Starting phenix.real_space_refine on Thu Jul 31 00:43:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.map" model { file = "/net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh1_31983/07_2025/7vh1_31983.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 96 5.16 5 C 8398 2.51 5 N 2202 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13156 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12817 SG CYS B 41 72.601 50.103 99.254 1.00 65.04 S ATOM 12823 SG CYS B 42 74.991 47.562 97.655 1.00 59.29 S ATOM 12957 SG CYS B 58 75.843 47.964 101.097 1.00 95.41 S ATOM 12982 SG CYS B 61 76.199 51.449 99.581 1.00 97.90 S ATOM 13072 SG CYS B 72 66.862 54.747 103.834 1.00112.88 S Time building chain proxies: 8.76, per 1000 atoms: 0.67 Number of scatterers: 13156 At special positions: 0 Unit cell: (102.4, 131.2, 124.8, 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 2 29.99 S 96 16.00 O 2458 8.00 N 2202 7.00 C 8398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.05 Simple disulfide: pdb=" SG CYS A1650 " - pdb=" SG CYS A1664 " distance=2.02 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 41 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " Number of angles added : 6 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3166 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 46.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.487A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 3.552A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 4.152A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.144A pdb=" N SER A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.711A pdb=" N HIS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.413A pdb=" N ALA A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.534A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.757A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 4.042A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.524A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 4.326A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.931A pdb=" N ILE A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.761A pdb=" N LYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 5.365A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.566A pdb=" N ILE A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.867A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.542A pdb=" N MET A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.608A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 574 through 578 removed outlier: 4.193A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 4.044A pdb=" N CYS A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 602 through 622 removed outlier: 3.768A pdb=" N ASP A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Proline residue: A 611 - end of helix removed outlier: 3.512A pdb=" N ARG A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.321A pdb=" N LEU A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 644 removed outlier: 3.588A pdb=" N MET A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.848A pdb=" N ARG A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.802A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.908A pdb=" N LEU A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 removed outlier: 3.744A pdb=" N GLU A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 3.690A pdb=" N LYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 removed outlier: 3.841A pdb=" N ILE A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.724A pdb=" N TYR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.646A pdb=" N LYS A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 Processing helix chain 'A' and resid 887 through 893 removed outlier: 3.778A pdb=" N SER A 891 " --> pdb=" O GLN A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 920 removed outlier: 3.845A pdb=" N SER A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 982 through 988 removed outlier: 3.610A pdb=" N ALA A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1024 through 1035 removed outlier: 3.892A pdb=" N GLY A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1085 removed outlier: 4.080A pdb=" N TYR A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.905A pdb=" N ASN A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A1094 " --> pdb=" O LEU A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1135 through 1155 removed outlier: 3.738A pdb=" N LEU A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1179 removed outlier: 