Starting phenix.real_space_refine on Mon Aug 25 22:12:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lmx_4088/08_2025/5lmx_4088.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 163 5.16 5 C 19712 2.51 5 N 5369 2.21 5 O 5868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31118 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 11207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11207 Classifications: {'peptide': 1420} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 5, 'PTRANS': 51, 'TRANS': 1363} Chain breaks: 12 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 8868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8868 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1058} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 133 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 706 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain breaks: 1 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 60} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 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 781 SG CYS A 102 81.235 143.935 102.211 1.00108.95 S ATOM 806 SG CYS A 105 81.956 144.524 105.827 1.00111.29 S ATOM 1605 SG CYS A 233 78.286 144.270 104.729 1.00112.17 S ATOM 1627 SG CYS A 236 80.825 147.328 103.737 1.00124.79 S ATOM 461 SG CYS A 62 112.034 102.890 105.075 1.00 94.92 S ATOM 480 SG CYS A 65 111.434 101.104 108.305 1.00 92.34 S ATOM 535 SG CYS A 72 109.280 100.351 105.593 1.00 92.92 S ATOM 19430 SG CYS B1104 103.375 109.213 119.291 1.00 81.64 S ATOM 19456 SG CYS B1107 101.709 110.626 116.529 1.00 88.74 S ATOM 19603 SG CYS B1128 105.249 109.693 116.137 1.00 84.61 S ATOM 19631 SG CYS B1131 104.195 112.665 118.462 1.00 88.47 S ATOM 27071 SG CYS I 13 40.531 119.968 38.049 1.00161.37 S ATOM 27191 SG CYS I 30 40.899 123.141 39.973 1.00194.69 S ATOM 27512 SG CYS J 7 72.653 36.641 87.226 1.00101.98 S ATOM 27535 SG CYS J 10 72.877 33.590 89.973 1.00 97.69 S ATOM 27815 SG CYS J 45 69.437 35.580 88.821 1.00101.16 S ATOM 27821 SG CYS J 46 71.420 33.107 86.927 1.00101.59 S ATOM 28889 SG CYS L 34 100.743 55.036 56.624 1.00127.07 S ATOM 28993 SG CYS L 48 103.667 57.086 57.459 1.00139.22 S Time building chain proxies: 6.36, per 1000 atoms: 0.20 Number of scatterers: 31118 At special positions: 0 Unit cell: (138.06, 169.92, 166.38, 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 163 16.00 O 5868 8.00 N 5369 7.00 C 19712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 21 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7382 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 45 sheets defined 38.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.706A pdb=" N SER A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.647A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.663A pdb=" N ARG A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.667A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.100A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 416 through 439 Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.521A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.508A pdb=" N THR A 570 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.590A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.781A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.813A pdb=" N ALA A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.772A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 849 through 862 removed outlier: 3.666A pdb=" N THR A 853 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.548A pdb=" N ILE A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.585A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1006 removed outlier: 3.872A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 removed outlier: 3.677A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.564A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.661A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1162 through 1176 removed outlier: 3.606A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1298 through 1306 Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.526A pdb=" N VAL A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1338 Processing helix chain 'A' and resid 1441 through 1452 Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.717A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.609A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.988A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.673A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.924A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1629 Processing helix chain 'A' and resid 1636 through 1644 Processing helix chain 'A' and resid 1649 through 1653 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 35 through 42 removed outlier: 4.007A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 55 through 58 removed outlier: 3.689A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.643A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.545A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.718A pdb=" N LEU B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.553A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.529A pdb=" N MET B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.794A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 4.094A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.840A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.694A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 4.006A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.524A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.571A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.539A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.805A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1136 through 1138 No H-bonds generated for 'chain 'B' and resid 1136 through 1138' Processing helix chain 'B' and resid 1180 through 1192 Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.641A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.560A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.903A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 309 through 330 removed outlier: 3.502A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.541A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.653A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.591A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.643A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.621A pdb=" N SER E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.519A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.559A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.666A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.940A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 132' Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.951A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 4.050A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.979A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 6.317A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.162A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 480 through 486 removed outlier: 5.863A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 510 removed outlier: 3.707A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'A' and resid 749 through 752 removed outlier: 3.657A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AA9, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.799A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id=AB2, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 3.694A pdb=" N ARG A1499 " --> pdb=" O VAL A1261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.481A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.691A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.793A pdb=" N ASP B 111 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 117 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB7, first strand: chain 'B' and resid 205 through 206 removed outlier: 6.445A pdb=" N MET B 205 " --> pdb=" O HIS B 504 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.775A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 550 through 551 removed outlier: 4.362A pdb=" N ARG B 550 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 650 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 removed outlier: 4.362A pdb=" N ARG B 550 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 650 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 571 through 572 removed outlier: 7.046A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.813A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.813A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AC6, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 7.718A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.555A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AC9, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD1, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD2, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD3, first strand: chain 'C' and resid 41 through 47 removed outlier: 5.540A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.359A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AD6, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.768A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD8, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AD9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.902A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.902A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.366A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.519A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 133 through 137 Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.521A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'N' and resid 69 through 71 removed outlier: 6.765A pdb=" N ILE M 88 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.986A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) 1314 hydrogen bonds defined for protein. 