Starting phenix.real_space_refine on Wed Mar 4 10:28:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh1_31983/03_2026/7vh1_31983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh1_31983/03_2026/7vh1_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_31983/03_2026/7vh1_31983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh1_31983/03_2026/7vh1_31983.map" model { file = "/net/cci-nas-00/data/ceres_data/7vh1_31983/03_2026/7vh1_31983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh1_31983/03_2026/7vh1_31983.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 7, 'HIS:plan': 4, 'GLU:plan': 11, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1} 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: 2.90, per 1000 atoms: 0.22 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: 1.04 Conformation dependent library (CDL) restraints added in 561.0 milliseconds 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: 0.53 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: 2.18 Time building geometry restraints manager: 1.45 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.520 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.002 ARG A1741 TYR 0.035 0.004 TYR A 695 PHE 0.037 0.005 PHE A1457 TRP 0.030 0.004 TRP A1717 HIS 0.011 0.004 HIS A1283 Details of bonding type rmsd covalent geometry : bond 0.00938 (13384) covalent geometry : angle 1.32028 (18053) SS BOND : bond 0.01462 ( 3) SS BOND : angle 1.85488 ( 6) hydrogen bonds : bond 0.21233 ( 394) hydrogen bonds : angle 7.88227 ( 1122) metal coordination : bond 0.13212 ( 6) metal coordination : angle 14.51831 ( 6) *********************** 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 : 0.517 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: 0.7064 (m90) REVERT: A 510 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5540 (pp) REVERT: A 850 GLU cc_start: 0.8123 (tt0) cc_final: 0.7812 (tm-30) REVERT: A 870 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8809 (tm) REVERT: A 910 TYR cc_start: 0.8108 (t80) cc_final: 0.7666 (t80) REVERT: A 1019 TYR cc_start: 0.5559 (t80) cc_final: 0.5336 (t80) REVERT: A 1028 PHE cc_start: 0.8793 (t80) cc_final: 0.8591 (t80) REVERT: A 1029 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8556 (mtmm) REVERT: A 1132 TYR cc_start: 0.7698 (m-10) cc_final: 0.7430 (m-80) REVERT: A 1207 MET cc_start: 0.8940 (mmt) cc_final: 0.8704 (mmm) REVERT: A 1285 MET cc_start: 0.6901 (ttm) cc_final: 0.6662 (mtp) REVERT: A 1308 GLN cc_start: 0.8668 (mm110) cc_final: 0.8430 (mm-40) REVERT: A 1495 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7981 (mtp180) REVERT: A 1496 ASN cc_start: 0.6155 (m-40) cc_final: 0.5907 (m-40) REVERT: A 1623 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8593 (ttpp) REVERT: A 1715 PHE cc_start: 0.6972 (t80) cc_final: 0.6290 (t80) REVERT: B 47 THR cc_start: 0.8682 (p) cc_final: 0.8202 (t) outliers start: 11 outliers final: 3 residues processed: 286 average time/residue: 0.1394 time to fit residues: 55.7859 Evaluate side-chains 146 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 288 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 A1406 ASN A1734 ASN ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.124003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097962 restraints weight = 33257.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100095 restraints weight = 21198.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101554 restraints weight = 15361.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102351 restraints weight = 12357.