3.916A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.742A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1227 through 1233 removed outlier: 3.731A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 3.575A pdb=" N ILE A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1244 through 1249' Processing helix chain 'A' and resid 1265 through 1271 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.250A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.050A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 4.517A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A1401 " --> pdb=" O THR A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 removed outlier: 3.513A pdb=" N THR A1418 " --> pdb=" O GLN A1414 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1449 removed outlier: 4.436A pdb=" N LYS A1441 " --> pdb=" O ALA A1437 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A1444 " --> pdb=" O SER A1440 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 4.108A pdb=" N GLN A1478 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A1484 " --> pdb=" O LYS A1480 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 4.321A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1535 removed outlier: 3.643A pdb=" N GLN A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 4.244A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 4.184A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1617 removed outlier: 3.658A pdb=" N SER A1616 " --> pdb=" O SER A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1623 Processing helix chain 'A' and resid 1640 through 1645 Processing helix chain 'A' and resid 1654 through 1658 removed outlier: 3.535A pdb=" N LEU A1657 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1658 " --> pdb=" O CYS A1655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1654 through 1658' Processing helix chain 'A' and resid 1665 through 1669 Processing helix chain 'A' and resid 1677 through 1693 removed outlier: 4.292A pdb=" N ASP A1681 " --> pdb=" O PRO A1677 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1739 Processing helix chain 'A' and resid 1743 through 1750 Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.684A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1792 Processing helix chain 'A' and resid 1806 through 1808 No H-bonds generated for 'chain 'A' and resid 1806 through 1808' Processing helix chain 'B' and resid 58 through 67 removed outlier: 4.141A pdb=" N GLN B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.687A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 removed outlier: 7.422A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 3.547A pdb=" N TYR A 545 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 543 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 558 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 3.730A pdb=" N GLY A1376 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A1185 " --> pdb=" O THR A1333 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1333 " --> pdb=" O CYS A1185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1549 through 1550 Processing sheet with id=AA7, first strand: chain 'A' and resid 1630 through 1631 removed outlier: 3.502A pdb=" N VAL A1630 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1718 394 hydrogen bonds defined for protein. 1122 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: 4.40 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3820 1.33 - 1.46: 2834 1.46 - 1.58: 6593 1.58 - 1.70: 0 1.70 - 1.82: 137 Bond restraints: 13384 Sorted by residual: bond pdb=" N ILE A 87 " pdb=" CA ILE A 87 " ideal model delta sigma weight residual 1.458 1.430 0.028 7.70e-03 1.69e+04 1.32e+01 bond pdb=" C GLU A 726 " pdb=" N PRO A 727 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.15e+01 bond pdb=" CA PRO A 624 " pdb=" C PRO A 624 " ideal model delta sigma weight residual 1.521 1.550 -0.029 9.30e-03 1.16e+04 9.74e+00 bond pdb=" C PRO A 624 " pdb=" O PRO A 624 " ideal model delta sigma weight residual 1.235 1.211 0.024 7.90e-03 1.60e+04 9.52e+00 bond pdb=" CB ARG A1479 " pdb=" CG ARG A1479 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.98e+00 ... (remaining 13379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 17428 3.12 - 6.24: 525 6.24 - 9.36: 84 9.36 - 12.47: 14 12.47 - 15.59: 2 Bond angle restraints: 18053 Sorted by residual: angle pdb=" N ILE A 364 " pdb=" CA ILE A 364 " pdb=" C ILE A 364 " ideal model delta sigma weight residual 112.96 105.33 7.63 1.00e+00 1.00e+00 5.82e+01 angle pdb=" N GLY