3660 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: 7.54 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7997 1.35 - 1.47: 8849 1.47 - 1.59: 14599 1.59 - 1.72: 10 1.72 - 1.84: 257 Bond restraints: 31712 Sorted by residual: bond pdb=" CA PRO C 252 " pdb=" C PRO C 252 " ideal model delta sigma weight residual 1.514 1.544 -0.030 5.50e-03 3.31e+04 3.00e+01 bond pdb=" N PRO A1181 " pdb=" CD PRO A1181 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.89e+01 bond pdb=" N PRO B 693 " pdb=" CD PRO B 693 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" N PRO A 508 " pdb=" CD PRO A 508 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.56e+01 bond pdb=" N PRO C 221 " pdb=" CD PRO C 221 " ideal model delta sigma weight residual 1.473 1.544 -0.071 1.40e-02 5.10e+03 2.56e+01 ... (remaining 31707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 40282 3.23 - 6.45: 2451 6.45 - 9.68: 92 9.68 - 12.90: 1 12.90 - 16.13: 9 Bond angle restraints: 42835 Sorted by residual: angle pdb=" N ILE A 670 " pdb=" CA ILE A 670 " pdb=" C ILE A 670 " ideal model delta sigma weight residual 111.56 118.13 -6.57 8.60e-01 1.35e+00 5.83e+01 angle pdb=" C GLY C 173 " pdb=" N ARG C 174 " pdb=" CA ARG C 174 " ideal model delta sigma weight residual 120.38 129.68 -9.30 1.37e+00 5.33e-01 4.61e+01 angle pdb=" C GLY A1218 " pdb=" N ILE A1219 " pdb=" CA ILE A1219 " ideal model delta sigma weight residual 120.24 124.42 -4.18 6.30e-01 2.52e+00 4.40e+01 angle pdb=" C THR C 151 " pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 120.51 129.40 -8.89 1.45e+00 4.76e-01 3.76e+01 angle pdb=" C ASN B1006 " pdb=" N TYR B1007 " pdb=" CA TYR B1007 " ideal model delta sigma weight residual 120.38 128.45 -8.07 1.37e+00 5.33e-01 3.47e+01 ... (remaining 42830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.37: 16765 18.37 - 36.75: 1743 36.75 - 55.12: 531 55.12 - 73.50: 221 73.50 - 91.87: 97 Dihedral angle restraints: 19357 sinusoidal: 7948 harmonic: 11409 Sorted by residual: dihedral pdb=" N VAL A1136 " pdb=" C VAL A1136 " pdb=" CA VAL A1136 " pdb=" CB VAL A1136 " ideal model delta harmonic sigma weight residual 123.40 114.56 8.84 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP B 369 " pdb=" CB ASP B 369 " pdb=" CG ASP B 369 " pdb=" OD1 ASP B 369 " ideal model delta sinusoidal sigma weight residual -30.00 -89.58 59.58 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" N VAL A 735 " pdb=" C VAL A 735 " pdb=" CA VAL A 735 " pdb=" CB VAL A 735 " ideal model delta harmonic sigma weight residual 123.40 132.00 -8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 19354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3794 0.077 - 0.155: 893 0.155 - 0.232: 94 0.232 - 0.310: 6 0.310 - 0.387: 1 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CG LEU C 120 " pdb=" CB LEU C 120 " pdb=" CD1 LEU C 120 " pdb=" CD2 LEU C 120 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA VAL A1136 " pdb=" N VAL A1136 " pdb=" C VAL A1136 " pdb=" CB VAL A1136 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB THR B1084 " pdb=" CA THR B1084 " pdb=" OG1 THR B1084 " pdb=" CG2 THR B1084 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4785 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 143 " 0.049 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP B 143 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B 143 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 143 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 143 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 143 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP B 143 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 143 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 143 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 143 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 832 " -0.039 2.00e-02 2.50e+03 1.97e-02 9.66e+00 pdb=" CG TRP B 832 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 832 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 832 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 832 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 832 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 832 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 832 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 832 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 832 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1032 " -0.042 2.00e-02 2.50e+03 2.16e-02 9.34e+00 pdb=" CG TYR B1032 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B1032 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B1032 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B1032 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1032 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B1032 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1032 " -0.020 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 0.61 - 1.47: 13 1.47 - 2.33: 113 2.33 - 3.19: 23407 3.19 - 4.04: 80708 4.04 - 4.90: 139965 Warning: very small nonbonded interaction distances. Nonbonded interactions: 244206 Sorted by model distance: nonbonded pdb=" OH TYR A 50 " pdb=" ND2 ASN A 383 " model vdw 0.614 3.120 nonbonded pdb=" OG SER A 988 " pdb=" CD GLU B 988 " model vdw 0.918 3.270 nonbonded pdb=" O LEU A 369 " pdb=" ND2 ASN A 380 " model vdw 1.106 3.120 nonbonded pdb=" O ALA A1658 " pdb=" O ILE G 105 " model vdw 1.255 3.040 nonbonded pdb=" CB SER A 988 " pdb=" CG GLU B 988 " model vdw 1.278 3.840 ... (remaining 244201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 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 : 0.012 0.792 31734 Z= 0.768 Angle : 1.556 21.383 42856 Z= 1.056 Chirality : 0.063 0.387 4788 Planarity : 0.006 0.041 5530 Dihedral : 18.691 91.872 11975 Min Nonbonded Distance : 0.614 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.51 % Favored : 92.86 % Rotamer: Outliers : 8.43 % Allowed : 10.57 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.11), residues: 3838 helix: -1.72 (0.11), residues: 1288 sheet: -1.45 (0.19), residues: 578 loop : -1.90 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1091 TYR 0.043 0.006 TYR A1174 PHE 0.034 0.005 PHE B 262 TRP 0.065 0.007 TRP B 143 HIS 0.017 0.003 HIS B 646 Details of bonding type rmsd covalent geometry : bond 0.01108 (31712) covalent geometry : angle 1.54800 (42835) hydrogen bonds : bond 0.24079 ( 1280) hydrogen bonds : angle 8.84958 ( 3660) metal coordination : bond 0.20964 ( 20) metal coordination : angle 7.16354 ( 21) Misc. bond : bond 0.22565 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 908 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.6397 (m-80) cc_final: 0.5945 (m-80) REVERT: A 324 LEU cc_start: 0.9334 (mt) cc_final: 0.8933 (mt) REVERT: A 398 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: A 469 LYS cc_start: 0.8467 (tttt) cc_final: 0.7919 (tppt) REVERT: A 587 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 588 LEU cc_start: 0.8757 (mt) cc_final: 0.8262 (tt) REVERT: A 596 HIS cc_start: 0.7236 (p-80) cc_final: 0.6513 (m90) REVERT: A 743 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.6691 (p0) REVERT: A 776 LEU cc_start: 0.9210 (tp) cc_final: 0.8918 (tp) REVERT: A 786 TYR cc_start: 0.6522 (p90) cc_final: 0.6271 (p90) REVERT: A 794 VAL cc_start: 0.9409 (t) cc_final: 0.9202 (p) REVERT: A 810 LEU cc_start: 0.9545 (mt) cc_final: 0.9308 (tp) REVERT: A 817 PHE cc_start: 0.8580 (m-80) cc_final: 0.8219 (m-80) REVERT: A 977 MET cc_start: 0.9104 (ttt) cc_final: 0.8808 (tpp) REVERT: A 981 TYR cc_start: 0.7866 (t80) cc_final: 0.7384 (t80) REVERT: A 1027 LEU cc_start: 0.9128 (mt) cc_final: 0.8691 (mt) REVERT: A 1056 ASP cc_start: 0.9062 (t0) cc_final: 0.8619 (t0) REVERT: A 1133 LEU cc_start: 0.7885 (tp) cc_final: 0.7624 (tp) REVERT: A 1136 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7331 (m) REVERT: A 1169 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9217 (mm) REVERT: A 1170 MET cc_start: 0.8987 (mmm) cc_final: 0.8377 (mmm) REVERT: A 1177 SER cc_start: 0.9493 (m) cc_final: 0.9196 (p) REVERT: A 1226 VAL cc_start: 0.9072 (t) cc_final: 0.8778 (t) REVERT: A 1238 MET cc_start: 0.7857 (mtm) cc_final: 0.7429 (mtp) REVERT: A 1313 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9097 (mt) REVERT: A 1321 PHE cc_start: 0.9057 (t80) cc_final: 0.8679 (t80) REVERT: A 1562 ILE cc_start: 0.9421 (mt) cc_final: 0.9171 (mt) REVERT: A 1629 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8475 (m110) REVERT: B 215 MET cc_start: 0.7926 (mtp) cc_final: 0.7394 (mmm) REVERT: B 250 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8750 (tp) REVERT: B 277 LEU cc_start: 0.8159 (mt) cc_final: 0.7839 (mt) REVERT: B 302 LEU cc_start: 0.9174 (mp) cc_final: 0.8784 (mt) REVERT: B 306 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8619 (mp) REVERT: B 374 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9157 (mt) REVERT: B 377 MET cc_start: 0.9234 (mtp) cc_final: 0.8287 (mtp) REVERT: B 381 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8161 (tp) REVERT: B 403 LEU cc_start: 0.8917 (tp) cc_final: 0.8431 (tt) REVERT: B 412 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 461 MET cc_start: 0.8628 (mmm) cc_final: 0.8371 (mmm) REVERT: B 485 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6502 (p) REVERT: B 496 PHE cc_start: 0.8678 (t80) cc_final: 0.8287 (t80) REVERT: B 502 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7553 (ptm) REVERT: B 519 LYS cc_start: 0.1081 (OUTLIER) cc_final: -0.0745 (tmtt) REVERT: B 545 PHE cc_start: 0.7440 (m-80) cc_final: 0.6749 (m-80) REVERT: B 592 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9159 (tt) REVERT: B 640 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 687 THR cc_start: 0.7842 (p) cc_final: 0.7372 (p) REVERT: B 692 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.7938 (p) REVERT: B 859 CYS cc_start: 0.5770 (OUTLIER) cc_final: 0.5305 (p) REVERT: B 887 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6060 (pt) REVERT: B 935 ASP cc_start: 0.8931 (m-30) cc_final: 0.8653 (t70) REVERT: B 965 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: B 1000 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7402 (mp) REVERT: B 1018 THR cc_start: 0.7179 (p) cc_final: 0.6885 (p) REVERT: B 1030 VAL cc_start: 0.8176 (t) cc_final: 0.7937 (t) REVERT: B 1085 SER cc_start: 0.8658 (m) cc_final: 0.7501 (p) REVERT: B 1180 PHE cc_start: 0.7331 (t80) cc_final: 0.6165 (t80) REVERT: C 67 PHE cc_start: 0.8272 (m-10) cc_final: 0.7955 (m-10) REVERT: C 83 VAL cc_start: 0.9030 (t) cc_final: 0.8782 (t) REVERT: C 136 LEU cc_start: 0.9384 (tp) cc_final: 0.9160 (mm) REVERT: C 193 LEU cc_start: 0.9403 (mt) cc_final: 0.8993 (mt) REVERT: C 216 HIS cc_start: 0.6819 (t70) cc_final: 0.5880 (t70) REVERT: C 220 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7336 (t) REVERT: C 229 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8259 (tp) REVERT: C 247 PHE cc_start: 0.8753 (t80) cc_final: 0.8134 (t80) REVERT: D 25 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8252 (p) REVERT: E 78 LEU cc_start: 0.9220 (tp) cc_final: 0.9004 (tp) REVERT: F 82 THR cc_start: 0.8785 (t) cc_final: 0.8580 (t) REVERT: F 84 TYR cc_start: 0.7119 (m-80) cc_final: 0.6409 (m-80) REVERT: F 94 LEU