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103028 restraints weight = 10821.700| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13393 Z= 0.136 Angle : 0.726 12.082 18065 Z= 0.369 Chirality : 0.044 0.223 2075 Planarity : 0.005 0.066 2279 Dihedral : 6.518 35.250 1770 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.13 % Allowed : 4.23 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.18), residues: 1629 helix: -2.15 (0.17), residues: 711 sheet: -3.01 (0.44), residues: 97 loop : -3.08 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 36 TYR 0.017 0.001 TYR A 214 PHE 0.018 0.002 PHE A 223 TRP 0.013 0.002 TRP A 245 HIS 0.005 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00300 (13384) covalent geometry : angle 0.70929 (18053) SS BOND : bond 0.00481 ( 3) SS BOND : angle 0.92327 ( 6) hydrogen bonds : bond 0.03871 ( 394) hydrogen bonds : angle 5.12994 ( 1122) metal coordination : bond 0.00951 ( 6) metal coordination : angle 8.46651 ( 6) *********************** 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 216 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.6522 (mmt) cc_final: 0.6196 (mmt) REVERT: A 836 ASP cc_start: 0.8367 (m-30) cc_final: 0.8026 (p0) REVERT: A 837 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6847 (mtmt) REVERT: A 850 GLU cc_start: 0.8211 (tt0) cc_final: 0.7912 (tm-30) REVERT: A 1028 PHE cc_start: 0.8724 (t80) cc_final: 0.8400 (t80) REVERT: A 1122 LYS cc_start: 0.8829 (tttp) cc_final: 0.8557 (tppt) REVERT: A 1207 MET cc_start: 0.8887 (mmt) cc_final: 0.8685 (mmm) REVERT: A 1274 MET cc_start: 0.5468 (mmt) cc_final: 0.4865 (mtt) REVERT: A 1285 MET cc_start: 0.7596 (ttm) cc_final: 0.7329 (mtp) REVERT: A 1290 MET cc_start: 0.6407 (ttt) cc_final: 0.5639 (tpt) REVERT: A 1308 GLN cc_start: 0.8647 (mm110) cc_final: 0.8263 (mm-40) REVERT: A 1419 ILE cc_start: 0.8653 (mt) cc_final: 0.8390 (mm) REVERT: A 1467 ASP cc_start: 0.7816 (p0) cc_final: 0.7599 (p0) REVERT: A 1543 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7487 (ptt-90) REVERT: A 1585 LEU cc_start: 0.7644 (mm) cc_final: 0.7396 (mt) REVERT: A 1715 PHE cc_start: 0.6844 (t80) cc_final: 0.6530 (t80) REVERT: B 47 THR cc_start: 0.8621 (p) cc_final: 0.8193 (t) outliers start: 2 outliers final: 1 residues processed: 216 average time/residue: 0.1068 time to fit residues: 33.6757 Evaluate side-chains 140 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 66 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.124584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099736 restraints weight = 33692.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101091 restraints weight = 22742.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.103138 restraints weight = 16321.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.103383 restraints weight = 13558.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.103455 restraints weight = 11254.767| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13393 Z= 0.115 Angle : 0.658 9.880 18065 Z= 0.333 Chirality : 0.042 0.192 2075 Planarity : 0.004 0.049 2279 Dihedral : 5.796 31.146 1770 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.19), residues: 1629 helix: -1.55 (0.18), residues: 721 sheet: -2.47 (0.50), residues: 91 loop : -2.83 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.015 0.001 TYR A 782 PHE 0.015 0.001 PHE A 852 TRP 0.013 0.001 TRP A1192 HIS 0.007 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00255 (13384) covalent geometry : angle 0.64550 (18053) SS BOND : bond 0.00607 ( 3) SS BOND : angle 0.94934 ( 6) hydrogen bonds : bond 0.03328 ( 394) hydrogen bonds : angle 4.62490 ( 1122) metal coordination : bond 0.00527 ( 6) metal coordination : angle 6.95866 ( 6) *********************** 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 196 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7854 (tpp) cc_final: 0.7226 (tpt) REVERT: A 836 ASP cc_start: 0.8431 (m-30) cc_final: 0.7902 (p0) REVERT: A 850 GLU cc_start: 0.8296 (tt0) cc_final: 0.7837 (tm-30) REVERT: A 1026 MET cc_start: 0.6574 (mmt) cc_final: 0.6315 (mmm) REVERT: A 1028 PHE cc_start: 0.8668 (t80) cc_final: 0.8443 (t80) REVERT: A 1122 