A1694 " pdb=" CA GLY A1694 " pdb=" C GLY A1694 " ideal model delta sigma weight residual 113.18 128.77 -15.59 2.37e+00 1.78e-01 4.33e+01 angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 109.34 121.60 -12.26 2.08e+00 2.31e-01 3.48e+01 angle pdb=" N VAL A 699 " pdb=" CA VAL A 699 " pdb=" C VAL A 699 " ideal model delta sigma weight residual 111.58 105.62 5.96 1.06e+00 8.90e-01 3.16e+01 angle pdb=" C TYR A1318 " pdb=" N ASP A1319 " pdb=" CA ASP A1319 " ideal model delta sigma weight residual 122.46 130.21 -7.75 1.41e+00 5.03e-01 3.02e+01 ... (remaining 18048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 7322 15.23 - 30.46: 672 30.46 - 45.69: 133 45.69 - 60.92: 15 60.92 - 76.15: 7 Dihedral angle restraints: 8149 sinusoidal: 3285 harmonic: 4864 Sorted by residual: dihedral pdb=" CA PRO A 581 " pdb=" C PRO A 581 " pdb=" N VAL A 582 " pdb=" CA VAL A 582 " ideal model delta harmonic sigma weight residual -180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" CA GLY A1694 " pdb=" C GLY A1694 " pdb=" N GLU A1695 " pdb=" CA GLU A1695 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA LEU A1693 " pdb=" C LEU A1693 " pdb=" N GLY A1694 " pdb=" CA GLY A1694 " ideal model delta harmonic sigma weight residual 180.00 147.76 32.24 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1578 0.075 - 0.151: 428 0.151 - 0.226: 51 0.226 - 0.301: 12 0.301 - 0.377: 6 Chirality restraints: 2075 Sorted by residual: chirality pdb=" CA LYS A 762 " pdb=" N LYS A 762 " pdb=" C LYS A 762 " pdb=" CB LYS A 762 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE A1280 " pdb=" CA ILE A1280 " pdb=" CG1 ILE A1280 " pdb=" CG2 ILE A1280 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL A1800 " pdb=" CA VAL A1800 " pdb=" CG1 VAL A1800 " pdb=" CG2 VAL A1800 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 2072 not shown) Planarity restraints: 2279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1289 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ASP A1289 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP A1289 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A1290 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 581 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C PRO A 581 " 0.047 2.00e-02 2.50e+03 pdb=" O PRO A 581 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 582 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 950 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO A 951 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 951 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 951 " -0.038 5.00e-02 4.00e+02 ... (remaining 2276 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2365 2.76 - 3.29: 12322 3.29 - 3.83: 20422 3.83 - 4.36: 23003 4.36 - 4.90: 38480 Nonbonded interactions: 96592 Sorted by model distance: nonbonded pdb=" O LEU A1668 " pdb=" OG SER A1672 " model vdw 2.222 3.040 nonbonded pdb=" O LEU A 497 " pdb=" OG SER A 500 " model vdw 2.222 3.040 nonbonded pdb=" OG SER A1098 " pdb=" OG SER A1101 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLU A1307 " pdb=" OG SER A1324 " model vdw 2.276 3.040 nonbonded pdb=" O SER A1327 " pdb=" OG SER A1327 " model vdw 2.290 3.040 ... (remaining 96587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.010 0.188 13393 Z= 0.446 Angle : 1.347 28.110 18065 Z= 0.710 Chirality : 0.070 0.377 2075 Planarity : 0.008 0.066 2279 Dihedral : 12.238 76.148 4974 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.91 % Favored : 87.85 % Rotamer: Outliers : 0.74 % Allowed : 6.72 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.15), residues: 1629 helix: -3.54 (0.12), residues: 718 sheet: -3.89 (0.47), residues: 78 loop : -3.52 (0.18), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A1717 HIS 0.011 0.004 HIS A1283 PHE 0.037 0.005 PHE A1457 TYR 0.035 0.004 TYR A 695 ARG 0.009 0.002 ARG A1741 Details of bonding type rmsd hydrogen bonds : bond 0.21233 ( 394) hydrogen bonds : angle 7.88227 ( 1122) metal coordination : bond 0.13212 ( 6) metal coordination : angle 14.51831 ( 6) SS BOND : bond 0.01462 ( 3) SS BOND : angle 1.85488 ( 6) covalent geometry : bond 0.00938 (13384) covalent geometry : angle 1.32028 (18053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 277 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.7390 (m90) cc_final: 0.7066 (m90) REVERT: A 510 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5466 (pp) REVERT: A 850 GLU cc_start: 0.8123 (tt0) cc_final: 0.7809 (tm-30) REVERT: A 870 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8810 (tm) REVERT: A 910 TYR cc_start: 0.8108 (t80) cc_final: 0.7668 (t80) REVERT: A 1019 TYR cc_start: 0.5559 (t80) cc_final: 0.5321 (t80) REVERT: A 1028 PHE cc_start: 0.8793 (t80) cc_final: 0.8589 (t80) REVERT: A 1029 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8547 (mtmm) REVERT: A 1132 TYR cc_start: 0.7698 (m-10) cc_final: 0.7423 (m-80) REVERT: A 1207 MET cc_start: 0.8940 (mmt) cc_final: 0.8707 (mmm) REVERT: A 1285 MET cc_start: 0.6901 (ttm) cc_final: 0.6635 (mtp) REVERT: A 1308 GLN cc_start: 0.8668 (mm110) cc_final: 0.8432 (mm-40) REVERT: A 1495 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7982 (mtp180) REVERT: A 1496 ASN cc_start: 0.6155 (m-40) cc_final: 0.5908 (m-40) REVERT: A 1623 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8599 (ttpp) REVERT: A 1715 PHE cc_start: 0.6972 (t80) cc_final: 0.6293 (t80) REVERT: B 47 THR cc_start: 0.8682 (p) cc_final: 0.8203 (t) outliers start: 11 outliers final: 3 residues processed: 286 average time/residue: 0.3048 time to fit residues: 121.9349 Evaluate side-chains 147 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 131 GLN A 149 ASN A 512 ASN A 522 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1206 GLN A1297 ASN A1405 HIS A1734 ASN ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.124281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098622 restraints weight = 32670.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100713 restraints weight = 20657.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102164 restraints weight = 15027.795| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13393 Z= 0.130 Angle : 0.725 12.344 18065 Z= 0.367 Chirality : 0.043 0.198 2075 Planarity : 0.005 0.068 2279 Dihedral : 6.547 34.808 1770 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.18), residues: 1629 helix: -2.21 (0.17), residues: 714 sheet: -3.30 (0.47), residues: 81 loop : -3.10 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 245 HIS 0.005 0.001 HIS A1812 PHE 0.018 0.002 PHE A 223 TYR 0.016 0.001 TYR A 214 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 394) hydrogen bonds : angle 5.15018 ( 1122) metal coordination : bond 0.00757 ( 6) metal coordination : angle 8.59767 ( 6) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.95822 ( 6) covalent geometry : bond 0.00282 (13384) covalent geometry : angle 0.70828 (18053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8943 (mp) cc_final: 0.8670 (mt) REVERT: A 836 ASP cc_start: 0.8399 (m-30) cc_final: 0.7888 (m-30) REVERT: A 837 LYS cc_start: 0.7369 (ttpt) cc_final: 0.7134 (mtmt) REVERT: A 850 GLU cc_start: 0.8231 (tt0) cc_final: 0.7907 (tm-30) REVERT: A 1028 PHE cc_start: 0.8750 (t80) cc_final: 0.8424 (t80) REVERT: A 1122 LYS cc_start: 0.8887 (tttp) cc_final: 0.8556 (tppt) REVERT: A 1207 MET cc_start: 0.8932 (mmt) cc_final: 0.8717 (mmm) REVERT: A 1271 HIS cc_start: 0.7128 (m-70) cc_final: 0.6818 (m-70) REVERT: A 1274 MET cc_start: 0.5742 (mmt) cc_final: 0.5031 (mtt) REVERT: A 1285 MET cc_start: 0.7608 (ttm) cc_final: 0.7310 (mtp) REVERT: A 1290 MET cc_start: 0.6252 (ttt) cc_final: 0.5503 (tpt) REVERT: A 1308 GLN cc_start: 0.8711 (mm110) cc_final: 0.8256 (mm-40) REVERT: A 1419 ILE cc_start: 0.8646 (mt) cc_final: 0.8374 (mm) REVERT: A 1495 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6894 (mtt90) REVERT: A 1585 LEU cc_start: 0.7629 (mm) cc_final: 0.7319 (mt) REVERT: A 1715 PHE cc_start: 0.6970 (t80) cc_final: 0.6632 (t80) REVERT: A 1772 PHE cc_start: 0.6822 (t80) cc_final: 0.6499 (t80) REVERT: B 47 THR cc_start: 0.8675 (p) cc_final: 0.8243 (t) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.2582 time to fit residues: 82.8829 Evaluate side-chains 135 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 35 optimal weight: 0.0770 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.125575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100497 restraints weight = 33672.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101906 restraints weight = 23184.