0.7585 (pm20) REVERT: C 179 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8029 (mm110) REVERT: E 166 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7057 (mmm160) REVERT: G 167 GLN cc_start: 0.0387 (OUTLIER) cc_final: 0.0156 (mp10) REVERT: J 35 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7907 (pp) REVERT: K 36 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8285 (p) REVERT: L 21 ILE cc_start: 0.8900 (mm) cc_final: 0.8685 (mt) outliers start: 175 outliers final: 112 residues processed: 595 average time/residue: 0.1823 time to fit residues: 177.7157 Evaluate side-chains 557 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 432 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1063 TYR Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 300 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1476 ASN A1486 ASN ** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS ** B 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN H 43 ASN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150204 restraints weight = 40239.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137882 restraints weight = 75729.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.134435 restraints weight = 65195.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.133434 restraints weight = 76429.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.134164 restraints weight = 54964.894| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30336 Z= 0.199 Angle : 0.722 23.089 40983 Z= 0.358 Chirality : 0.045 0.215 4577 Planarity : 0.005 0.088 5268 Dihedral : 5.852 53.677 4074 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.95 % Favored : 90.02 % Rotamer: Outliers : 4.88 % Allowed : 23.11 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.87 (0.13), residues: 3688 helix: 0.25 (0.15), residues: 1253 sheet: -1.92 (0.22), residues: 517 loop : -2.11 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 13 TYR 0.037 0.002 TYR H 120 PHE 0.026 0.002 PHE A 786 TRP 0.009 0.001 TRP I 24 HIS 0.011 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00474 (30316) covalent geometry : angle 0.68895 (40960) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.74903 ( 2) hydrogen bonds : bond 0.04042 ( 1088) hydrogen bonds : angle 5.07998 ( 3078) metal coordination : bond 0.00951 ( 19) metal coordination : angle 9.54565 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 444 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: A 334 ARG cc_start: 0.6881 (ttm110) cc_final: 0.6563 (ptm160) REVERT: A 602 MET cc_start: 0.7832 (mmt) cc_final: 0.7496 (mmt) REVERT: A 634 TYR cc_start: 0.8273 (m-80) cc_final: 0.7952 (m-10) REVERT: A 662 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8212 (pp20) REVERT: A 691 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8835 (t) REVERT: A 860 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: A 909 MET cc_start: 0.8059 (mmm) cc_final: 0.7414 (mmt) REVERT: A 1053 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8628 (m-30) REVERT: A 1155 LYS cc_start: 0.7651 (mmmt) cc_final: 0.7373 (mmtp) REVERT: A 1184 GLN cc_start: 0.8899 (tt0) cc_final: 0.8425 (tt0) REVERT: A 1277 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7484 (ttm110) REVERT: A 1300 ARG cc_start: 0.7421 (ttt180) cc_final: 0.7194 (ttt90) REVERT: A 1557 ASN cc_start: 0.7442 (m110) cc_final: 0.6977 (p0) REVERT: A 1626 ILE cc_start: 0.8372 (mt) cc_final: 0.8059 (tt) REVERT: B 1 MET cc_start: 0.3516 (tpt) cc_final: 0.2161 (tpt) REVERT: B 80 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: B 264 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 289 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7662 (mp) REVERT: B 346 PHE cc_start: 0.9128 (t80) cc_final: 0.8780 (t80) REVERT: B 626 TYR cc_start: 0.8914 (m-80) cc_final: 0.8643 (m-80) REVERT: B 688 MET cc_start: 0.8068 (mtm) cc_final: 0.7791 (mtm) REVERT: B 747 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9039 (mm) REVERT: B 943 MET cc_start: 0.9047 (mmt) cc_final: 0.8333 (mmt) REVERT: B 1024 MET cc_start: 0.6432 (ppp) cc_final: 0.5001 (tpt) REVERT: B 1169 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8187 (ptp) REVERT: E 20 GLN cc_start: 0.8436 (mt0) cc_final: 0.8162 (mt0) REVERT: E 195 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7297 (mpp80) REVERT: G 67 SER cc_start: 0.8398 (t) cc_final: 0.7333 (m) REVERT: G 167 GLN cc_start: 0.1127 (OUTLIER) cc_final: -0.1001 (tp40) REVERT: J 35 