LYS cc_start: 0.8931 (tttp) cc_final: 0.8728 (tptp) REVERT: A 1207 MET cc_start: 0.8873 (mmt) cc_final: 0.8641 (mmm) REVERT: A 1271 HIS cc_start: 0.8031 (m-70) cc_final: 0.7685 (m-70) REVERT: A 1274 MET cc_start: 0.5591 (mmt) cc_final: 0.4899 (mtm) REVERT: A 1285 MET cc_start: 0.7625 (ttm) cc_final: 0.7422 (mtp) REVERT: A 1290 MET cc_start: 0.6229 (ttt) cc_final: 0.5654 (tpt) REVERT: A 1308 GLN cc_start: 0.8722 (mm110) cc_final: 0.8396 (mm-40) REVERT: A 1495 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.6778 (mtt90) REVERT: A 1543 ARG cc_start: 0.7746 (ptt-90) cc_final: 0.7506 (ptt-90) REVERT: A 1715 PHE cc_start: 0.6702 (t80) cc_final: 0.6324 (t80) REVERT: B 47 THR cc_start: 0.8765 (p) cc_final: 0.8317 (t) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1096 time to fit residues: 31.8813 Evaluate side-chains 134 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 153 optimal weight: 0.0020 chunk 104 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 472 HIS A 704 HIS A1111 ASN ** A1124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.124663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100296 restraints weight = 32965.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.101879 restraints weight = 22128.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103030 restraints weight = 15553.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103570 restraints weight = 13914.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.103549 restraints weight = 11757.880| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13393 Z= 0.111 Angle : 0.631 10.048 18065 Z= 0.319 Chirality : 0.042 0.194 2075 Planarity : 0.004 0.044 2279 Dihedral : 5.379 27.292 1770 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.20), residues: 1629 helix: -1.10 (0.19), residues: 719 sheet: -2.13 (0.52), residues: 94 loop : -2.68 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.014 0.001 TYR A 782 PHE 0.021 0.001 PHE A1772 TRP 0.013 0.001 TRP A1192 HIS 0.006 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00245 (13384) covalent geometry : angle 0.62120 (18053) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.72965 ( 6) hydrogen bonds : bond 0.03007 ( 394) hydrogen bonds : angle 4.41669 ( 1122) metal coordination : bond 0.00481 ( 6) metal coordination : angle 6.00118 ( 6) *********************** 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 186 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 PHE cc_start: 0.7051 (m-80) cc_final: 0.5693 (t80) REVERT: A 355 LEU cc_start: 0.9013 (mp) cc_final: 0.8429 (tp) REVERT: A 361 MET cc_start: 0.8156 (tpt) cc_final: 0.7949 (tpp) REVERT: A 393 VAL cc_start: 0.8647 (t) cc_final: 0.8446 (t) REVERT: A 445 ILE cc_start: 0.9151 (mm) cc_final: 0.8784 (mm) REVERT: A 458 MET cc_start: 0.7865 (tpp) cc_final: 0.6745 (tpt) REVERT: A 850 GLU cc_start: 0.8237 (tt0) cc_final: 0.7809 (tm-30) REVERT: A 892 LEU cc_start: 0.5850 (tp) cc_final: 0.5405 (mt) REVERT: A 893 MET cc_start: 0.8625 (ptt) cc_final: 0.8375 (ptt) REVERT: A 1030 TYR cc_start: 0.8003 (m-80) cc_final: 0.7586 (m-80) REVERT: A 1122 LYS cc_start: 0.8961 (tttp) cc_final: 0.8747 (tptp) REVERT: A 1143 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7922 (mtp85) REVERT: A 1160 CYS cc_start: 0.8366 (p) cc_final: 0.8105 (p) REVERT: A 1271 HIS cc_start: 0.8087 (m-70) cc_final: 0.7886 (m-70) REVERT: A 1274 MET cc_start: 0.5846 (mmt) cc_final: 0.5140 (mtm) REVERT: A 1308 GLN cc_start: 0.8716 (mm110) cc_final: 0.8475 (mm-40) REVERT: A 1495 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6805 (mtt90) REVERT: A 1715 PHE cc_start: 0.6637 (t80) cc_final: 0.6333 (t80) REVERT: B 47 THR cc_start: 0.8868 (p) cc_final: 0.8400 (t) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0994 time to fit residues: 27.8603 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 : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 ASN A1712 ASN A1713 GLN A1714 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094641 restraints weight = 33996.