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102822 restraints weight = 16556.270| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13393 Z= 0.111 Angle : 0.648 9.968 18065 Z= 0.327 Chirality : 0.042 0.193 2075 Planarity : 0.004 0.048 2279 Dihedral : 5.726 31.238 1770 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.19), residues: 1629 helix: -1.49 (0.18), residues: 715 sheet: -2.46 (0.49), residues: 91 loop : -2.80 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1192 HIS 0.004 0.001 HIS A1812 PHE 0.014 0.001 PHE A 852 TYR 0.014 0.001 TYR A 782 ARG 0.004 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 394) hydrogen bonds : angle 4.60477 ( 1122) metal coordination : bond 0.00487 ( 6) metal coordination : angle 6.77950 ( 6) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.03444 ( 6) covalent geometry : bond 0.00239 (13384) covalent geometry : angle 0.63595 (18053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8848 (mp) cc_final: 0.8566 (mt) REVERT: A 836 ASP cc_start: 0.8407 (m-30) cc_final: 0.7989 (m-30) REVERT: A 850 GLU cc_start: 0.8308 (tt0) cc_final: 0.7839 (tm-30) REVERT: A 893 MET cc_start: 0.8834 (ptt) cc_final: 0.8623 (ptt) REVERT: A 1026 MET cc_start: 0.6506 (mmt) cc_final: 0.6248 (mmm) REVERT: A 1028 PHE cc_start: 0.8666 (t80) cc_final: 0.8448 (t80) REVERT: A 1095 CYS cc_start: 0.8708 (p) cc_final: 0.8497 (p) REVERT: A 1122 LYS cc_start: 0.8861 (tttp) cc_final: 0.8625 (tptp) REVERT: A 1207 MET cc_start: 0.8856 (mmt) cc_final: 0.8590 (mmm) REVERT: A 1271 HIS cc_start: 0.7319 (m-70) cc_final: 0.6945 (m-70) REVERT: A 1274 MET cc_start: 0.5911 (mmt) cc_final: 0.5094 (mtm) REVERT: A 1285 MET cc_start: 0.7538 (ttm) cc_final: 0.7338 (mtp) REVERT: A 1290 MET cc_start: 0.6232 (ttt) cc_final: 0.5862 (tpp) REVERT: A 1308 GLN cc_start: 0.8656 (mm110) cc_final: 0.8264 (mm-40) REVERT: A 1495 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.6866 (mtt90) REVERT: A 1715 PHE cc_start: 0.7065 (t80) cc_final: 0.6600 (t80) REVERT: B 47 THR cc_start: 0.8837 (p) cc_final: 0.8418 (t) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2707 time to fit residues: 78.9415 Evaluate side-chains 138 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.0670 chunk 110 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 472 HIS A 704 HIS A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1712 ASN A1713 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.119956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093911 restraints weight = 33277.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095856 restraints weight = 21767.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097188 restraints weight = 16164.669| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13393 Z= 0.192 Angle : 0.723 9.405 18065 Z= 0.368 Chirality : 0.046 0.195 2075 Planarity : 0.004 0.046 2279 Dihedral : 5.830 30.893 1770 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1629 helix: -1.29 (0.18), residues: 727 sheet: -2.05 (0.57), residues: 82 loop : -2.71 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1192 HIS 0.004 0.001 HIS A 472 PHE 0.020 0.002 PHE A 642 TYR 0.021 0.002 TYR A 695 ARG 0.005 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 394) hydrogen bonds : angle 4.84244 ( 1122) metal coordination : bond 0.01110 ( 6) metal coordination : angle 7.45751 ( 6) SS BOND : bond 0.00550 ( 3) SS BOND : angle 1.07930 ( 6) covalent geometry : bond 0.00439 (13384) covalent geometry : angle 0.71043 (18053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.7149 (m110) cc_final: 0.6165 (t0) REVERT: A 151 PHE cc_start: 0.7244 (m-80) cc_final: 0.6346 (t80) REVERT: A 385 MET cc_start: 0.7669 (ppp) cc_final: 0.7430 (ppp) REVERT: A 393 VAL cc_start: 0.8824 (t) cc_final: 0.8611 (t) REVERT: A 458 MET cc_start: 0.7283 (tpt) cc_final: 0.7072 (tpt) REVERT: A 850 GLU cc_start: 0.8215 (tt0) cc_final: 0.7888 (tm-30) REVERT: A 1026 MET cc_start: 0.6708 (mmt) cc_final: 0.6410 (mmm) REVERT: A 1028 PHE cc_start: 0.8796 (t80) cc_final: 0.8544 (t80) REVERT: A 1030 TYR cc_start: 0.7983 (m-80) cc_final: 0.7501 (m-80) REVERT: A 1271 HIS cc_start: 0.7228 (m-70) cc_final: 0.6945 (m-70) REVERT: A 1274 MET cc_start: 0.5687 (mmt) cc_final: 0.4912 (mtm) REVERT: A 1290 MET cc_start: 0.6670 (ttt) cc_final: 0.6161 (tpp) REVERT: A 1308 GLN cc_start: 0.8743 (mm110) cc_final: 0.8447 (mm-40) REVERT: B 47 THR cc_start: 0.8733 (p) cc_final: 0.8170 (t) REVERT: B 77 LYS cc_start: 0.8941 (mptt) cc_final: 0.8473 (mmmt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2518 time to fit residues: 63.9164 Evaluate side-chains 123 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1713 GLN A1714 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100120 restraints weight = 33009.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101755 restraints weight = 21985.