cc_start: 0.9679 (mt) cc_final: 0.9464 (pp) REVERT: F 153 VAL cc_start: 0.8356 (t) cc_final: 0.7682 (p) REVERT: G 43 ILE cc_start: 0.9027 (pt) cc_final: 0.8816 (tt) REVERT: G 66 LEU cc_start: 0.9021 (mt) cc_final: 0.8759 (mt) REVERT: H 42 ILE cc_start: 0.8185 (pp) cc_final: 0.7843 (pp) REVERT: H 43 ASN cc_start: 0.9008 (t0) cc_final: 0.8614 (t0) REVERT: H 55 LEU cc_start: 0.9311 (mt) cc_final: 0.9082 (mt) REVERT: H 95 TYR cc_start: 0.7593 (t80) cc_final: 0.7251 (t80) REVERT: I 26 SER cc_start: 0.7020 (t) cc_final: 0.6665 (p) REVERT: I 60 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8396 (tt) REVERT: J 48 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.8695 (ttp80) REVERT: J 56 LEU cc_start: 0.9349 (mt) cc_final: 0.8606 (tp) REVERT: J 60 PHE cc_start: 0.7028 (m-80) cc_final: 0.4863 (m-80) REVERT: K 86 VAL cc_start: 0.9337 (t) cc_final: 0.9110 (p) REVERT: K 121 LEU cc_start: 0.9254 (mt) cc_final: 0.8820 (mt) REVERT: K 130 VAL cc_start: 0.8999 (t) cc_final: 0.8720 (t) REVERT: K 135 PHE cc_start: 0.6465 (t80) cc_final: 0.5611 (t80) REVERT: L 40 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7984 (tp) REVERT: M 38 PHE cc_start: 0.9470 (m-80) cc_final: 0.9007 (m-80) REVERT: M 65 TYR cc_start: 0.8425 (p90) cc_final: 0.8172 (m-80) REVERT: N 173 THR cc_start: 0.3459 (p) cc_final: 0.3218 (p) outliers start: 292 outliers final: 41 residues processed: 1120 average time/residue: 0.1757 time to fit residues: 310.2205 Evaluate side-chains 609 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 540 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 260 GLN A 263 ASN A 332 GLN A 383 ASN A 435 ASN A 537 GLN A 580 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 738 ASN A 748 ASN A 753 ASN A 798 HIS A 840 ASN A1020 GLN A1047 GLN A1293 HIS A1314 GLN A1323 HIS ** A1599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 GLN B 43 GLN B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 HIS B 400 GLN B 427 GLN B 433 ASN B 575 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 HIS B 724 GLN B 735 HIS B 975 HIS B 987 ASN B 999 GLN B1008 HIS C 216 HIS C 323 ASN D 23 HIS ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 147 HIS E 179 GLN F 59 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 21 ASN J 64 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN K 118 GLN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.064093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048988 restraints weight = 232486.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.050286 restraints weight = 173552.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051294 restraints weight = 138061.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052094 restraints weight = 114782.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052732 restraints weight = 98556.486| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 31734 Z= 0.211 Angle : 0.769 19.279 42856 Z= 0.398 Chirality : 0.046 0.195 4788 Planarity : 0.005 0.072 5530 Dihedral : 4.660 71.079 4239 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.20 % Allowed : 3.72 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.13), residues: 3838 helix: 0.42 (0.14), residues: 1290 sheet: -1.07 (0.18), residues: 632 loop : -1.23 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 368 TYR 0.036 0.002 TYR H 93 PHE 0.034 0.002 PHE E 82 TRP 0.046 0.002 TRP B 143 HIS 0.014 0.002 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00466 (31712) covalent geometry : angle 0.75632 (42835) hydrogen bonds : bond 0.05283 ( 1280) hydrogen bonds : angle 6.09634 ( 3660) metal coordination : bond 0.00513 ( 20) metal coordination : angle 6.26358 ( 21) Misc. bond : bond 0.01174 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 607 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.9169 (m-80) cc_final: 0.8380 (m-80) REVERT: A 424 MET cc_start: 0.8860 (ttt) cc_final: 0.8613 (mmm) REVERT: A 469 LYS cc_start: 0.9218 (tttt) cc_final: 0.8964 (tppt) REVERT: A 509 GLU cc_start: 0.9383 (mm-30) cc_final: 0.8905 (mm-30) REVERT: A 578 TYR cc_start: 0.8933 (m-10) cc_final: 0.8588 (m-80) REVERT: A 614 LEU cc_start: 0.9493 (mt) cc_final: 0.9262 (mt) REVERT: A 624 TYR cc_start: 0.7971 (m-80) cc_final: 0.6010 (m-80) REVERT: A 633 MET cc_start: 0.9628 (mmp) cc_final: 0.8887 (mmp) REVERT: A 654 ASP cc_start: 0.9665 (t70) cc_final: 0.9382 (m-30) REVERT: A 669 LEU cc_start: 0.7766 (mt) cc_final: 0.6510 (mm) REVERT: A 687 PHE cc_start: 0.9505 (m-80) cc_final: 0.8859 (m-80) REVERT: A 760 TRP cc_start: 0.8361 (m100) cc_final: 0.8142 (m100) REVERT: A 821 ILE cc_start: 0.9562 (tp) cc_final: 0.9329 (mm) REVERT: A 977 MET cc_start: 0.9620 (ttt) cc_final: 0.8998 (tpp) REVERT: A 981 TYR cc_start: 0.9276 (t80) cc_final: 0.8980 (t80) REVERT: A 1027 LEU cc_start: 0.8904 (mt) cc_final: 0.8435 (mt) REVERT: A 1056 ASP cc_start: 0.7727 (t0) cc_final: 0.7493 (t0) REVERT: A 1133 LEU cc_start: 0.8989 (tp) cc_final: 0.8573 (tp) REVERT: A 1170 MET cc_start: 0.9722 (mmm) cc_final: 0.9294 (mmm) REVERT: A 1238 MET cc_start: 0.8435 (mtm) cc_final: 0.8229 (mtp) REVERT: A 1483 LEU cc_start: 0.8674 (tt) cc_final: 0.8153 (tt) REVERT: A 1556 GLU cc_start: 0.8767 (pm20) cc_final: 0.8459 (pp20) REVERT: A 1588 MET cc_start: 0.9554 (mmp) cc_final: 0.9086 (mmm) REVERT: A 1598 PHE cc_start: 0.9024 (m-80) cc_final: 0.8463 (m-80) REVERT: A 1603 MET cc_start: 0.8915 (ttp) cc_final: 0.8260 (ptt) REVERT: A 1621 PHE cc_start: 0.9182 (m-80) cc_final: 0.8953 (m-10) REVERT: B 205 MET cc_start: 0.8508 (mmt) cc_final: 0.7890 (mmt) REVERT: B 250 LEU cc_start: 0.9358 (mp) cc_final: 0.8638 (tp) REVERT: B 277 LEU cc_start: 0.8938 (mt) cc_final: 0.8536 (mt) REVERT: B 373 MET cc_start: 0.9770 (tpt) cc_final: 0.9012 (mmm) REVERT: B 374 LEU cc_start: 0.9689 (tt) cc_final: 0.9463 (pp) REVERT: B 378 ILE cc_start: 0.9900 (mt) cc_final: 0.9694 (mt) REVERT: B 402 VAL cc_start: 0.9605 (t) cc_final: 0.9385 (t) REVERT: B 457 ILE cc_start: 0.8670 (mm) cc_final: 0.8325 (mm) REVERT: B 496 PHE cc_start: 0.9514 (t80) cc_final: 0.9213 (t80) REVERT: B 532 HIS cc_start: 0.8178 (t-170) cc_final: 0.6549 (m90) REVERT: B 545 PHE cc_start: 0.9265 (m-80) cc_final: 0.8549 (m-80) REVERT: B 629 VAL cc_start: 0.9384 (t) cc_final: 0.8915 (t) REVERT: B 640 LEU cc_start: 0.9132 (tt) cc_final: 0.8692 (mt) REVERT: B 649 MET cc_start: 0.9169 (tpt) cc_final: 0.8532 (tpt) REVERT: B 663 ILE cc_start: 0.8379 (mp) cc_final: 0.7413 (tp) REVERT: B 785 ASP cc_start: 0.8589 (m-30) cc_final: 0.8360 (p0) REVERT: B 884 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8652 (tm-30) REVERT: B 927 CYS cc_start: 0.8827 (t) cc_final: 0.8216 (t) REVERT: B 930 LYS cc_start: 0.8145 (mttt) cc_final: 0.7772 (mmtt) REVERT: B 959 THR cc_start: 0.8867 (p) cc_final: 0.8520 (t) REVERT: B 965 GLU cc_start: 0.8672 (tt0) cc_final: 0.7653 (tm-30) REVERT: B 1005 TYR cc_start: 0.6733 (m-80) cc_final: 0.6357 (m-10) REVERT: B 1030 VAL cc_start: 0.9667 (t) cc_final: 0.9392 (t) REVERT: B 1176 VAL cc_start: 0.9020 (t) cc_final: 0.8802 (t) REVERT: B 1194 ILE cc_start: 0.8099 (mp) cc_final: 0.7864 (mp) REVERT: B 1198 TYR cc_start: 0.9587 (m-80) cc_final: 0.9358 (m-80) REVERT: C 63 ILE cc_start: 0.9352 (mp) cc_final: 0.8768 (mp) REVERT: C 67 PHE cc_start: 0.9355 (m-10) cc_final: 0.9049 (m-80) REVERT: C 92 ILE cc_start: 0.8524 (mp) cc_final: 0.7657 (mp) REVERT: C 94 ASP cc_start: 0.9176 (m-30) cc_final: 0.8866 (m-30) REVERT: C 193 LEU cc_start: 0.9821 (mt) cc_final: 0.9417 (mt) REVERT: C 247 PHE cc_start: 0.9428 (t80) cc_final: 0.8637 (t80) REVERT: E 135 PHE cc_start: 0.9312 (m-10) cc_final: 0.9064 (m-80) REVERT: E 168 TYR cc_start: 0.8501 (m-80) cc_final: 0.8175 (m-80) REVERT: E 215 MET cc_start: 0.9202 (mpp) cc_final: 0.8759 (mpp) REVERT: F 112 GLU cc_start: 0.8478 (pm20) cc_final: 0.8259 (mp0) REVERT: F 132 LEU cc_start: 0.9149 (mm) cc_final: 0.8773 (mm) REVERT: G 54 LEU cc_start: 0.8380 (pp) cc_final: 0.8071 (pp) REVERT: G 115 PHE cc_start: 0.8460 (m-80) cc_final: 0.8082 (m-80) REVERT: H 42 ILE cc_start: 0.9525 (pt) cc_final: 0.9059 (mp) REVERT: H 95 TYR cc_start: 0.8671 (t80) cc_final: 0.7898 (t80) REVERT: J 49 MET cc_start: 0.8806 (mmm) cc_final: 0.8486 (mmm) REVERT: K 57 ASP cc_start: 0.9197 (m-30) cc_final: 0.8948 (m-30) REVERT: K 87 GLU cc_start: 0.9278 (tt0) cc_final: 0.8191 (tm-30) REVERT: K 98 GLU cc_start: 0.9238 (mp0) cc_final: 0.9018 (mp0) REVERT: K 135 PHE cc_start: 0.9230 (t80) cc_final: 0.8638 (t80) REVERT: M 67 ASP cc_start: 0.8780 (t0) cc_final: 0.8520 (t0) REVERT: N 58 PHE cc_start: 0.9523 (m-80) cc_final: 0.8957 (m-80) REVERT: N 170 HIS cc_start: 0.9135 (t70) cc_final: 0.8881 (p-80) REVERT: N 173 THR cc_start: 0.3272 (p) cc_final: 0.2908 (p) outliers start: 7 outliers final: 2 residues processed: 610 average time/residue: 0.1668 time to fit residues: 164.5694 Evaluate side-chains 452 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 450 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 202 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 chunk 356 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 470 HIS A 560 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN A 673 HIS A 706 HIS A 880 GLN A1532 GLN B 45 HIS B 151 ASN B 197 ASN B 213 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 ASN B 480 GLN B 587 GLN B 683 ASN ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B 923 GLN D 23 HIS E 61 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 26 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 71 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.058704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.044696 restraints weight = 236751.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045871 restraints weight = 176638.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.046794 restraints weight = 139718.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047473 restraints weight = 115939.