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095849 restraints weight = 22963.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097041 restraints weight = 16814.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097516 restraints weight = 14680.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097526 restraints weight = 12487.196| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13393 Z= 0.205 Angle : 0.742 9.857 18065 Z= 0.376 Chirality : 0.046 0.198 2075 Planarity : 0.004 0.057 2279 Dihedral : 5.708 27.773 1770 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.20), residues: 1629 helix: -1.09 (0.18), residues: 745 sheet: -1.84 (0.58), residues: 80 loop : -2.73 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 553 TYR 0.023 0.002 TYR A 695 PHE 0.018 0.002 PHE A1457 TRP 0.016 0.002 TRP A1192 HIS 0.005 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00467 (13384) covalent geometry : angle 0.73053 (18053) SS BOND : bond 0.00471 ( 3) SS BOND : angle 1.21853 ( 6) hydrogen bonds : bond 0.03681 ( 394) hydrogen bonds : angle 4.75314 ( 1122) metal coordination : bond 0.01153 ( 6) metal coordination : angle 7.05546 ( 6) *********************** 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 152 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6871 (m110) cc_final: 0.6040 (t0) REVERT: A 151 PHE cc_start: 0.7173 (m-80) cc_final: 0.6241 (t80) REVERT: A 355 LEU cc_start: 0.9111 (mp) cc_final: 0.8841 (tp) REVERT: A 565 MET cc_start: 0.6593 (tmm) cc_final: 0.6373 (tmm) REVERT: A 850 GLU cc_start: 0.8316 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 893 MET cc_start: 0.8697 (ptt) cc_final: 0.8453 (ptt) REVERT: A 973 ASP cc_start: 0.8313 (t70) cc_final: 0.7972 (m-30) REVERT: A 1030 TYR cc_start: 0.8392 (m-80) cc_final: 0.7694 (m-80) REVERT: A 1207 MET cc_start: 0.8519 (mmm) cc_final: 0.8280 (mmm) REVERT: A 1271 HIS cc_start: 0.8017 (m-70) cc_final: 0.7510 (m-70) REVERT: A 1274 MET cc_start: 0.5451 (mmt) cc_final: 0.4971 (mtm) REVERT: A 1308 GLN cc_start: 0.8874 (mm110) cc_final: 0.8381 (mm-40) REVERT: A 1696 TRP cc_start: 0.6582 (p-90) cc_final: 0.6164 (p-90) REVERT: B 47 THR cc_start: 0.8824 (p) cc_final: 0.8233 (t) REVERT: B 77 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8478 (mmmt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.1047 time to fit residues: 24.4194 Evaluate side-chains 117 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3954 r_free = 0.3954 target = 0.120417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096118 restraints weight = 33784.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097143 restraints weight = 23215.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098348 restraints weight = 16842.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098875 restraints weight = 14341.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098901 restraints weight = 12445.887| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13393 Z= 0.155 Angle : 0.688 9.424 18065 Z= 0.350 Chirality : 0.045 0.174 2075 Planarity : 0.004 0.047 2279 Dihedral : 5.512 29.592 1770 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1629 helix: -0.80 (0.19), residues: 742 sheet: -2.34 (0.50), residues: 94 loop : -2.57 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.020 0.001 TYR A 450 PHE 0.012 0.001 PHE A 852 TRP 0.012 0.001 TRP A1192 HIS 0.005 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00353 (13384) covalent geometry : angle 0.68055 (18053) SS BOND : bond 0.00429 ( 3) SS BOND : angle 0.97289 ( 6) hydrogen bonds : bond 0.03207 ( 394) hydrogen bonds : angle 4.62977 ( 1122) metal coordination : bond 0.00778 ( 6) metal coordination : angle 5.69632 ( 6) *********************** 