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102732 restraints weight = 15755.702| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13393 Z= 0.108 Angle : 0.634 10.062 18065 Z= 0.317 Chirality : 0.042 0.215 2075 Planarity : 0.004 0.048 2279 Dihedral : 5.247 28.321 1770 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1629 helix: -0.83 (0.19), residues: 722 sheet: -1.63 (0.56), residues: 85 loop : -2.58 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 76 HIS 0.002 0.001 HIS A 647 PHE 0.012 0.001 PHE A 852 TYR 0.012 0.001 TYR A 782 ARG 0.006 0.000 ARG A1092 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 394) hydrogen bonds : angle 4.36259 ( 1122) metal coordination : bond 0.00330 ( 6) metal coordination : angle 5.34697 ( 6) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.57533 ( 6) covalent geometry : bond 0.00233 (13384) covalent geometry : angle 0.62693 (18053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6993 (m110) cc_final: 0.6025 (t0) REVERT: A 151 PHE cc_start: 0.7074 (m-80) cc_final: 0.6294 (t80) REVERT: A 445 ILE cc_start: 0.9209 (mm) cc_final: 0.8636 (tp) REVERT: A 850 GLU cc_start: 0.8227 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 973 ASP cc_start: 0.7518 (t0) cc_final: 0.7304 (m-30) REVERT: A 1026 MET cc_start: 0.6224 (mmt) cc_final: 0.6024 (mmm) REVERT: A 1028 PHE cc_start: 0.8744 (t80) cc_final: 0.8536 (t80) REVERT: A 1030 TYR cc_start: 0.8086 (m-80) cc_final: 0.7461 (m-80) REVERT: A 1271 HIS cc_start: 0.7771 (m-70) cc_final: 0.7347 (m-70) REVERT: A 1274 MET cc_start: 0.5549 (mmt) cc_final: 0.4942 (mtt) REVERT: A 1285 MET cc_start: 0.6571 (mtp) cc_final: 0.6265 (mtp) REVERT: A 1308 GLN cc_start: 0.8701 (mm110) cc_final: 0.8474 (mm-40) REVERT: A 1495 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.6831 (mtt90) REVERT: A 1623 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8433 (ttpp) REVERT: A 1772 PHE cc_start: 0.6974 (t80) cc_final: 0.6698 (t80) REVERT: B 47 THR cc_start: 0.8911 (p) cc_final: 0.8378 (t) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2411 time to fit residues: 66.0552 Evaluate side-chains 131 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 120 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1713 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100788 restraints weight = 33329.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101971 restraints weight = 23341.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.103428 restraints weight = 16819.087| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13393 Z= 0.103 Angle : 0.622 9.357 18065 Z= 0.312 Chirality : 0.042 0.236 2075 Planarity : 0.004 0.053 2279 Dihedral : 4.998 25.919 1770 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.20), residues: 1629 helix: -0.60 (0.20), residues: 718 sheet: -1.53 (0.55), residues: 87 loop : -2.45 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1549 HIS 0.006 0.001 HIS A 647 PHE 0.012 0.001 PHE A 852 TYR 0.016 0.001 TYR A 450 ARG 0.007 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 394) hydrogen bonds : angle 4.28321 ( 1122) metal coordination : bond 0.00348 ( 6) metal coordination : angle 4.75597 ( 6) SS BOND : bond 0.00505 ( 3) SS BOND : angle 0.92505 ( 6) covalent geometry : bond 0.00224 (13384) covalent geometry : angle 0.61594 (18053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6867 (m110) cc_final: 0.6044 (t0) REVERT: A 151 PHE cc_start: 0.6946 (m-80) cc_final: 0.6240 (t80) REVERT: A 355 LEU cc_start: 0.9115 (mp) cc_final: 0.8665 (tp) REVERT: A 848 MET cc_start: 0.7360 (mmt) cc_final: 0.7127 (mmt) REVERT: A 850 GLU cc_start: 0.8300 (tt0) cc_final: 0.7896 (tm-30) REVERT: A 1030 TYR cc_start: 0.8094 (m-80) cc_final: 0.7457 (m-80) REVERT: A 1271 HIS cc_start: 0.7681 (m-70) cc_final: 0.7205 (m-70) REVERT: A 1274 MET cc_start: 0.5377 (mmt) cc_final: 0.4676 (mtm) REVERT: A 1285 MET cc_start: 0.6525 (mtp) cc_final: 0.6217 (mtp) REVERT: A 1308 GLN cc_start: 0.8671 (mm110) cc_final: 0.8399 (mm-40) REVERT: A 1495 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.6717 (mtt90) REVERT: A 1623 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8406 (ttpp) REVERT: B 47 THR cc_start: 0.8903 (p) cc_final: 0.8389 (t) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2348 time to fit residues: 64.3031 Evaluate side-chains 135 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 3 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1154 ASN ** A1726 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 = 0.3987 r_free = 0.3987 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097837 restraints weight = 33673.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098999 restraints weight = 23070.