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048006 restraints weight = 100161.258| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 31734 Z= 0.190 Angle : 0.684 17.560 42856 Z= 0.354 Chirality : 0.044 0.235 4788 Planarity : 0.005 0.052 5530 Dihedral : 4.759 89.058 4239 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 3838 helix: 0.75 (0.14), residues: 1296 sheet: -0.82 (0.18), residues: 634 loop : -1.01 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 591 TYR 0.031 0.002 TYR H 95 PHE 0.031 0.002 PHE B 222 TRP 0.052 0.002 TRP B 143 HIS 0.007 0.002 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00427 (31712) covalent geometry : angle 0.67519 (42835) hydrogen bonds : bond 0.04401 ( 1280) hydrogen bonds : angle 5.58753 ( 3660) metal coordination : bond 0.00872 ( 20) metal coordination : angle 4.97872 ( 21) Misc. bond : bond 0.00842 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9139 (mp10) cc_final: 0.8851 (mp10) REVERT: A 108 PHE cc_start: 0.9128 (m-80) cc_final: 0.8365 (m-80) REVERT: A 424 MET cc_start: 0.8847 (ttt) cc_final: 0.8613 (mmm) REVERT: A 519 LEU cc_start: 0.9682 (mt) cc_final: 0.9218 (mt) REVERT: A 578 TYR cc_start: 0.9127 (m-10) cc_final: 0.8766 (m-80) REVERT: A 589 MET cc_start: 0.9674 (mmp) cc_final: 0.9436 (mmp) REVERT: A 624 TYR cc_start: 0.6991 (m-80) cc_final: 0.6370 (m-80) REVERT: A 633 MET cc_start: 0.9538 (mmp) cc_final: 0.9206 (mmp) REVERT: A 654 ASP cc_start: 0.9551 (t70) cc_final: 0.9315 (m-30) REVERT: A 687 PHE cc_start: 0.9537 (m-80) cc_final: 0.8860 (m-80) REVERT: A 744 MET cc_start: 0.7506 (mmt) cc_final: 0.7296 (mmm) REVERT: A 786 TYR cc_start: 0.9216 (p90) cc_final: 0.8951 (p90) REVERT: A 821 ILE cc_start: 0.9619 (tp) cc_final: 0.9362 (mm) REVERT: A 965 THR cc_start: 0.9171 (p) cc_final: 0.8755 (p) REVERT: A 977 MET cc_start: 0.9678 (ttt) cc_final: 0.9271 (tpt) REVERT: A 981 TYR cc_start: 0.9382 (t80) cc_final: 0.8935 (t80) REVERT: A 1027 LEU cc_start: 0.8831 (mt) cc_final: 0.8436 (mt) REVERT: A 1170 MET cc_start: 0.9647 (mmm) cc_final: 0.9127 (mmm) REVERT: A 1224 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8791 (mt-10) REVERT: A 1294 MET cc_start: 0.9449 (mmm) cc_final: 0.9113 (mmm) REVERT: A 1588 MET cc_start: 0.9585 (mmp) cc_final: 0.9348 (mmm) REVERT: A 1598 PHE cc_start: 0.9378 (m-80) cc_final: 0.8943 (m-80) REVERT: A 1603 MET cc_start: 0.9244 (ttp) cc_final: 0.8595 (ptm) REVERT: A 1621 PHE cc_start: 0.9093 (m-80) cc_final: 0.8711 (m-10) REVERT: B 108 MET cc_start: 0.8663 (mmt) cc_final: 0.8291 (mmm) REVERT: B 296 ASP cc_start: 0.8976 (m-30) cc_final: 0.8332 (p0) REVERT: B 388 GLU cc_start: 0.9047 (mp0) cc_final: 0.8818 (pm20) REVERT: B 457 ILE cc_start: 0.8996 (mm) cc_final: 0.8694 (mm) REVERT: B 496 PHE cc_start: 0.9532 (t80) cc_final: 0.9294 (t80) REVERT: B 502 MET cc_start: 0.9472 (ptm) cc_final: 0.9005 (ptp) REVERT: B 545 PHE cc_start: 0.9403 (m-80) cc_final: 0.8652 (m-80) REVERT: B 640 LEU cc_start: 0.9265 (tt) cc_final: 0.8515 (mt) REVERT: B 649 MET cc_start: 0.9166 (tpt) cc_final: 0.8449 (tpt) REVERT: B 663 ILE cc_start: 0.8741 (mp) cc_final: 0.7951 (tp) REVERT: B 721 MET cc_start: 0.9475 (mmp) cc_final: 0.9056 (mmp) REVERT: B 726 MET cc_start: 0.8892 (tpt) cc_final: 0.8531 (mmm) REVERT: B 760 TYR cc_start: 0.9209 (m-10) cc_final: 0.8957 (m-10) REVERT: B 785 ASP cc_start: 0.8668 (m-30) cc_final: 0.8336 (p0) REVERT: B 874 TYR cc_start: 0.9328 (t80) cc_final: 0.9128 (t80) REVERT: B 884 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8769 (tm-30) REVERT: B 927 CYS cc_start: 0.9412 (t) cc_final: 0.8644 (t) REVERT: B 930 LYS cc_start: 0.8255 (mttt) cc_final: 0.8021 (mmtt) REVERT: B 959 THR cc_start: 0.9409 (p) cc_final: 0.8905 (t) REVERT: B 963 PHE cc_start: 0.8878 (m-80) cc_final: 0.8431 (m-80) REVERT: B 965 GLU cc_start: 0.8681 (tt0) cc_final: 0.8449 (tm-30) REVERT: B 1030 VAL cc_start: 0.9832 (t) cc_final: 0.9576 (t) REVERT: B 1198 TYR cc_start: 0.9236 (m-80) cc_final: 0.8997 (m-80) REVERT: C 63 ILE cc_start: 0.9435 (mp) cc_final: 0.8703 (mp) REVERT: C 67 PHE cc_start: 0.9471 (m-10) cc_final: 0.9193 (m-80) REVERT: C 71 MET cc_start: 0.9212 (mtt) cc_final: 0.8834 (mmm) REVERT: C 94 ASP cc_start: 0.8856 (m-30) cc_final: 0.8480 (m-30) REVERT: C 193 LEU cc_start: 0.9882 (mt) cc_final: 0.9613 (mt) REVERT: C 247 PHE cc_start: 0.9368 (t80) cc_final: 0.9163 (t80) REVERT: C 308 MET cc_start: 0.7482 (ttt) cc_final: 0.7273 (ttt) REVERT: C 313 ILE cc_start: 0.9841 (mp) cc_final: 0.9469 (mp) REVERT: C 314 PHE cc_start: 0.9585 (t80) cc_final: 0.9093 (t80) REVERT: E 58 MET cc_start: 0.9425 (mpp) cc_final: 0.9084 (mpp) REVERT: E 82 PHE cc_start: 0.9068 (m-10) cc_final: 0.8792 (m-10) REVERT: E 135 PHE cc_start: 0.9550 (m-10) cc_final: 0.9255 (m-80) REVERT: E 215 MET cc_start: 0.9355 (mpp) cc_final: 0.8908 (mpp) REVERT: F 100 GLN cc_start: 0.9720 (mt0) cc_final: 0.9365 (tp-100) REVERT: F 103 MET cc_start: 0.9265 (tpt) cc_final: 0.8828 (tpp) REVERT: F 110 ASP cc_start: 0.9052 (t70) cc_final: 0.8693 (t0) REVERT: F 112 GLU cc_start: 0.8918 (pm20) cc_final: 0.8700 (mp0) REVERT: G 54 LEU cc_start: 0.8245 (pp) cc_final: 0.7443 (pp) REVERT: G 71 MET cc_start: 0.8439 (ptm) cc_final: 0.8033 (ppp) REVERT: G 115 PHE cc_start: 0.8370 (m-80) cc_final: 0.8085 (m-80) REVERT: G 121 ASN cc_start: 0.9560 (m-40) cc_final: 0.9358 (t0) REVERT: H 55 LEU cc_start: 0.9655 (mt) cc_final: 0.9395 (mt) REVERT: H 116 TYR cc_start: 0.9498 (m-10) cc_final: 0.9283 (m-80) REVERT: J 1 MET cc_start: 0.8757 (tpp) cc_final: 0.8371 (tpp) REVERT: J 49 MET cc_start: 0.9108 (mmm) cc_final: 0.8614 (mmm) REVERT: K 63 PHE cc_start: 0.9583 (m-80) cc_final: 0.9361 (m-80) REVERT: N 109 LEU cc_start: 0.8464 (pt) cc_final: 0.8026 (pt) REVERT: N 170 HIS cc_start: 0.9098 (t70) cc_final: 0.8553 (t70) outliers start: 1 outliers final: 0 residues processed: 523 average time/residue: 0.1665 time to fit residues: 141.2599 Evaluate side-chains 406 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 221 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 230 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 341 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A1647 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 243 GLN B 248 ASN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** K 64 GLN ** 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 = 0.3203 r_free = 0.3203 target = 0.056145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042678 restraints weight = 241779.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.043868 restraints weight = 178591.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044666 restraints weight = 140439.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.045035 restraints weight = 116893.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045710 restraints weight = 104873.951| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 31734 Z= 0.167 Angle : 0.640 17.322 42856 Z= 0.330 Chirality : 0.044 0.209 4788 Planarity : 0.004 0.054 5530 Dihedral : 4.612 60.594 4239 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 3838 helix: 0.98 (0.14), residues: 1302 sheet: -0.62 (0.19), residues: 609 loop : -0.95 (0.14), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 957 TYR 0.035 0.002 TYR H 93 PHE 0.050 0.002 PHE C 315 TRP 0.035 0.002 TRP B 143 HIS 0.026 0.001 HIS K 95 Details of bonding type rmsd covalent geometry : bond 0.00365 (31712) covalent geometry : angle 0.62954 (42835) hydrogen bonds : bond 0.04054 ( 1280) hydrogen bonds : angle 5.40714 ( 3660) metal coordination : bond 0.00816 ( 20) metal coordination : angle 5.21922 ( 21) Misc. bond : bond 0.00713 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9134 (mp10) cc_final: 0.8920 (mp10) REVERT: A 108 PHE cc_start: 0.9194 (m-80) cc_final: 0.8480 (m-10) REVERT: A 223 PHE cc_start: 0.9676 (t80) cc_final: 0.9445 (t80) REVERT: A 324 LEU cc_start: 0.9633 (mt) cc_final: 0.9388 (mt) REVERT: A 471 MET cc_start: 0.8239 (mpp) cc_final: 0.8022 (mpp) REVERT: A 509 GLU cc_start: 0.9601 (tp30) cc_final: 0.8986 (tm-30) REVERT: A 519 LEU cc_start: 0.9708 (mt) cc_final: 0.9122 (mt) REVERT: A 578 TYR cc_start: 0.9147 (m-10) cc_final: 0.8816 (m-80) REVERT: A 589 MET cc_start: 0.9666 (mmp) cc_final: 0.9405 (mmp) REVERT: A 600 MET cc_start: 0.9672 (mmp) cc_final: 0.9341 (mmm) REVERT: A 601 MET cc_start: 0.9494 (mmm) cc_final: 0.9062 (mmm) REVERT: A 606 ARG cc_start: 0.8685 (tpp80) cc_final: 0.8288 (tpp80) REVERT: A 624 TYR cc_start: 0.7472 (m-80) cc_final: 0.5997 (m-80) REVERT: A 633 MET cc_start: 0.9626 (mmp) cc_final: 0.9307 (mmp) REVERT: A 669 LEU cc_start: 0.8437 (mm) cc_final: 0.8048 (mm) REVERT: A 680 LEU cc_start: 0.9894 (tt) cc_final: 0.9671 (tp) REVERT: A 687 PHE cc_start: 0.9538 (m-80) cc_final: 0.8753 (m-80) REVERT: A 760 TRP cc_start: 0.8456 (m100) cc_final: 0.8245 (m100) REVERT: A 770 LEU cc_start: 0.9505 (tp) cc_final: 0.9270 (mm) REVERT: A 776 LEU cc_start: 0.9450 (tp) cc_final: 0.9224 (tp) REVERT: A 786 TYR cc_start: 0.9312 (p90) cc_final: 0.9000 (p90) REVERT: A 821 ILE cc_start: 0.9560 (tp) cc_final: 0.9269 (mm) REVERT: A 917 MET cc_start: 0.9491 (tmm) cc_final: 0.9128 (tmm) REVERT: A 928 MET cc_start: 0.9158 (mmp) cc_final: 0.8721 (mpp) REVERT: A 977 MET cc_start: 0.9697 (ttt) cc_final: 0.9312 (tpt) REVERT: A 981 TYR cc_start: 0.9448 (t80) cc_final: 0.8979 (t80) REVERT: A 1027 LEU cc_start: 0.9022 (mt) cc_final: 0.8661 (mt) REVERT: A 1170 MET cc_start: 0.9626 (mmm) cc_final: 0.9153 (mmm) REVERT: A 1183 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8795 (mp0) REVERT: A 1294 MET cc_start: 0.9510 (mmm) cc_final: 0.9080 (mmm) REVERT: A 1588 MET cc_start: 0.9578 (mmp) cc_final: 0.9344 (mmm) REVERT: A 1603 MET cc_start: 0.9350 (ttp) cc_final: 0.8614 (ptm) REVERT: A 1621 PHE cc_start: 0.9146 (m-80) cc_final: 0.8828 (m-10) REVERT: A 1648 ASN cc_start: 0.8288 (p0) cc_final: 0.7933 (p0) REVERT: B 108 MET cc_start: 0.9106 (mmt) cc_final: 0.8090 (tpp) REVERT: B 205 MET cc_start: 0.9117 (mmt) cc_final: 0.8557 (mmt) REVERT: B 296 ASP cc_start: 0.9208 (m-30) cc_final: 0.8558 (p0) REVERT: B 334 PHE cc_start: 0.8984 (m-80) cc_final: 0.8738 (m-80) REVERT: B 377 MET cc_start: 0.9875 (ppp) cc_final: 0.9626 (ppp) REVERT: B 496 PHE cc_start: 0.9571 (t80) cc_final: 0.9148 (t80) REVERT: B 502 MET cc_start: 0.9501 (ptm) cc_final: 0.9187 (ptm) REVERT: B 545 PHE cc_start: 0.9476 (m-80) cc_final: 0.8794 (m-80) REVERT: B 595 TRP cc_start: 0.8414 (m100) cc_final: 0.8113 (m100) REVERT: B 640 LEU cc_start: 0.9375 (tt) cc_final: 0.8822 (pp) REVERT: B 641 TYR cc_start: 0.9566 (m-80) cc_final: 0.9350 (m-10) REVERT: B 649 MET cc_start: 0.9262 (tpt) cc_final: 0.8813 (tpp) REVERT: B 672 MET cc_start: 0.8460 (ptp) cc_final: 0.8230 (ptp) REVERT: B 674 ILE cc_start: 0.9539 (pt) cc_final: 0.8986 (mm) REVERT: B 726 MET cc_start: 0.9011 (tpt) cc_final: 0.8631 (mmm) REVERT: B 783 MET cc_start: 0.6327 (mpp) cc_final: 0.5674 (mpp) REVERT: B 785 ASP cc_start: 0.8637 (m-30) cc_final: 0.8358 (p0) REVERT: B 927 CYS cc_start: 0.9251 (t) cc_final: 0.8481 (t) REVERT: B 959 THR cc_start: 0.9488 (p) cc_final: 0.8752 (t) REVERT: B 963 PHE cc_start: 0.9082 (m-80) cc_final: 0.8735 (m-80) REVERT: B 965 GLU cc_start: 0.8704 (tt0) cc_final: 0.8048 (tm-30) REVERT: B 1030 VAL cc_start: 0.9881 (t) cc_final: 0.9674 (t) REVERT: B 1031 VAL cc_start: 0.9490 (t) cc_final: 0.9144 (t) REVERT: B 1198 TYR cc_start: 0.9325 (m-80) cc_final: 0.8839 (m-80) REVERT: C 63 ILE cc_start: 0.9516 (mp) cc_final: 0.8818 (mp) REVERT: C 67 PHE cc_start: 0.9508 (m-10) cc_final: 0.9257 (m-80) REVERT: C 71 MET cc_start: 0.9204 (mtt) cc_final: 0.8898 (mmm) REVERT: C 94 ASP cc_start: 0.8948 (m-30) cc_final: 0.8542 (m-30) REVERT: C 193 LEU cc_start: 0.9859 (mt) cc_final: 0.9619 (mp) REVERT: C 308 MET cc_start: 0.7640 (ttt) cc_final: 0.7431 (ttt) REVERT: C 313 ILE cc_start: 0.9872 (mp) cc_final: 0.9518 (mp) REVERT: E 58 MET cc_start: 0.9526 (mpp) cc_final: 0.8681 (mpp) REVERT: E 82 PHE cc_start: 0.9065 (m-10) cc_final: 0.8784 (m-10) REVERT: E 135 PHE cc_start: 0.9684 (m-10) cc_final: 0.9458 (m-80) REVERT: E 168 TYR cc_start: 0.7772 (m-80) cc_final: 0.7347 (m-80) REVERT: E 215 MET cc_start: 0.9275 (mpp) cc_final: 0.8933 (mpp) REVERT: F 89 GLU cc_start: 0.9575 (mp0) cc_final: 0.9215 (mp0) REVERT: F 100 GLN cc_start: 0.9725 (mt0) cc_final: 0.9362 (tp-100) REVERT: F 103 MET cc_start: 0.9434 (tpt) cc_final: 0.9069 (tpp) REVERT: G 54 LEU cc_start: 0.8005 (pp) cc_final: 0.7410 (pp) REVERT: G 55 GLU cc_start: 0.7323 (pp20) cc_final: 0.7065 (pm20) REVERT: G 87 LEU cc_start: 0.8424 (pp) cc_final: 0.7963 (tt) REVERT: H 42 ILE cc_start: 0.9543 (pt) cc_final: 0.8999 (mp) REVERT: H 55 LEU cc_start: 0.9678 (mt) cc_final: 0.9425 (mt) REVERT: H 97 MET cc_start: 0.8713 (mpp) cc_final: 0.7836 (mpp) REVERT: H 142 LEU cc_start: 0.9802 (tp) cc_final: 0.9564 (tp) REVERT: J 1 MET cc_start: 0.8821 (tpp) cc_final: 0.8420 (tpp) REVERT: J 49 MET cc_start: 0.9213 (mmm) cc_final: 0.8857 (mmm) REVERT: K 46 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7679 (mtpt) REVERT: N 107 MET cc_start: 0.6368 (tmm) cc_final: 0.5874 (tmm) REVERT: N 170 HIS cc_start: 0.9110 (t70) cc_final: 0.8582 (t70) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.1593 time to fit residues: 126.3463 Evaluate side-chains 377 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 379 optimal weight: 30.0000 chunk 315 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 906 GLN A 942 GLN A1151 ASN A1180 ASN A1314 GLN A1320 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN E 8 ASN G 64 GLN J 23 ASN J 26 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.038188 restraints weight = 262512.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.039243 restraints weight = 192121.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.039991 restraints weight = 149648.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040542 restraints weight = 123725.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.040983 restraints weight = 106850.368| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 31734 Z= 0.230 Angle : 0.722 17.295 42856 Z= 0.376 Chirality : 0.045 0.241 4788 Planarity : 0.005 0.058 5530 Dihedral : 4.987 73.674 4239 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 3838 helix: 0.63 (0.14), residues: 1316 sheet: -0.55 (0.19), residues: 616 loop : -0.96 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1076 TYR 0.036 0.002 TYR H 95 PHE 0.031 0.003 PHE E 96 TRP 0.040 0.003 TRP B 143 HIS 0.008 0.002 HIS B1008 Details of bonding type rmsd covalent geometry : bond 0.00484 (31712) covalent geometry : angle 0.71331 (42835) hydrogen bonds : bond 0.04333 ( 1280) hydrogen bonds : angle 5.53688 ( 3660) metal coordination : bond 0.01045 ( 20) metal coordination : angle 5.11238 ( 21) Misc. bond : bond 0.00680 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9281 (mp10) cc_final: 0.9027 (mp10) REVERT: A 108 PHE cc_start: 0.9223 (m-80) cc_final: 0.8500 (m-10) REVERT: A 424 MET cc_start: 0.8535 (mtt) cc_final: 0.8124 (mmm) REVERT: A 437 PHE cc_start: 0.8787 (t80) cc_final: 0.8050 (t80) REVERT: A 471 MET cc_start: 0.8241 (mpp) cc_final: 0.7927 (mpp) REVERT: A 478 TYR cc_start: 0.8410 (m-80) cc_final: 0.8196 (m-80) REVERT: A 509 GLU cc_start: 0.9645 (tp30) cc_final: 0.9048 (tm-30) REVERT: A 519 LEU cc_start: 0.9797 (mt) cc_final: 0.9362 (mt) REVERT: A 578 TYR cc_start: 0.9264 (m-10) cc_final: 0.8911 (m-80) REVERT: A 589 MET cc_start: 0.9755 (mmp) cc_final: 0.9522 (mmp) REVERT: A 594 THR cc_start: 0.4653 (m) cc_final: 0.4038 (m) REVERT: A 600 MET cc_start: 0.9687 (mmp) cc_final: 0.9409 (mmm) REVERT: A 601 MET cc_start: 0.9391 (mmm) cc_final: 0.8948 (mmm) REVERT: A 624 TYR cc_start: 0.8172 (m-80) cc_final: 0.7709 (m-80) REVERT: A 625 ASN cc_start: 0.9489 (t0) cc_final: 0.9241 (m-40) REVERT: A 633 MET cc_start: 0.9494 (mmp) cc_final: 0.9060 (mmp) REVERT: A 635 MET cc_start: 0.9754 (ptt) cc_final: 0.9538 (ppp) REVERT: A 669 LEU cc_start: 0.8489 (mm) cc_final: 0.7932 (mm) REVERT: A 687 PHE cc_start: 0.9542 (m-80) cc_final: 0.8793 (m-80) REVERT: A 917 MET cc_start: 0.9586 (tmm) cc_final: 0.9260 (tmm) REVERT: A 925 MET cc_start: 0.9542 (tpt) cc_final: 0.9175 (mmm) REVERT: A 977 MET cc_start: 0.9789 (ttt) cc_final: 0.9406 (mmm) REVERT: A 981 TYR cc_start: 0.9504 (t80) cc_final: 0.9221 (t80) REVERT: A 1025 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8509 (ptpt) REVERT: A 1026 GLN cc_start: 0.9083 (tp40) cc_final: 0.8868 (mt0) REVERT: A 1170 MET cc_start: 0.9563 (mmm) cc_final: 0.8782 (mmm) REVERT: A 1294 MET cc_start: 0.9555 (mmm) cc_final: 0.9226 (mmm) REVERT: A 1529 MET cc_start: 0.9651 (mpp) cc_final: 0.9383 (mpp) REVERT: A 1621 PHE cc_start: 0.9200 (m-80) cc_final: 0.8863 (m-10) REVERT: A 1648 ASN cc_start: 0.8536 (p0) cc_final: 0.8227 (p0) REVERT: A 1656 VAL cc_start: 0.7374 (t) cc_final: 0.7017 (m) REVERT: B 108 MET cc_start: 0.9206 (mmt) cc_final: 0.8366 (tpp) REVERT: B 205 MET cc_start: 0.9273 (mmt) cc_final: 0.8871 (mmt) REVERT: B 250 LEU cc_start: 0.9453 (tp) cc_final: 0.9220 (tp) REVERT: B 330 LEU cc_start: 0.9687 (mt) cc_final: 0.9484 (mt) REVERT: B 377 MET cc_start: 0.9657 (ppp) cc_final: 0.9306 (ppp) REVERT: B 496 PHE cc_start: 0.9670 (t80) cc_final: 0.9146 (t80) REVERT: B 502 MET cc_start: 0.9707 (ptm) cc_final: 0.9419 (ptm) REVERT: B 545 PHE cc_start: 0.9435 (m-80) cc_final: 0.8875 (m-80) REVERT: B 595 TRP cc_start: 0.8722 (m100) cc_final: 0.8404 (m100) REVERT: B 640 LEU cc_start: 0.9383 (tt) cc_final: 0.8796 (mt) REVERT: B 649 MET cc_start: 0.9318 (tpt) cc_final: 0.8884 (tpp) REVERT: B 782 ASP cc_start: 0.7418 (p0) cc_final: 0.7180 (p0) REVERT: B 783 MET cc_start: 0.6898 (mpp) cc_final: 0.5691 (mpp) REVERT: B 785 ASP cc_start: 0.8666 (m-30) cc_final: 0.8464 (p0) REVERT: B 839 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8491 (mttt) REVERT: B 936 MET cc_start: 0.9390 (mmt) cc_final: 0.8904 (mmm) REVERT: B 958 MET cc_start: 0.8984 (mpp) cc_final: 0.8769 (mpp) REVERT: B 963 PHE cc_start: 0.9061 (m-80) cc_final: 0.8597 (m-80) REVERT: B 965 GLU cc_start: 0.8906 (tt0) cc_final: 0.8243 (tm-30) REVERT: B 986 PHE cc_start: 0.8502 (m-80) cc_final: 0.7953 (m-80) REVERT: B 1026 ILE cc_start: 0.9645 (mm) cc_final: 0.9434 (tp) REVERT: B 1031 VAL cc_start: 0.9489 (t) cc_final: 0.8754 (t) REVERT: B 1198 TYR cc_start: 0.9456 (m-80) cc_final: 0.9191 (m-80) REVERT: C 63 ILE cc_start: 0.9582 (mp) cc_final: 0.9291 (mp) REVERT: C 71 MET cc_start: 0.9257 (mtt) cc_final: 0.8753 (mmm) REVERT: C 314 PHE cc_start: 0.9373 (t80) cc_final: 0.9060 (t80) REVERT: E 58 MET cc_start: 0.9611 (mpp) cc_final: 0.8570 (mpp) REVERT: E 82 PHE cc_start: 0.9116 (m-10) cc_final: 0.8717 (m-80) REVERT: E 168 TYR cc_start: 0.8197 (m-80) cc_final: 0.7686 (m-80) REVERT: E 215 MET cc_start: 0.9283 (mpp) cc_final: 0.9007 (mpp) REVERT: F 85 MET cc_start: 0.9106 (ptp) cc_final: 0.8341 (ttp) REVERT: F 89 GLU cc_start: 0.9756 (mp0) cc_final: 0.9162 (mp0) REVERT: F 103 MET cc_start: 0.9642 (tpt) cc_final: 0.9130 (tpp) REVERT: F 132 LEU cc_start: 0.9059 (mm) cc_final: 0.8535 (mm) REVERT: G 52 MET cc_start: 0.9173 (mmp) cc_final: 0.8938 (mmp) REVERT: G 71 MET cc_start: 0.8409 (ptm) cc_final: 0.8132 (ppp) REVERT: G 72 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8316 (ptpp) REVERT: G 87 LEU cc_start: 0.8549 (pp) cc_final: 0.8201 (pp) REVERT: H 55 LEU cc_start: 0.9612 (mt) cc_final: 0.9150 (mt) REVERT: H 97 MET cc_start: 0.8675 (mpp) cc_final: 0.7860 (mpp) REVERT: H 142 LEU cc_start: 0.9758 (tp) cc_final: 0.9377 (tp) REVERT: J 1 MET cc_start: 0.8872 (tpp) cc_final: 0.8250 (tpp) REVERT: J 49 MET cc_start: 0.9468 (mmm) cc_final: 0.9167 (mmm) REVERT: J 50 ILE cc_start: 0.9529 (mm) cc_final: 0.9279 (tp) REVERT: M 67 ASP cc_start: 0.9015 (t0) cc_final: 0.8678 (t0) REVERT: M 108 LEU cc_start: 0.7807 (pt) cc_final: 0.7487 (tp) REVERT: N 58 PHE cc_start: 0.9661 (m-80) cc_final: 0.9440 (m-80) REVERT: N 80 MET cc_start: 0.8396 (mmp) cc_final: 0.8193 (mmm) REVERT: N 82 ILE cc_start: 0.8416 (mp) cc_final: 0.8203 (mp) REVERT: N 170 HIS cc_start: 0.9116 (t70) cc_final: 0.8701 (t-170) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1513 time to fit residues: 111.7313 Evaluate side-chains 337 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 107 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 353 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 553 GLN A 950 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 433 ASN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN G 67 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.037204 restraints weight = 259836.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.038229 restraints weight = 187670.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.038972 restraints weight = 145909.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.039511 restraints weight = 120367.