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 156 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6847 (m110) cc_final: 0.5809 (t0) REVERT: A 355 LEU cc_start: 0.9105 (mp) cc_final: 0.8796 (tp) REVERT: A 356 ILE cc_start: 0.9192 (mt) cc_final: 0.8982 (mt) REVERT: A 565 MET cc_start: 0.6471 (tmm) cc_final: 0.6220 (tmm) REVERT: A 850 GLU cc_start: 0.8300 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 893 MET cc_start: 0.8673 (ptt) cc_final: 0.8440 (ptt) REVERT: A 973 ASP cc_start: 0.8138 (t70) cc_final: 0.7824 (m-30) REVERT: A 1030 TYR cc_start: 0.8401 (m-80) cc_final: 0.7703 (m-80) REVERT: A 1207 MET cc_start: 0.8581 (mmm) cc_final: 0.8362 (mmm) REVERT: A 1271 HIS cc_start: 0.7989 (m-70) cc_final: 0.7554 (m-70) REVERT: A 1274 MET cc_start: 0.5463 (mmt) cc_final: 0.4892 (mtm) REVERT: A 1308 GLN cc_start: 0.8711 (mm110) cc_final: 0.8328 (mm-40) REVERT: A 1696 TRP cc_start: 0.6428 (p-90) cc_final: 0.6128 (p-90) REVERT: B 47 THR cc_start: 0.8905 (p) cc_final: 0.8336 (t) REVERT: B 77 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8567 (mmmt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0950 time to fit residues: 23.2027 Evaluate side-chains 121 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ** A1231 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.118315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094246 restraints weight = 34103.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095475 restraints weight = 22933.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.095932 restraints weight = 17133.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096148 restraints weight = 16413.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096276 restraints weight = 14932.593| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.004 0.043 13393 Z= 0.180 Angle : 0.719 9.738 18065 Z= 0.362 Chirality : 0.045 0.172 2075 Planarity : 0.004 0.050 2279 Dihedral : 5.542 27.974 1770 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.20), residues: 1629 helix: -0.72 (0.19), residues: 737 sheet: -2.43 (0.51), residues: 94 loop : -2.53 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 553 TYR 0.019 0.002 TYR A 450 PHE 0.017 0.002 PHE A 151 TRP 0.016 0.002 TRP A1192 HIS 0.005 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00413 (13384) covalent geometry : angle 0.70985 (18053) SS BOND : bond 0.00435 ( 3) SS BOND : angle 1.15950 ( 6) hydrogen bonds : bond 0.03399 ( 394) hydrogen bonds : angle 4.73175 ( 1122) metal coordination : bond 0.01018 ( 6) metal coordination : angle 6.20619 ( 6) *********************** 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 154 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6788 (m110) cc_final: 0.6036 (t0) REVERT: A 355 LEU cc_start: 0.9077 (mp) cc_final: 0.8856 (tp) REVERT: A 356 ILE cc_start: 0.9206 (mt) cc_final: 0.8981 (mt) REVERT: A 458 MET cc_start: 0.6476 (tpp) cc_final: 0.5149 (tpt) REVERT: A 490 LEU cc_start: 0.8697 (tp) cc_final: 0.8484 (tp) REVERT: A 565 MET cc_start: 0.6494 (tmm) cc_final: 0.6246 (tmm) REVERT: A 850 GLU cc_start: 0.8330 (tt0) cc_final: 0.7930 (tm-30) REVERT: A 973 ASP cc_start: 0.8238 (t70) cc_final: 0.7915 (m-30) REVERT: A 1030 TYR cc_start: 0.8383 (m-80) cc_final: 0.7651 (m-80) REVERT: A 1207 MET cc_start: 0.8541 (mmm) cc_final: 0.8276 (mmm) REVERT: A 1271 HIS cc_start: 0.7782 (m-70) cc_final: 0.7195 (m-70) REVERT: A 1274 MET cc_start: 0.5435 (mmt) cc_final: 0.4837 (mtt) REVERT: A 1308 GLN cc_start: 0.8706 (mm110) cc_final: 0.8188 (mm-40) REVERT: A 1696 TRP cc_start: 0.6561 (p-90) cc_final: 0.6295 (p-90) REVERT: B 47 THR cc_start: 0.8649 (p) cc_final: 0.8103 (t) REVERT: B 77 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8505 (mmmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1040 time to fit residues: 24.3634 Evaluate side-chains 118 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 111 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 105 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 A1445 GLN ** A1726 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 = 0.3976 r_free = 0.3976 target = 0.121269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096702 restraints weight = 33273.