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099551 restraints weight = 16561.090| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13393 Z= 0.137 Angle : 0.660 9.395 18065 Z= 0.331 Chirality : 0.044 0.186 2075 Planarity : 0.004 0.043 2279 Dihedral : 5.084 27.089 1770 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1629 helix: -0.47 (0.20), residues: 728 sheet: -1.65 (0.55), residues: 82 loop : -2.47 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1192 HIS 0.004 0.001 HIS A1812 PHE 0.010 0.001 PHE A 852 TYR 0.016 0.001 TYR A 695 ARG 0.006 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.02902 ( 394) hydrogen bonds : angle 4.43090 ( 1122) metal coordination : bond 0.00734 ( 6) metal coordination : angle 5.26312 ( 6) SS BOND : bond 0.00455 ( 3) SS BOND : angle 0.79403 ( 6) covalent geometry : bond 0.00314 (13384) covalent geometry : angle 0.65349 (18053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6868 (m110) cc_final: 0.5936 (t0) REVERT: A 151 PHE cc_start: 0.6931 (m-80) cc_final: 0.6192 (t80) REVERT: A 848 MET cc_start: 0.7361 (mmt) cc_final: 0.7137 (mmt) REVERT: A 850 GLU cc_start: 0.8294 (tt0) cc_final: 0.7891 (tm-30) REVERT: A 893 MET cc_start: 0.8674 (ptt) cc_final: 0.8473 (ptt) REVERT: A 1030 TYR cc_start: 0.8352 (m-80) cc_final: 0.7752 (m-80) REVERT: A 1271 HIS cc_start: 0.7633 (m-70) cc_final: 0.7070 (m-70) REVERT: A 1274 MET cc_start: 0.5350 (mmt) cc_final: 0.4819 (mtm) REVERT: A 1308 GLN cc_start: 0.8605 (mm110) cc_final: 0.8310 (mm-40) REVERT: B 47 THR cc_start: 0.8989 (p) cc_final: 0.8439 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2289 time to fit residues: 57.1743 Evaluate side-chains 124 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 130 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1714 ASN A1726 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.123580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099109 restraints weight = 33718.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100320 restraints weight = 23204.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101916 restraints weight = 16805.967| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13393 Z= 0.111 Angle : 0.635 9.449 18065 Z= 0.315 Chirality : 0.043 0.191 2075 Planarity : 0.003 0.044 2279 Dihedral : 4.932 26.624 1770 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1629 helix: -0.33 (0.20), residues: 725 sheet: -1.45 (0.55), residues: 80 loop : -2.37 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1549 HIS 0.004 0.001 HIS A1812 PHE 0.011 0.001 PHE A 223 TYR 0.013 0.001 TYR A 450 ARG 0.005 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 394) hydrogen bonds : angle 4.32811 ( 1122) metal coordination : bond 0.00474 ( 6) metal coordination : angle 4.64085 ( 6) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.66672 ( 6) covalent geometry : bond 0.00250 (13384) covalent geometry : angle 0.62900 (18053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6715 (m110) cc_final: 0.5807 (t0) REVERT: A 376 ARG cc_start: 0.8296 (mmp80) cc_final: 0.8022 (mmp80) REVERT: A 848 MET cc_start: 0.7282 (mmt) cc_final: 0.7069 (mmt) REVERT: A 850 GLU cc_start: 0.8302 (tt0) cc_final: 0.7885 (tm-30) REVERT: A 1030 TYR cc_start: 0.8282 (m-80) cc_final: 0.7774 (m-80) REVERT: A 1271 HIS cc_start: 0.7342 (m-70) cc_final: 0.6684 (m-70) REVERT: A 1274 MET cc_start: 0.5120 (mmt) cc_final: 0.4587 (mtm) REVERT: A 1308 GLN cc_start: 0.8617 (mm110) cc_final: 0.8304 (mm-40) REVERT: A 1495 ARG cc_start: 0.7244 (mtm-85) cc_final: 0.5965 (mtt90) REVERT: A 1623 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8494 (ttpp) REVERT: B 47 THR cc_start: 0.8936 (p) cc_final: 0.8403 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2380 time to fit residues: 59.8249 Evaluate side-chains 128 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.122459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098124 restraints weight = 33302.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099337 restraints weight = 22741.