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7979 (pp) REVERT: K 36 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8294 (p) outliers start: 161 outliers final: 114 residues processed: 563 average time/residue: 0.1826 time to fit residues: 170.2466 Evaluate side-chains 551 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 422 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 79 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 812 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1063 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1277 ARG Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1504 LEU Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1598 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 167 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 69 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 359 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 309 optimal weight: 0.0980 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 311 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 590 ASN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.154867 restraints weight = 40246.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142816 restraints weight = 71964.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.141370 restraints weight = 58121.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139869 restraints weight = 61582.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140351 restraints weight = 48438.540| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30336 Z= 0.126 Angle : 0.674 18.548 40983 Z= 0.334 Chirality : 0.043 0.193 4577 Planarity : 0.004 0.087 5268 Dihedral : 5.604 53.142 4074 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.24 % Allowed : 23.90 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.20 % 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: -1.70 (0.14), residues: 3688 helix: 0.44 (0.15), residues: 1257 sheet: -1.86 (0.22), residues: 538 loop : -2.04 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 13 TYR 0.030 0.001 TYR A 896 PHE 0.017 0.001 PHE A1644 TRP 0.011 0.001 TRP B 916 HIS 0.026 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00289 (30316) covalent geometry : angle 0.64794 (40960) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.67383 ( 2) hydrogen bonds : bond 0.03558 ( 1088) hydrogen bonds : angle 4.88247 ( 3078) metal coordination : bond 0.00835 ( 19) metal coordination : angle 8.19958 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 462 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.5947 (t70) cc_final: 0.5611 (t-90) REVERT: A 334 ARG cc_start: 0.6856 (ttm110) cc_final: 0.6576 (ptm160) REVERT: A 479 MET cc_start: 0.7595 (mmm) cc_final: 0.7317 (mmt) REVERT: A 501 ASN cc_start: 0.8174 (m-40) cc_final: 0.7880 (m110) REVERT: A 602 MET cc_start: 0.7796 (mmt) cc_final: 0.7508 (mmt) REVERT: A 617 MET cc_start: 0.9181 (mtm) cc_final: 0.8959 (mtt) REVERT: A 634 TYR cc_start: 0.8146 (m-80) cc_final: 0.7858 (m-10) REVERT: A 670 ASP cc_start: 0.7602 (p0) cc_final: 0.7346 (p0) REVERT: A 692 MET cc_start: 0.8861 (mmm) cc_final: 0.8597 (mmm) REVERT: A 860 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: A 909 MET cc_start: 0.7951 (mmm) cc_final: 0.7366 (mmt) REVERT: A 1053 ASP cc_start: 0.8866 (t0) cc_final: 0.8609 (m-30) REVERT: A 1155 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7378 (mmtp) REVERT: A 1184 GLN cc_start: 0.8763 (tt0) cc_final: 0.8243 (tt0) REVERT: A 1284 LYS cc_start: 0.5520 (tptp) cc_final: 0.5071 (mptt) REVERT: A 1300 ARG cc_start: 0.7430 (ttt180) cc_final: 0.7211 (ttt90) REVERT: A 1480 LEU cc_start: 0.7451 (tt) cc_final: 0.7064 (mm) REVERT: A 1489 TRP cc_start: 0.7917 (p-90) cc_final: 0.7693 (p-90) REVERT: A 1557 ASN cc_start: 0.7383 (m110) cc_final: 0.7016 (p0) REVERT: A 1626 ILE cc_start: 0.8482 (mt) cc_final: 0.8143 (tt) REVERT: B 1 MET cc_start: 0.3540 (tpt) cc_final: 0.2169 (tpt) REVERT: B 80 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6995 (m-30) REVERT: B 264 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8026 (t0) REVERT: B 289 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7435 (mp) REVERT: B 346 PHE cc_start: 0.9051 (t80) cc_final: 0.8676 (t80) REVERT: B 626 TYR cc_start: 0.8800 (m-80) cc_final: 0.8512 (m-80) REVERT: B 688 MET cc_start: 0.8160 (mtm) cc_final: 0.7916 (mtm) REVERT: B 705 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7019 (tp-100) REVERT: B 709 GLN cc_start: 0.7464 (mt0) cc_final: 