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039954 restraints weight = 103972.124| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 31734 Z= 0.188 Angle : 0.661 15.453 42856 Z= 0.342 Chirality : 0.044 0.226 4788 Planarity : 0.006 0.238 5530 Dihedral : 4.901 67.090 4239 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.13), residues: 3838 helix: 0.69 (0.14), residues: 1334 sheet: -0.42 (0.20), residues: 585 loop : -0.96 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 448 TYR 0.036 0.002 TYR H 93 PHE 0.032 0.002 PHE C 315 TRP 0.039 0.002 TRP B 143 HIS 0.009 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00402 (31712) covalent geometry : angle 0.65268 (42835) hydrogen bonds : bond 0.04085 ( 1280) hydrogen bonds : angle 5.45753 ( 3660) metal coordination : bond 0.00965 ( 20) metal coordination : angle 4.63134 ( 21) Misc. bond : bond 0.00645 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9185 (mp10) cc_final: 0.8950 (mp10) REVERT: A 108 PHE cc_start: 0.9209 (m-80) cc_final: 0.8594 (m-10) REVERT: A 437 PHE cc_start: 0.8803 (t80) cc_final: 0.7969 (t80) REVERT: A 471 MET cc_start: 0.8387 (mpp) cc_final: 0.8032 (mpp) REVERT: A 578 TYR cc_start: 0.9323 (m-10) cc_final: 0.9000 (m-80) REVERT: A 588 LEU cc_start: 0.9233 (tp) cc_final: 0.9027 (tp) REVERT: A 589 MET cc_start: 0.9757 (mmp) cc_final: 0.9436 (mmp) REVERT: A 594 THR cc_start: 0.4479 (m) cc_final: 0.4030 (m) REVERT: A 600 MET cc_start: 0.9659 (mmp) cc_final: 0.9428 (mmm) REVERT: A 601 MET cc_start: 0.9301 (mmm) cc_final: 0.8634 (mmm) REVERT: A 614 LEU cc_start: 0.9643 (mt) cc_final: 0.9280 (mt) REVERT: A 625 ASN cc_start: 0.9508 (t0) cc_final: 0.9282 (m-40) REVERT: A 633 MET cc_start: 0.9536 (mmp) cc_final: 0.9327 (mmp) REVERT: A 635 MET cc_start: 0.9821 (ptt) cc_final: 0.9584 (mmp) REVERT: A 669 LEU cc_start: 0.8381 (mm) cc_final: 0.7833 (mm) REVERT: A 687 PHE cc_start: 0.9547 (m-80) cc_final: 0.8864 (m-80) REVERT: A 776 LEU cc_start: 0.9518 (tp) cc_final: 0.9225 (tp) REVERT: A 786 TYR cc_start: 0.9337 (p90) cc_final: 0.9032 (p90) REVERT: A 917 MET cc_start: 0.9591 (tmm) cc_final: 0.9275 (tmm) REVERT: A 925 MET cc_start: 0.9524 (tpt) cc_final: 0.9201 (mmm) REVERT: A 977 MET cc_start: 0.9783 (ttt) cc_final: 0.9296 (mmm) REVERT: A 994 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8428 (mm-30) REVERT: A 1170 MET cc_start: 0.9539 (mmm) cc_final: 0.8736 (mmp) REVERT: A 1294 MET cc_start: 0.9538 (mmm) cc_final: 0.9240 (mmm) REVERT: A 1529 MET cc_start: 0.9675 (mpp) cc_final: 0.9433 (mpp) REVERT: A 1588 MET cc_start: 0.9307 (mmp) cc_final: 0.9031 (mmm) REVERT: A 1621 PHE cc_start: 0.9200 (m-80) cc_final: 0.8870 (m-10) REVERT: A 1645 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7959 (tmtt) REVERT: A 1648 ASN cc_start: 0.8472 (p0) cc_final: 0.8053 (p0) REVERT: A 1656 VAL cc_start: 0.7969 (t) cc_final: 0.7669 (m) REVERT: B 205 MET cc_start: 0.9230 (mmt) cc_final: 0.8811 (mmp) REVERT: B 377 MET cc_start: 0.9752 (ppp) cc_final: 0.9513 (ppp) REVERT: B 378 ILE cc_start: 0.9733 (tp) cc_final: 0.9280 (tp) REVERT: B 382 TYR cc_start: 0.9458 (m-10) cc_final: 0.8853 (m-80) REVERT: B 494 TYR cc_start: 0.9607 (m-80) cc_final: 0.9375 (m-80) REVERT: B 496 PHE cc_start: 0.9710 (t80) cc_final: 0.9257 (t80) REVERT: B 502 MET cc_start: 0.9711 (ptm) cc_final: 0.9415 (ptm) REVERT: B 545 PHE cc_start: 0.9423 (m-80) cc_final: 0.8942 (m-80) REVERT: B 595 TRP cc_start: 0.8724 (m100) cc_final: 0.8375 (m100) REVERT: B 640 LEU cc_start: 0.9383 (tt) cc_final: 0.8608 (mt) REVERT: B 649 MET cc_start: 0.9508 (tpt) cc_final: 0.9109 (tpp) REVERT: B 674 ILE cc_start: 0.9248 (tt) cc_final: 0.8863 (tt) REVERT: B 782 ASP cc_start: 0.8120 (p0) cc_final: 0.7911 (p0) REVERT: B 783 MET cc_start: 0.7178 (mpp) cc_final: 0.6018 (mpp) REVERT: B 785 ASP cc_start: 0.8771 (m-30) cc_final: 0.8484 (p0) REVERT: B 839 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8572 (mttt) REVERT: B 927 CYS cc_start: 0.9151 (t) cc_final: 0.8871 (t) REVERT: B 936 MET cc_start: 0.9398 (mmt) cc_final: 0.8986 (mmm) REVERT: B 958 MET cc_start: 0.9012 (mpp) cc_final: 0.8812 (mpp) REVERT: B 963 PHE cc_start: 0.9115 (m-80) cc_final: 0.8589 (m-80) REVERT: B 965 GLU cc_start: 0.8991 (tt0) cc_final: 0.8384 (tm-30) REVERT: B 970 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8953 (mtmt) REVERT: B 986 PHE cc_start: 0.8622 (m-80) cc_final: 0.8113 (m-80) REVERT: B 1000 LEU cc_start: 0.9563 (mm) cc_final: 0.9279 (mm) REVERT: B 1030 VAL cc_start: 0.9871 (t) cc_final: 0.9611 (t) REVERT: C 229 LEU cc_start: 0.9567 (mp) cc_final: 0.9318 (tt) REVERT: C 314 PHE cc_start: 0.9373 (t80) cc_final: 0.9064 (t80) REVERT: C 321 LEU cc_start: 0.9636 (tp) cc_final: 0.9131 (pp) REVERT: E 58 MET cc_start: 0.9638 (mpp) cc_final: 0.8617 (mpp) REVERT: E 82 PHE cc_start: 0.9146 (m-10) cc_final: 0.8682 (m-80) REVERT: E 168 TYR cc_start: 0.8453 (m-80) cc_final: 0.8008 (m-80) REVERT: F 85 MET cc_start: 0.9321 (ptp) cc_final: 0.8620 (ttp) REVERT: F 89 GLU cc_start: 0.9700 (mp0) cc_final: 0.9289 (mp0) REVERT: F 103 MET cc_start: 0.9658 (tpt) cc_final: 0.9099 (tpp) REVERT: G 52 MET cc_start: 0.9184 (mmp) cc_final: 0.8799 (mmp) REVERT: G 55 GLU cc_start: 0.7966 (pp20) cc_final: 0.7577 (pm20) REVERT: G 71 MET cc_start: 0.8277 (ptm) cc_final: 0.7918 (ppp) REVERT: G 87 LEU cc_start: 0.8592 (pp) cc_final: 0.8282 (pp) REVERT: G 89 ILE cc_start: 0.8238 (mp) cc_final: 0.7998 (mp) REVERT: H 55 LEU cc_start: 0.9651 (mt) cc_final: 0.9202 (mt) REVERT: H 97 MET cc_start: 0.8866 (mpp) cc_final: 0.7957 (mpp) REVERT: H 138 GLU cc_start: 0.9091 (pm20) cc_final: 0.8743 (pp20) REVERT: H 142 LEU cc_start: 0.9765 (tp) cc_final: 0.9374 (tp) REVERT: J 8 PHE cc_start: 0.9457 (m-80) cc_final: 0.9168 (m-80) REVERT: J 49 MET cc_start: 0.9478 (mmm) cc_final: 0.9139 (mmm) REVERT: J 50 ILE cc_start: 0.9584 (mm) cc_final: 0.9337 (tp) REVERT: K 100 LEU cc_start: 0.9035 (mp) cc_final: 0.8036 (tt) REVERT: M 67 ASP cc_start: 0.9013 (t0) cc_final: 0.8738 (t0) REVERT: N 58 PHE cc_start: 0.9659 (m-80) cc_final: 0.9434 (m-80) REVERT: N 170 HIS cc_start: 0.9212 (t70) cc_final: 0.8843 (t-170) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.1558 time to fit residues: 108.1281 Evaluate side-chains 327 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 351 optimal weight: 5.9990 chunk 279 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 366 optimal weight: 7.9990 chunk 341 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 767 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 26 GLN ** K 64 GLN ** 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 = 0.3008 r_free = 0.3008 target = 0.047225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.035536 restraints weight = 272793.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.036538 restraints weight = 194342.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.037220 restraints weight = 149522.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.037811 restraints weight = 122661.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.038204 restraints weight = 104752.247| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.8715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 31734 Z= 0.206 Angle : 0.685 15.599 42856 Z= 0.356 Chirality : 0.044 0.252 4788 Planarity : 0.006 0.166 5530 Dihedral : 5.036 70.902 4239 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.13), residues: 3838 helix: 0.64 (0.14), residues: 1325 sheet: -0.62 (0.20), residues: 580 loop : -0.92 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 136 TYR 0.032 0.002 TYR H 95 PHE 0.051 0.002 PHE B 496 TRP 0.040 0.002 TRP B 143 HIS 0.006 0.002 HIS B1008 Details of bonding type rmsd covalent geometry : bond 0.00442 (31712) covalent geometry : angle 0.67617 (42835) hydrogen bonds : bond 0.04167 ( 1280) hydrogen bonds : angle 5.54262 ( 3660) metal coordination : bond 0.01316 ( 20) metal coordination : angle 4.96966 ( 21) Misc. bond : bond 0.00678 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.9210 (m-80) cc_final: 0.8614 (m-10) REVERT: A 424 MET cc_start: 0.8993 (mtt) cc_final: 0.8695 (mmm) REVERT: A 437 PHE cc_start: 0.8862 (t80) cc_final: 0.8102 (t80) REVERT: A 478 TYR cc_start: 0.8077 (m-80) cc_final: 0.7795 (m-80) REVERT: A 549 MET cc_start: 0.8864 (mmp) cc_final: 0.8640 (mmm) REVERT: A 578 TYR cc_start: 0.9393 (m-10) cc_final: 0.9006 (m-80) REVERT: A 601 MET cc_start: 0.9448 (mmm) cc_final: 0.8912 (mmm) REVERT: A 625 ASN cc_start: 0.9536 (t0) cc_final: 0.9276 (m-40) REVERT: A 635 MET cc_start: 0.9834 (ptt) cc_final: 0.9585 (ppp) REVERT: A 669 LEU cc_start: 0.8425 (mm) cc_final: 0.7835 (mm) REVERT: A 671 GLN cc_start: 0.9308 (mt0) cc_final: 0.9098 (pt0) REVERT: A 687 PHE cc_start: 0.9537 (m-80) cc_final: 0.8882 (m-80) REVERT: A 917 MET cc_start: 0.9593 (tmm) cc_final: 0.9241 (tmm) REVERT: A 925 MET cc_start: 0.9578 (tpt) cc_final: 0.9009 (mmp) REVERT: A 977 MET cc_start: 0.9805 (ttt) cc_final: 0.9372 (mmm) REVERT: A 994 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8394 (mm-30) REVERT: A 1019 LEU cc_start: 0.9323 (mp) cc_final: 0.9082 (mp) REVERT: A 1027 LEU cc_start: 0.9409 (mt) cc_final: 0.8812 (pp) REVERT: A 1028 GLU cc_start: 0.9302 (pt0) cc_final: 0.9055 (pm20) REVERT: A 1170 MET cc_start: 0.9543 (mmm) cc_final: 0.8770 (mmp) REVERT: A 1294 MET cc_start: 0.9698 (mmm) cc_final: 0.9378 (mmm) REVERT: A 1588 MET cc_start: 0.9565 (mmp) cc_final: 0.9208 (mmm) REVERT: A 1621 PHE cc_start: 0.9197 (m-80) cc_final: 0.8958 (m-10) REVERT: A 1648 ASN cc_start: 0.8042 (p0) cc_final: 0.7763 (p0) REVERT: B 40 GLU cc_start: 0.9473 (mt-10) cc_final: 0.9127 (tm-30) REVERT: B 205 MET cc_start: 0.9156 (mmt) cc_final: 0.8616 (mmp) REVERT: B 292 ILE cc_start: 0.9247 (tt) cc_final: 0.9008 (tp) REVERT: B 334 PHE cc_start: 0.9111 (m-80) cc_final: 0.8445 (m-80) REVERT: B 378 ILE cc_start: 0.9727 (tp) cc_final: 0.9282 (tp) REVERT: B 382 TYR cc_start: 0.9515 (m-10) cc_final: 0.9066 (m-80) REVERT: B 494 TYR cc_start: 0.9673 (m-80) cc_final: 0.9387 (m-80) REVERT: B 496 PHE cc_start: 0.9678 (t80) cc_final: 0.9435 (t80) REVERT: B 502 MET cc_start: 0.9695 (ptm) cc_final: 0.9475 (ptm) REVERT: B 523 GLU cc_start: 0.8984 (mp0) cc_final: 0.8462 (mt-10) REVERT: B 545 PHE cc_start: 0.9423 (m-80) cc_final: 0.9029 (m-80) REVERT: B 595 TRP cc_start: 0.8799 (m100) cc_final: 0.8400 (m100) REVERT: B 640 LEU cc_start: 0.9426 (tt) cc_final: 0.8641 (mt) REVERT: B 649 MET cc_start: 0.9478 (tpt) cc_final: 0.9242 (tpp) REVERT: B 767 ASN cc_start: 0.9651 (p0) cc_final: 0.9373 (p0) REVERT: B 783 MET cc_start: 0.7395 (mpp) cc_final: 0.6335 (mpp) REVERT: B 785 ASP cc_start: 0.8794 (m-30) cc_final: 0.8552 (p0) REVERT: B 936 MET cc_start: 0.9421 (mmt) cc_final: 0.8975 (mmm) REVERT: B 963 PHE cc_start: 0.9145 (m-80) cc_final: 0.8620 (m-80) REVERT: B 986 PHE cc_start: 0.8544 (m-80) cc_final: 0.7873 (m-80) REVERT: B 1000 LEU cc_start: 0.9599 (mm) cc_final: 0.9263 (mm) REVERT: B 1198 TYR cc_start: 0.9760 (m-80) cc_final: 0.9500 (m-80) REVERT: C 67 PHE cc_start: 0.9645 (m-80) cc_final: 0.9383 (m-80) REVERT: C 229 LEU cc_start: 0.9545 (mp) cc_final: 0.9312 (tt) REVERT: C 314 PHE cc_start: 0.9421 (t80) cc_final: 0.9068 (t80) REVERT: E 58 MET cc_start: 0.9664 (mpp) cc_final: 0.8669 (mpp) REVERT: E 82 PHE cc_start: 0.9200 (m-10) cc_final: 0.8716 (m-80) REVERT: E 135 PHE cc_start: 0.9589 (m-80) cc_final: 0.9235 (m-80) REVERT: E 168 TYR cc_start: 0.8519 (m-80) cc_final: 0.8074 (m-80) REVERT: E 215 MET cc_start: 0.9315 (mpp) cc_final: 0.9084 (mpp) REVERT: F 85 MET cc_start: 0.9280 (ptp) cc_final: 0.8800 (ttp) REVERT: F 103 MET cc_start: 0.9619 (tpt) cc_final: 0.8929 (tpp) REVERT: G 52 MET cc_start: 0.9301 (mmp) cc_final: 0.8838 (mmp) REVERT: G 71 MET cc_start: 0.8324 (ptm) cc_final: 0.7985 (ppp) REVERT: G 87 LEU cc_start: 0.8505 (pp) cc_final: 0.8219 (pp) REVERT: H 55 LEU cc_start: 0.9685 (mt) cc_final: 0.9236 (mt) REVERT: H 97 MET cc_start: 0.8979 (mpp) cc_final: 0.8109 (mpp) REVERT: H 138 GLU cc_start: 0.9156 (pm20) cc_final: 0.8840 (pp20) REVERT: H 142 LEU cc_start: 0.9803 (tp) cc_final: 0.9445 (tp) REVERT: J 8 PHE cc_start: 0.9536 (m-80) cc_final: 0.9111 (m-80) REVERT: J 49 MET cc_start: 0.9497 (mmm) cc_final: 0.9154 (mmm) REVERT: K 125 MET cc_start: 0.9821 (ptp) cc_final: 0.9411 (ptp) REVERT: M 53 LEU cc_start: 0.8890 (tp) cc_final: 0.8666 (pp) REVERT: M 67 ASP cc_start: 0.8881 (t0) cc_final: 0.8626 (t0) REVERT: N 58 PHE cc_start: 0.9707 (m-80) cc_final: 0.9474 (m-80) REVERT: N 170 HIS cc_start: 0.8788 (t70) cc_final: 0.8439 (t-170) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.1526 time to fit residues: 99.8067 Evaluate side-chains 305 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 78 optimal weight: 20.0000 chunk 349 optimal weight: 0.4980 chunk 323 optimal weight: 30.0000 chunk 32 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 367 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 339 optimal weight: 9.9990 chunk 275 optimal weight: 0.0570 chunk 27 optimal weight: 30.0000 chunk 317 optimal weight: 4.