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100932 restraints weight = 16446.874| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13393 Z= 0.130 Angle : 0.662 9.326 18065 Z= 0.331 Chirality : 0.043 0.193 2075 Planarity : 0.003 0.043 2279 Dihedral : 4.953 26.986 1770 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1629 helix: -0.30 (0.20), residues: 720 sheet: -1.61 (0.56), residues: 82 loop : -2.29 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1192 HIS 0.004 0.001 HIS A1812 PHE 0.021 0.001 PHE A1772 TYR 0.013 0.001 TYR A 782 ARG 0.005 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 394) hydrogen bonds : angle 4.53846 ( 1122) metal coordination : bond 0.00659 ( 6) metal coordination : angle 4.75787 ( 6) SS BOND : bond 0.00266 ( 3) SS BOND : angle 0.84769 ( 6) covalent geometry : bond 0.00293 (13384) covalent geometry : angle 0.65649 (18053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6709 (m110) cc_final: 0.5840 (t0) REVERT: A 850 GLU cc_start: 0.8317 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 903 GLU cc_start: 0.8289 (mp0) cc_final: 0.8002 (mp0) REVERT: A 1030 TYR cc_start: 0.8243 (m-80) cc_final: 0.7797 (m-80) REVERT: A 1271 HIS cc_start: 0.7271 (m-70) cc_final: 0.6582 (m-70) REVERT: A 1274 MET cc_start: 0.5160 (mmt) cc_final: 0.4666 (mtt) REVERT: A 1307 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6354 (tm-30) REVERT: A 1308 GLN cc_start: 0.8321 (mm110) cc_final: 0.7894 (mm-40) REVERT: B 47 THR cc_start: 0.8950 (p) cc_final: 0.8391 (t) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2408 time to fit residues: 57.1216 Evaluate side-chains 129 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 10.0000 chunk 156 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1154 ASN ** A1711 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.124263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099903 restraints weight = 33420.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101515 restraints weight = 22240.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.103136 restraints weight = 15790.819| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13393 Z= 0.109 Angle : 0.645 9.311 18065 Z= 0.319 Chirality : 0.043 0.194 2075 Planarity : 0.003 0.041 2279 Dihedral : 4.820 26.815 1770 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1629 helix: -0.19 (0.20), residues: 719 sheet: -1.36 (0.57), residues: 80 loop : -2.24 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1549 HIS 0.005 0.001 HIS A1812 PHE 0.019 0.001 PHE A1772 TYR 0.022 0.001 TYR A1312 ARG 0.007 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 394) hydrogen bonds : angle 4.44816 ( 1122) metal coordination : bond 0.00449 ( 6) metal coordination : angle 4.21800 ( 6) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.71458 ( 6) covalent geometry : bond 0.00244 (13384) covalent geometry : angle 0.64048 (18053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6513 (m110) cc_final: 0.5555 (t0) REVERT: A 376 ARG cc_start: 0.8233 (mmp80) cc_final: 0.7896 (mmp80) REVERT: A 850 GLU cc_start: 0.8343 (tt0) cc_final: 0.7977 (tm-30) REVERT: A 860 LEU cc_start: 0.8354 (tp) cc_final: 0.8088 (tp) REVERT: A 861 ASP cc_start: 0.7898 (m-30) cc_final: 0.7569 (m-30) REVERT: A 903 GLU cc_start: 0.8135 (mp0) cc_final: 0.7926 (mp0) REVERT: A 1026 MET cc_start: 0.7437 (mmm) cc_final: 0.7176 (mmm) REVERT: A 1030 TYR cc_start: 0.7929 (m-80) cc_final: 0.7509 (m-80) REVERT: A 1196 MET cc_start: 0.7769 (mtt) cc_final: 0.7491 (mtt) REVERT: A 1271 HIS cc_start: 0.7549 (m-70) cc_final: 0.6811 (m-70) REVERT: A 1274 MET cc_start: 0.4942 (mmt) cc_final: 0.4446 (mtt) REVERT: A 1308 GLN cc_start: 0.8425 (mm110) cc_final: 0.8076 (mm-40) REVERT: B 47 THR cc_start: 0.8931 (p) cc_final: 0.8389 (t) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2355 time to fit residues: 58.5864 Evaluate side-chains 129 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.120347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.095762 restraints weight = 33631.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097498 restraints weight = 21291.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.099702 restraints weight = 14767.769| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13393 Z= 0.160 Angle : 0.699 9.401 18065 Z= 0.349 Chirality : 0.045 0.194 2075 Planarity : 0.004 0.041 2279 Dihedral : 5.090 27.396 1770 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1629 helix: -0.41 (0.19), residues: 741 sheet: -1.55 (0.57), residues: 82 loop : -2.21 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 155 HIS 0.005 0.001 HIS A1812 PHE 0.018 0.002 PHE A1772 TYR 0.015 0.001 TYR A 695 ARG 0.006 0.000 ARG A1543 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 394) hydrogen bonds : angle 4.66179 ( 1122) metal coordination : bond 0.00905 ( 6) metal coordination : angle 5.08734 ( 6) SS BOND : bond 0.00377 ( 3) SS BOND : angle 0.68500 ( 6) covalent geometry : bond 0.00367 (13384) covalent geometry : angle 0.69301 (18053) =============================================================================== Job complete usr+sys time: 3726.02 seconds wall clock time: 66 minutes 2.24 seconds (3962.24 seconds total)