0.7189 (mt0) REVERT: B 747 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8961 (mm) REVERT: B 820 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6034 (mtm110) REVERT: B 943 MET cc_start: 0.8886 (mmt) cc_final: 0.8163 (mmt) REVERT: B 998 MET cc_start: 0.8993 (mtp) cc_final: 0.8777 (mtp) REVERT: B 1024 MET cc_start: 0.6467 (ppp) cc_final: 0.5089 (tpt) REVERT: B 1055 ARG cc_start: 0.7856 (tpt90) cc_final: 0.7645 (tpt90) REVERT: B 1169 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8108 (ptp) REVERT: J 35 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7890 (pp) REVERT: K 34 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.7919 (p) REVERT: K 36 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8255 (p) outliers start: 140 outliers final: 100 residues processed: 564 average time/residue: 0.1870 time to fit residues: 171.3174 Evaluate side-chains 536 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 426 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1063 TYR Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1601 ASP Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 870 GLU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 248 optimal weight: 8.9990 chunk 366 optimal weight: 30.0000 chunk 7 optimal weight: 0.0770 chunk 167 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A1643 HIS B 475 HIS B 887 HIS C 94 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN G 167 GLN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.155211 restraints weight = 40050.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142986 restraints weight = 75159.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139465 restraints weight = 66329.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.138901 restraints weight = 83875.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.139308 restraints weight = 62971.440| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30336 Z= 0.136 Angle : 0.685 19.053 40983 Z= 0.338 Chirality : 0.044 0.221 4577 Planarity : 0.005 0.087 5268 Dihedral : 5.533 52.787 4074 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.18 % Allowed : 24.14 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.17 % 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: -1.63 (0.14), residues: 3688 helix: 0.50 (0.15), residues: 1257 sheet: -1.78 (0.22), residues: 543 loop : -2.00 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 13 TYR 0.031 0.001 TYR A 896 PHE 0.019 0.001 PHE G 69 TRP 0.008 0.001 TRP B 916 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00318 (30316) covalent geometry : angle 0.65633 (40960) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.55894 ( 2) hydrogen bonds : bond 0.03576 ( 1088) hydrogen bonds : angle 4.83060 ( 3078) metal coordination : bond 0.00838 ( 19) metal coordination : angle 8.62926 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 435 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.5946 (t70) cc_final: 0.5585 (t-90) REVERT: A 334 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6560 (ptm160) REVERT: A 479 MET cc_start: 0.7599 (mmm) cc_final: 0.7360 (mmt) REVERT: A 501 ASN cc_start: 0.8252 (m-40) cc_final: 0.7961 (m110) REVERT: A 602 MET cc_start: 0.7776 (mmt) cc_final: 0.7455 (mmt) REVERT: A 617 MET cc_start: 0.9190 (mtm) cc_final: 0.8934 (mtt) REVERT: A 634 TYR cc_start: 0.8230 (m-80) cc_final: 0.7974 (m-10) REVERT: A 670 ASP cc_start: 0.7505 (p0) cc_final: 0.7238 (p0) REVERT: A 691 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8776 (t) REVERT: A 860 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6682 (mp10) REVERT: A 1053 ASP cc_start: 0.8849 (t0) cc_final: 0.8580 (m-30) REVERT: A 1155 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7389 (mmtp) REVERT: A 1184 GLN cc_start: 0.8767 (tt0) cc_final: 0.8259 (tt0) REVERT: A 1236 MET cc_start: 0.6786 (ttp) cc_final: 0.6450 (ptm) REVERT: A 1284 LYS cc_start: 0.5541 (tptp) cc_final: 0.5098 (mptt) REVERT: A 1557 ASN cc_start: 0.7396 (m110) cc_final: 0.7010 (p0) REVERT: B 1 MET cc_start: 0.3800 (tpt) cc_final: 0.2426 (tpt) REVERT: B 264 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 289 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7477 (mp) REVERT: B 329 PHE cc_start: 0.7967 (t80) cc_final: 0.7661 (t80) REVERT: B 346 PHE cc_start: 0.9063 (t80) cc_final: 0.8688 (t80) REVERT: B 626 TYR cc_start: 0.8798 (m-80) cc_final: 0.8547 (m-80) REVERT: B 657 MET cc_start: 0.7247 (mtt) cc_final: 0.6932 (mtt) REVERT: B 688 MET cc_start: 0.8109 (mtm) cc_final: 0.7850 (mtm) REVERT: B 705 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7434 (tp-100) REVERT: B 747 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8995 (mm) REVERT: B 820 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6128 (mtm110) REVERT: B 943 MET cc_start: 0.8889 (mmt) cc_final: 0.8124 (mmt) REVERT: B 998 MET cc_start: 0.8905 (mtp) cc_final: 0.8622 (mtp) REVERT: B 1024 MET cc_start: 0.6463 (ppp) cc_final: 0.5041 (tpt) REVERT: B 1042 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7131 (ttp-110) REVERT: B 1055 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7633 (tpt90) REVERT: B 1169 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8172 (ptp) REVERT: J 35 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7931 (pp) REVERT: L 47 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7107 (mtm-85) outliers start: 138 outliers final: 111 residues processed: 542 average time/residue: 0.1853 time to fit residues: 164.8262 Evaluate side-chains 541 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 422 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 637 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1063 TYR Chi-restraints excluded: chain A residue 1069 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1282 THR Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 802 ARG Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 CYS Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 26 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 0.0370 chunk 273 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 329 optimal weight: 8.9990 chunk 166 optimal weight: 0.0040 chunk 196 optimal weight: 10.0000 overall best weight: 0.9674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A1643 HIS B 147 ASN B 475 HIS B 887 HIS ** B1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156647 restraints weight = 40046.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.144399 restraints weight = 73326.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.140922 restraints weight = 59143.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140155 restraints weight = 76420.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.140726 restraints weight = 60647.231| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30336 Z= 0.121 Angle : 0.678 26.326 40983 Z= 0.333 Chirality : 0.043 0.215 4577 Planarity : 0.005 0.087 5268 Dihedral : 5.473 52.792 4074 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.45 % Allowed : 24.96 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.17 % 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: -1.56 (0.14), residues: 3688 helix: 0.55 (0.15), residues: 1262 sheet: -1.74 (0.22), residues: 540 loop : -1.97 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 13 TYR 0.029 0.001 TYR A 896 PHE 0.017 0.001 PHE A 247 TRP 0.037 0.001 TRP A1489 HIS 0.011 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00278 (30316) covalent geometry : angle 0.64691 (40960) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.50666 ( 2) hydrogen bonds : bond 0.03434 ( 1088) hydrogen bonds : angle 4.77940 ( 3078) metal coordination : bond 0.00736 ( 19) metal coordination : angle 9.02567 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 453 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.5965 (t70) cc_final: 0.5586 (t-90) REVERT: A 334 ARG cc_start: 0.6844 (ttm110) cc_final: 0.6525 (ptm160) REVERT: A 479 MET cc_start: 0.7626 (mmm) cc_final: 0.7341 (mmt) REVERT: A 501 ASN cc_start: 0.8181 (m-40) cc_final: 0.7878 (m110) REVERT: A 617 MET cc_start: 0.9171 (mtm) cc_final: 0.8938 (mtt) REVERT: A 634 TYR cc_start: 0.8063 (m-80) cc_final: 0.7853 (m-10) REVERT: A 670 ASP cc_start: 0.7592 (p0) cc_final: 0.7306 (p0) REVERT: A 691 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8762 (t) REVERT: A 860 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 1053 ASP cc_start: 0.8839 (t0) cc_final: 0.8593 (m-30) REVERT: A 1155 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7384 (mmtp) REVERT: A 1184 GLN cc_start: 0.8755 (tt0) cc_final: 0.8255 (tt0) REVERT: A 1236 MET cc_start: 0.6751 (ttp) cc_final: 0.6417 (ptm) REVERT: A 1248 THR cc_start: 0.8613 (m) cc_final: 0.8213 (p) REVERT: A 1284 LYS cc_start: 0.5438 (tptp) cc_final: 0.5047 (mptt) REVERT: A 1557 ASN cc_start: 0.7383 (m110) cc_final: 0.6985 (p0) REVERT: B 1 MET cc_start: 0.3698 (tpt) cc_final: 0.2456 (tpt) REVERT: B 24 ASP cc_start: 