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN B 62 ASN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS C 158 ASN C 335 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 23 ASN ** K 64 GLN ** 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 = 0.3033 r_free = 0.3033 target = 0.048585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.036476 restraints weight = 266122.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037547 restraints weight = 189185.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.038301 restraints weight = 144894.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.038821 restraints weight = 118013.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.039209 restraints weight = 101267.461| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 31734 Z= 0.121 Angle : 0.610 11.206 42856 Z= 0.310 Chirality : 0.044 0.246 4788 Planarity : 0.005 0.160 5530 Dihedral : 4.717 68.799 4239 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 3838 helix: 1.02 (0.14), residues: 1311 sheet: -0.36 (0.20), residues: 591 loop : -0.80 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 136 TYR 0.033 0.001 TYR H 95 PHE 0.023 0.002 PHE C 315 TRP 0.035 0.002 TRP B 143 HIS 0.004 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00271 (31712) covalent geometry : angle 0.60329 (42835) hydrogen bonds : bond 0.03785 ( 1280) hydrogen bonds : angle 5.22330 ( 3660) metal coordination : bond 0.00609 ( 20) metal coordination : angle 4.13124 ( 21) Misc. bond : bond 0.00643 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 402 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9225 (mp10) cc_final: 0.8983 (mp10) REVERT: A 108 PHE cc_start: 0.9211 (m-80) cc_final: 0.8838 (m-10) REVERT: A 424 MET cc_start: 0.8996 (mtt) cc_final: 0.8735 (mmm) REVERT: A 437 PHE cc_start: 0.8803 (t80) cc_final: 0.8006 (t80) REVERT: A 471 MET cc_start: 0.8212 (mpp) cc_final: 0.7247 (ptt) REVERT: A 589 MET cc_start: 0.9726 (mmp) cc_final: 0.9473 (mmp) REVERT: A 594 THR cc_start: 0.4831 (m) cc_final: 0.3694 (m) REVERT: A 600 MET cc_start: 0.9733 (mmp) cc_final: 0.9391 (mmm) REVERT: A 601 MET cc_start: 0.9418 (mmm) cc_final: 0.8907 (mmm) REVERT: A 625 ASN cc_start: 0.9548 (t0) cc_final: 0.9177 (m-40) REVERT: A 669 LEU cc_start: 0.8345 (mm) cc_final: 0.7758 (mm) REVERT: A 687 PHE cc_start: 0.9539 (m-80) cc_final: 0.8908 (m-80) REVERT: A 917 MET cc_start: 0.9653 (tmm) cc_final: 0.9300 (tmm) REVERT: A 925 MET cc_start: 0.9360 (tpt) cc_final: 0.8976 (mmp) REVERT: A 994 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8268 (mm-30) REVERT: A 1027 LEU cc_start: 0.9166 (mt) cc_final: 0.8729 (pp) REVERT: A 1028 GLU cc_start: 0.9213 (pt0) cc_final: 0.8993 (pm20) REVERT: A 1170 MET cc_start: 0.9505 (mmm) cc_final: 0.8701 (mmp) REVERT: A 1294 MET cc_start: 0.9673 (mmm) cc_final: 0.9341 (mmm) REVERT: A 1598 PHE cc_start: 0.9519 (m-80) cc_final: 0.9055 (m-80) REVERT: A 1621 PHE cc_start: 0.9163 (m-80) cc_final: 0.8847 (m-10) REVERT: A 1645 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8085 (tmtt) REVERT: A 1648 ASN cc_start: 0.8443 (p0) cc_final: 0.7927 (p0) REVERT: B 164 MET cc_start: 0.8949 (ttm) cc_final: 0.8745 (ttp) REVERT: B 205 MET cc_start: 0.9146 (mmt) cc_final: 0.8643 (mmp) REVERT: B 292 ILE cc_start: 0.9189 (tt) cc_final: 0.8945 (tp) REVERT: B 330 LEU cc_start: 0.9631 (mt) cc_final: 0.9316 (mt) REVERT: B 377 MET cc_start: 0.9817 (ppp) cc_final: 0.9534 (ppp) REVERT: B 378 ILE cc_start: 0.9736 (tp) cc_final: 0.9252 (tp) REVERT: B 382 TYR cc_start: 0.9532 (m-10) cc_final: 0.9079 (m-80) REVERT: B 403 LEU cc_start: 0.9046 (pp) cc_final: 0.8662 (pp) REVERT: B 494 TYR cc_start: 0.9646 (m-80) cc_final: 0.9387 (m-80) REVERT: B 502 MET cc_start: 0.9710 (ptm) cc_final: 0.9493 (ptm) REVERT: B 523 GLU cc_start: 0.9111 (mp0) cc_final: 0.8466 (mt-10) REVERT: B 545 PHE cc_start: 0.9367 (m-80) cc_final: 0.9019 (m-80) REVERT: B 595 TRP cc_start: 0.8739 (m100) cc_final: 0.8347 (m100) REVERT: B 640 LEU cc_start: 0.9509 (tt) cc_final: 0.8929 (mt) REVERT: B 649 MET cc_start: 0.9436 (tpt) cc_final: 0.9227 (mmm) REVERT: B 715 ASN cc_start: 0.8929 (m-40) cc_final: 0.8708 (m-40) REVERT: B 767 ASN cc_start: 0.9669 (p0) cc_final: 0.9463 (p0) REVERT: B 783 MET cc_start: 0.6869 (mpp) cc_final: 0.6197 (mpp) REVERT: B 785 ASP cc_start: 0.8774 (m-30) cc_final: 0.8523 (p0) REVERT: B 839 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8819 (mttp) REVERT: B 936 MET cc_start: 0.9431 (mmt) cc_final: 0.8999 (mmm) REVERT: B 986 PHE cc_start: 0.8554 (m-80) cc_final: 0.7928 (m-80) REVERT: B 1000 LEU cc_start: 0.9541 (mm) cc_final: 0.9282 (mm) REVERT: C 229 LEU cc_start: 0.9561 (mp) cc_final: 0.9332 (tt) REVERT: C 247 PHE cc_start: 0.9394 (t80) cc_final: 0.9185 (t80) REVERT: E 58 MET cc_start: 0.9664 (mpp) cc_final: 0.8745 (mpp) REVERT: E 82 PHE cc_start: 0.9175 (m-10) cc_final: 0.8678 (m-80) REVERT: E 135 PHE cc_start: 0.9584 (m-80) cc_final: 0.9135 (m-80) REVERT: E 168 TYR cc_start: 0.8714 (m-80) cc_final: 0.8175 (m-80) REVERT: F 85 MET cc_start: 0.9239 (ptp) cc_final: 0.8675 (ttp) REVERT: F 89 GLU cc_start: 0.9546 (mp0) cc_final: 0.9162 (mp0) REVERT: F 92 ARG cc_start: 0.9435 (mmm160) cc_final: 0.9001 (tpp-160) REVERT: F 103 MET cc_start: 0.9575 (tpt) cc_final: 0.8912 (tpp) REVERT: G 52 MET cc_start: 0.9226 (mmp) cc_final: 0.8722 (mmp) REVERT: G 55 GLU cc_start: 0.8115 (pp20) cc_final: 0.7676 (pm20) REVERT: G 71 MET cc_start: 0.8281 (ptm) cc_final: 0.8038 (ppp) REVERT: G 72 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8454 (ptpt) REVERT: G 87 LEU cc_start: 0.8464 (pp) cc_final: 0.8187 (pp) REVERT: H 55 LEU cc_start: 0.9679 (mt) cc_final: 0.9213 (mt) REVERT: H 97 MET cc_start: 0.8995 (mpp) cc_final: 0.8064 (mpp) REVERT: H 138 GLU cc_start: 0.9224 (pm20) cc_final: 0.8978 (pp20) REVERT: H 142 LEU cc_start: 0.9798 (tp) cc_final: 0.9422 (tp) REVERT: J 8 PHE cc_start: 0.9565 (m-80) cc_final: 0.9197 (m-80) REVERT: J 49 MET cc_start: 0.9556 (mmm) cc_final: 0.9135 (mmm) REVERT: L 70 ARG cc_start: 0.7307 (mpp80) cc_final: 0.6116 (mpp80) REVERT: M 67 ASP cc_start: 0.8893 (t0) cc_final: 0.8666 (t0) REVERT: N 58 PHE cc_start: 0.9693 (m-80) cc_final: 0.9450 (m-80) REVERT: N 107 MET cc_start: 0.7791 (tmm) cc_final: 0.7193 (tmm) REVERT: N 170 HIS cc_start: 0.8823 (t70) cc_final: 0.8388 (t-170) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.1449 time to fit residues: 97.4432 Evaluate side-chains 315 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 339 optimal weight: 0.1980 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 325 optimal weight: 40.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN C 99 HIS ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035021 restraints weight = 279880.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.036018 restraints weight = 198582.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.036752 restraints weight = 150951.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.037270 restraints weight = 122847.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.037657 restraints weight = 105312.324| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.9285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 31734 Z= 0.200 Angle : 0.672 13.511 42856 Z= 0.347 Chirality : 0.044 0.221 4788 Planarity : 0.005 0.143 5530 Dihedral : 4.919 70.095 4239 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.13), residues: 3838 helix: 0.74 (0.14), residues: 1325 sheet: -0.47 (0.20), residues: 577 loop : -0.89 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 136 TYR 0.032 0.002 TYR H 95 PHE 0.024 0.002 PHE E 96 TRP 0.050 0.002 TRP G 125 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00426 (31712) covalent geometry : angle 0.66450 (42835) hydrogen bonds : bond 0.04056 ( 1280) hydrogen bonds : angle 5.46867 ( 3660) metal coordination : bond 0.01128 ( 20) metal coordination : angle 4.53873 ( 21) Misc. bond : bond 0.00709 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9272 (mp10) cc_final: 0.9028 (mp10) REVERT: A 108 PHE cc_start: 0.9223 (m-80) cc_final: 0.8644 (m-10) REVERT: A 424 MET cc_start: 0.9008 (mtt) cc_final: 0.8719 (mmm) REVERT: A 437 PHE cc_start: 0.8876 (t80) cc_final: 0.8078 (t80) REVERT: A 471 MET cc_start: 0.8281 (mpp) cc_final: 0.7607 (ptt) REVERT: A 549 MET cc_start: 0.8892 (mmp) cc_final: 0.8624 (mmm) REVERT: A 589 MET cc_start: 0.9731 (mmp) cc_final: 0.9506 (mmp) REVERT: A 594 THR cc_start: 0.5419 (m) cc_final: 0.3977 (m) REVERT: A 600 MET cc_start: 0.9673 (mmp) cc_final: 0.9370 (mmm) REVERT: A 601 MET cc_start: 0.9322 (mmm) cc_final: 0.8754 (mmm) REVERT: A 625 ASN cc_start: 0.9578 (t0) cc_final: 0.9188 (m-40) REVERT: A 687 PHE cc_start: 0.9519 (m-80) cc_final: 0.8912 (m-80) REVERT: A 770 LEU cc_start: 0.9817 (tp) cc_final: 0.9377 (pp) REVERT: A 771 PHE cc_start: 0.9450 (m-10) cc_final: 0.9184 (m-80) REVERT: A 917 MET cc_start: 0.9680 (tmm) cc_final: 0.9382 (tmm) REVERT: A 925 MET cc_start: 0.9519 (tpt) cc_final: 0.8983 (mmp) REVERT: A 994 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8282 (mm-30) REVERT: A 1170 MET cc_start: 0.9491 (mmm) cc_final: 0.8740 (mmp) REVERT: A 1294 MET cc_start: 0.9697 (mmm) cc_final: 0.9414 (mmm) REVERT: A 1588 MET cc_start: 0.9575 (tpt) cc_final: 0.8981 (tpp) REVERT: A 1598 PHE cc_start: 0.9490 (m-80) cc_final: 0.9188 (m-80) REVERT: A 1603 MET cc_start: 0.9208 (ttp) cc_final: 0.8681 (ptp) REVERT: A 1621 PHE cc_start: 0.9170 (m-80) cc_final: 0.8959 (m-10) REVERT: A 1648 ASN cc_start: 0.8702 (p0) cc_final: 0.8325 (p0) REVERT: B 205 MET cc_start: 0.9179 (mmt) cc_final: 0.8723 (mmp) REVERT: B 377 MET cc_start: 0.9819 (ppp) cc_final: 0.9575 (ppp) REVERT: B 494 