0.8063 (m-30) cc_final: 0.7858 (m-30) REVERT: B 134 MET cc_start: 0.8303 (mtm) cc_final: 0.7850 (mtp) REVERT: B 143 MET cc_start: 0.9012 (tpp) cc_final: 0.8728 (tpp) REVERT: B 264 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8087 (t0) REVERT: B 289 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7511 (mp) REVERT: B 329 PHE cc_start: 0.7947 (t80) cc_final: 0.7668 (t80) REVERT: B 346 PHE cc_start: 0.9031 (t80) cc_final: 0.8623 (t80) REVERT: B 626 TYR cc_start: 0.8758 (m-80) cc_final: 0.8454 (m-80) REVERT: B 657 MET cc_start: 0.7263 (mtt) cc_final: 0.6795 (mtt) REVERT: B 688 MET cc_start: 0.8145 (mtm) cc_final: 0.7861 (mtm) REVERT: B 705 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7428 (tp-100) REVERT: B 747 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 820 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6105 (mtm110) REVERT: B 943 MET cc_start: 0.8797 (mmt) cc_final: 0.8056 (mmt) REVERT: B 1024 MET cc_start: 0.6495 (ppp) cc_final: 0.5062 (tpt) REVERT: B 1042 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.7120 (ttp-110) REVERT: B 1055 ARG cc_start: 0.7847 (tpt90) cc_final: 0.7596 (tpt90) REVERT: B 1169 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8138 (ptp) REVERT: J 35 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7920 (pp) REVERT: L 47 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7161 (mtm-85) outliers start: 114 outliers final: 94 residues processed: 540 average time/residue: 0.1860 time to fit residues: 163.8956 Evaluate side-chains 527 residues out of total 3301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 425 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 515 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 964 GLU Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1063 TYR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1131 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 VAL Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1566 THR Chi-restraints excluded: chain A residue 1575 ILE Chi-restraints excluded: chain A residue 1605 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 608 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 752 ASN Chi-restraints excluded: chain B residue 806 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 820 ARG Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 842 ASP Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 THR Chi-restraints excluded: chain B residue 1033 THR Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1095 ILE Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1172 GLU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 319 optimal weight: 8.9990 chunk 313 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN A 364 ASN ** A1629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 HIS B 147 ASN B 402 GLN B 887 HIS C 94 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 GLN ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151639 restraints weight = 38661.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.143952 restraints weight = 65549.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141258 restraints weight = 56133.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141228 restraints weight = 53209.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.141510 restraints weight = 46512.810| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30336 Z= 0.132 Angle : 0.681 24.222 40983 Z= 0.335 Chirality : 0.044 0.204 4577 Planarity : 0.005 0.088 5268 Dihedral : 5.429 53.502 4074 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.70 % Allowed : 25.02 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.14 % Twisted Proline : 0.57 % Twisted General : 0.17 % 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: -1.54 (0.14), residues: 3688 helix: 0.55 (0.15), residues: 1271 sheet: -1.71 (0.22), residues: 531 loop : -1.97 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 13 TYR 0.030 0.001 TYR A 896 PHE 0.018 0.001 PHE G 69 TRP 0.020 0.001 TRP A1489 HIS 0.009 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00308 (30316) covalent geometry : angle 0.65092 (40960) SS BOND : bond 0.00224 ( 1) SS BOND : angle 1.46067 ( 2) hydrogen bonds : bond 0.03461 ( 1088) hydrogen bonds : angle 4.75925 ( 3078) metal coordination : bond 0.00779 ( 19) metal coordination : angle 8.78352 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.83 seconds wall clock time: 87 minutes 0.63 seconds (5220.63 seconds total)