TYR cc_start: 0.9619 (m-80) cc_final: 0.9389 (m-80) REVERT: B 523 GLU cc_start: 0.9051 (mp0) cc_final: 0.8473 (mt-10) REVERT: B 545 PHE cc_start: 0.9330 (m-80) cc_final: 0.9039 (m-80) REVERT: B 595 TRP cc_start: 0.8826 (m100) cc_final: 0.8465 (m100) REVERT: B 640 LEU cc_start: 0.9536 (tt) cc_final: 0.8940 (mt) REVERT: B 649 MET cc_start: 0.9334 (mmm) cc_final: 0.9128 (tpp) REVERT: B 715 ASN cc_start: 0.9190 (m-40) cc_final: 0.8989 (m110) REVERT: B 767 ASN cc_start: 0.9728 (p0) cc_final: 0.9442 (p0) REVERT: B 783 MET cc_start: 0.6384 (mpp) cc_final: 0.6170 (mpp) REVERT: B 785 ASP cc_start: 0.8862 (m-30) cc_final: 0.8593 (p0) REVERT: B 936 MET cc_start: 0.9474 (mmt) cc_final: 0.9012 (mmm) REVERT: B 986 PHE cc_start: 0.8555 (m-80) cc_final: 0.7909 (m-80) REVERT: B 1000 LEU cc_start: 0.9622 (mm) cc_final: 0.9395 (mm) REVERT: B 1013 MET cc_start: 0.9302 (tpt) cc_final: 0.9047 (tpp) REVERT: B 1082 HIS cc_start: 0.6269 (m90) cc_final: 0.6032 (m90) REVERT: C 229 LEU cc_start: 0.9547 (mp) cc_final: 0.9325 (tt) REVERT: C 247 PHE cc_start: 0.9431 (t80) cc_final: 0.9226 (t80) REVERT: E 58 MET cc_start: 0.9648 (mpp) cc_final: 0.8553 (mpp) REVERT: E 82 PHE cc_start: 0.9191 (m-10) cc_final: 0.8712 (m-80) REVERT: E 135 PHE cc_start: 0.9590 (m-80) cc_final: 0.9093 (m-80) REVERT: E 168 TYR cc_start: 0.8575 (m-80) cc_final: 0.8314 (m-80) REVERT: F 85 MET cc_start: 0.9263 (ptp) cc_final: 0.8529 (ttp) REVERT: F 89 GLU cc_start: 0.9541 (mp0) cc_final: 0.9157 (mp0) REVERT: F 92 ARG cc_start: 0.9436 (mmm160) cc_final: 0.9041 (tpp-160) REVERT: F 103 MET cc_start: 0.9625 (tpt) cc_final: 0.8996 (tpp) REVERT: G 52 MET cc_start: 0.9196 (mmp) cc_final: 0.8507 (mmp) REVERT: G 71 MET cc_start: 0.8310 (ptm) cc_final: 0.7962 (ppp) REVERT: G 87 LEU cc_start: 0.8541 (pp) cc_final: 0.8287 (pp) REVERT: H 55 LEU cc_start: 0.9678 (mt) cc_final: 0.9225 (mt) REVERT: H 138 GLU cc_start: 0.9179 (pm20) cc_final: 0.8832 (pp20) REVERT: J 8 PHE cc_start: 0.9604 (m-80) cc_final: 0.9335 (m-80) REVERT: J 48 ARG cc_start: 0.9769 (ptt90) cc_final: 0.9517 (ptm160) REVERT: M 53 LEU cc_start: 0.8763 (tp) cc_final: 0.8487 (pp) REVERT: M 67 ASP cc_start: 0.9037 (t0) cc_final: 0.8763 (t0) REVERT: N 58 PHE cc_start: 0.9718 (m-80) cc_final: 0.9482 (m-80) REVERT: N 90 MET cc_start: 0.8423 (mpp) cc_final: 0.8187 (mpp) REVERT: N 107 MET cc_start: 0.7653 (tmm) cc_final: 0.7345 (tmm) REVERT: N 170 HIS cc_start: 0.8471 (t70) cc_final: 0.8179 (t-170) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.1463 time to fit residues: 91.3793 Evaluate side-chains 293 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 95 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 206 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 268 optimal weight: 0.2980 chunk 230 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS B 62 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.037292 restraints weight = 261117.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.038340 restraints weight = 185230.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.039109 restraints weight = 142064.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.039614 restraints weight = 115973.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.040035 restraints weight = 100093.745| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.9279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 31734 Z= 0.113 Angle : 0.621 10.143 42856 Z= 0.313 Chirality : 0.044 0.228 4788 Planarity : 0.005 0.138 5530 Dihedral : 4.629 69.264 4239 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.14), residues: 3838 helix: 1.06 (0.14), residues: 1303 sheet: -0.29 (0.20), residues: 606 loop : -0.83 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 743 TYR 0.032 0.001 TYR H 95 PHE 0.023 0.001 PHE C 315 TRP 0.034 0.002 TRP B 143 HIS 0.006 0.001 HIS A 224 Details of bonding type rmsd covalent geometry : bond 0.00258 (31712) covalent geometry : angle 0.61573 (42835) hydrogen bonds : bond 0.03657 ( 1280) hydrogen bonds : angle 5.15425 ( 3660) metal coordination : bond 0.00537 ( 20) metal coordination : angle 3.84807 ( 21) Misc. bond : bond 0.00751 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9225 (mp10) cc_final: 0.9005 (mp10) REVERT: A 108 PHE cc_start: 0.9133 (m-80) cc_final: 0.8719 (m-10) REVERT: A 424 MET cc_start: 0.9048 (mtt) cc_final: 0.8786 (mmm) REVERT: A 437 PHE cc_start: 0.8895 (t80) cc_final: 0.8100 (t80) REVERT: A 471 MET cc_start: 0.8544 (mpp) cc_final: 0.7522 (ptt) REVERT: A 490 ILE cc_start: 0.7451 (tt) cc_final: 0.7192 (tt) REVERT: A 549 MET cc_start: 0.8874 (mmp) cc_final: 0.8588 (mmm) REVERT: A 594 THR cc_start: 0.5165 (m) cc_final: 0.3761 (m) REVERT: A 600 MET cc_start: 0.9737 (mmp) cc_final: 0.9452 (mmm) REVERT: A 601 MET cc_start: 0.9465 (mmm) cc_final: 0.9221 (mmm) REVERT: A 614 LEU cc_start: 0.9579 (mt) cc_final: 0.9372 (mt) REVERT: A 625 ASN cc_start: 0.9562 (t0) cc_final: 0.9186 (m-40) REVERT: A 635 MET cc_start: 0.9566 (ppp) cc_final: 0.9334 (ppp) REVERT: A 687 PHE cc_start: 0.9497 (m-80) cc_final: 0.8898 (m-80) REVERT: A 770 LEU cc_start: 0.9824 (tp) cc_final: 0.9453 (pp) REVERT: A 771 PHE cc_start: 0.9483 (m-10) cc_final: 0.9199 (m-80) REVERT: A 917 MET cc_start: 0.9657 (tmm) cc_final: 0.9361 (tmm) REVERT: A 925 MET cc_start: 0.9389 (tpt) cc_final: 0.8820 (tpp) REVERT: A 928 MET cc_start: 0.9409 (mmp) cc_final: 0.9186 (mtt) REVERT: A 960 MET cc_start: 0.8036 (mpp) cc_final: 0.7784 (ptp) REVERT: A 977 MET cc_start: 0.9755 (ttt) cc_final: 0.9136 (tpp) REVERT: A 994 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8547 (mt-10) REVERT: A 1049 MET cc_start: 0.9716 (mmp) cc_final: 0.9117 (tpp) REVERT: A 1170 MET cc_start: 0.9459 (mmm) cc_final: 0.8721 (mmp) REVERT: A 1294 MET cc_start: 0.9644 (mmm) cc_final: 0.9318 (tpp) REVERT: A 1588 MET cc_start: 0.9488 (tpt) cc_final: 0.9009 (tpp) REVERT: A 1598 PHE cc_start: 0.9625 (m-80) cc_final: 0.9185 (m-80) REVERT: A 1616 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7554 (tp30) REVERT: A 1621 PHE cc_start: 0.9127 (m-80) cc_final: 0.8735 (m-10) REVERT: B 108 MET cc_start: 0.9203 (mmt) cc_final: 0.8872 (mmp) REVERT: B 205 MET cc_start: 0.9160 (mmt) cc_final: 0.8665 (mmp) REVERT: B 334 PHE cc_start: 0.9108 (m-80) cc_final: 0.8369 (m-80) REVERT: B 403 LEU cc_start: 0.9085 (pp) cc_final: 0.8829 (pp) REVERT: B 494 TYR cc_start: 0.9610 (m-80) cc_final: 0.9399 (m-80) REVERT: B 502 MET cc_start: 0.9650 (ptt) cc_final: 0.9322 (ptm) REVERT: B 523 GLU cc_start: 0.9040 (mp0) cc_final: 0.8336 (mt-10) REVERT: B 545 PHE cc_start: 0.9288 (m-80) cc_final: 0.9026 (m-80) REVERT: B 595 TRP cc_start: 0.8704 (m100) cc_final: 0.8309 (m100) REVERT: B 640 LEU cc_start: 0.9540 (tt) cc_final: 0.8917 (mt) REVERT: B 649 MET cc_start: 0.9406 (mmm) cc_final: 0.8867 (mmm) REVERT: B 767 ASN cc_start: 0.9642 (p0) cc_final: 0.9384 (p0) REVERT: B 785 ASP cc_start: 0.8849 (m-30) cc_final: 0.8508 (p0) REVERT: B 839 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8866 (mttp) REVERT: B 927 CYS cc_start: 0.8752 (t) cc_final: 0.8481 (t) REVERT: B 936 MET cc_start: 0.9453 (mmt) cc_final: 0.8898 (mmm) REVERT: B 962 MET cc_start: 0.9376 (mtt) cc_final: 0.9162 (mmm) REVERT: B 986 PHE cc_start: 0.8530 (m-80) cc_final: 0.7779 (m-80) REVERT: B 1000 LEU cc_start: 0.9623 (mm) cc_final: 0.9396 (mm) REVERT: B 1013 MET cc_start: 0.9348 (tpt) cc_final: 0.9030 (tpp) REVERT: C 229 LEU cc_start: 0.9588 (mp) cc_final: 0.9360 (tt) REVERT: C 335 GLN cc_start: 0.8360 (pt0) cc_final: 0.8007 (pm20) REVERT: E 58 MET cc_start: 0.9613 (mpp) cc_final: 0.8602 (mpp) REVERT: E 82 PHE cc_start: 0.9141 (m-10) cc_final: 0.8680 (m-80) REVERT: E 135 PHE cc_start: 0.9585 (m-80) cc_final: 0.9062 (m-80) REVERT: E 168 TYR cc_start: 0.8612 (m-80) cc_final: 0.8087 (m-80) REVERT: E 215 MET cc_start: 0.9338 (mpp) cc_final: 0.9089 (mpp) REVERT: F 89 GLU cc_start: 0.9555 (mp0) cc_final: 0.9277 (mp0) REVERT: F 92 ARG cc_start: 0.9491 (mmm160) cc_final: 0.9041 (tpp-160) REVERT: F 103 MET cc_start: 0.9601 (tpt) cc_final: 0.8904 (tpp) REVERT: G 52 MET cc_start: 0.9158 (mmp) cc_final: 0.8441 (mmp) REVERT: G 55 GLU cc_start: 0.8131 (pp20) cc_final: 0.7662 (pm20) REVERT: G 71 MET cc_start: 0.8416 (ptm) cc_final: 0.8007 (ppp) REVERT: G 122 LEU cc_start: 0.9329 (mm) cc_final: 0.9004 (tp) REVERT: H 55 LEU cc_start: 0.9568 (mt) cc_final: 0.9091 (mt) REVERT: H 97 MET cc_start: 0.9002 (mpp) cc_final: 0.8011 (mpp) REVERT: H 142 LEU cc_start: 0.9781 (tp) cc_final: 0.9300 (tp) REVERT: J 8 PHE cc_start: 0.9604 (m-80) cc_final: 0.9292 (m-80) REVERT: K 57 ASP cc_start: 0.9247 (m-30) cc_final: 0.8860 (m-30) REVERT: K 125 MET cc_start: 0.9602 (ptp) cc_final: 0.9300 (ptt) REVERT: M 53 LEU cc_start: 0.8557 (tp) cc_final: 0.8325 (pp) REVERT: N 58 PHE cc_start: 0.9664 (m-80) cc_final: 0.9420 (m-80) REVERT: N 107 MET cc_start: 0.7574 (tmm) cc_final: 0.7275 (tmm) REVERT: N 170 HIS cc_start: 0.8483 (t70) cc_final: 0.8166 (t-170) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1458 time to fit residues: 96.6063 Evaluate side-chains 314 residues out of total 3476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 6 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 chunk 297 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 148 optimal weight: 0.0870 chunk 197 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.035717 restraints weight = 267967.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036737 restraints weight = 188922.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.037503 restraints weight = 144645.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.038062 restraints weight = 117224.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.038441 restraints weight = 99975.968| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.9422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 31734 Z= 0.116 Angle : 0.598 9.899 42856 Z= 0.303 Chirality : 0.043 0.225 4788 Planarity : 0.004 0.123 5530 Dihedral : 4.527 69.648 4239 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3838 helix: 1.12 (0.14), residues: 1308 sheet: -0.22 (0.21), residues: 579 loop : -0.82 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 136 TYR 0.032 0.001 TYR H 95 PHE 0.018 0.001 PHE E 96 TRP 0.035 0.001 TRP B 143 HIS 0.005 0.001 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00268 (31712) covalent geometry : angle 0.59323 (42835) hydrogen bonds : bond 0.03534 ( 1280) hydrogen bonds : angle 5.09902 ( 3660) metal coordination : bond 0.00537 ( 20) metal coordination : angle 3.60275 ( 21) Misc. bond : bond 0.00722 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.80 seconds wall clock time: 74 minutes 48.55 seconds (4488.55 seconds total)