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098318 restraints weight = 21558.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100001 restraints weight = 15184.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100391 restraints weight = 12765.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100270 restraints weight = 10959.796| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13393 Z= 0.116 Angle : 0.656 9.512 18065 Z= 0.327 Chirality : 0.043 0.185 2075 Planarity : 0.003 0.044 2279 Dihedral : 5.201 29.089 1770 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.20), residues: 1629 helix: -0.45 (0.19), residues: 731 sheet: -2.24 (0.52), residues: 90 loop : -2.37 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 376 TYR 0.014 0.001 TYR A 450 PHE 0.013 0.001 PHE A 852 TRP 0.019 0.001 TRP A 155 HIS 0.005 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00263 (13384) covalent geometry : angle 0.65077 (18053) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.72678 ( 6) hydrogen bonds : bond 0.02912 ( 394) hydrogen bonds : angle 4.44730 ( 1122) metal coordination : bond 0.00462 ( 6) metal coordination : angle 4.68569 ( 6) *********************** 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 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6402 (m110) cc_final: 0.5532 (t0) REVERT: A 356 ILE cc_start: 0.9176 (mt) cc_final: 0.8957 (mt) REVERT: A 458 MET cc_start: 0.6258 (tpp) cc_final: 0.5606 (tpt) REVERT: A 565 MET cc_start: 0.6482 (tmm) cc_final: 0.6229 (tmm) REVERT: A 850 GLU cc_start: 0.8329 (tt0) cc_final: 0.7911 (tm-30) REVERT: A 973 ASP cc_start: 0.7979 (t70) cc_final: 0.7728 (m-30) REVERT: A 1026 MET cc_start: 0.7516 (mmm) cc_final: 0.6983 (mmm) REVERT: A 1030 TYR cc_start: 0.8333 (m-80) cc_final: 0.7594 (m-80) REVERT: A 1271 HIS cc_start: 0.7630 (m-70) cc_final: 0.7089 (m-70) REVERT: A 1274 MET cc_start: 0.5231 (mmt) cc_final: 0.4736 (mtt) REVERT: A 1285 MET cc_start: 0.6640 (mtp) cc_final: 0.6278 (mtp) REVERT: A 1308 GLN cc_start: 0.8657 (mm110) cc_final: 0.8350 (mm-40) REVERT: A 1623 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8491 (ttpp) REVERT: B 47 THR cc_start: 0.8633 (p) cc_final: 0.8132 (t) REVERT: B 55 HIS cc_start: 0.3328 (p90) cc_final: 0.3083 (p90) REVERT: B 77 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8446 (mmmt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1022 time to fit residues: 25.5698 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.119716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095610 restraints weight = 34079.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096949 restraints weight = 22654.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097171 restraints weight = 16471.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.097512 restraints weight = 16030.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097603 restraints weight = 14976.799| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13393 Z= 0.147 Angle : 0.682 8.842 18065 Z= 0.340 Chirality : 0.044 0.187 2075 Planarity : 0.004 0.046 2279 Dihedral : 5.227 27.434 1770 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.21), residues: 1629 helix: -0.41 (0.19), residues: 739 sheet: -2.21 (0.54), residues: 90 loop : -2.31 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.018 0.001 TYR A1312 PHE 0.012 0.001 PHE A 852 TRP 0.015 0.001 TRP A1192 HIS 0.004 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00338 (13384) covalent geometry : angle 0.67511 (18053) SS BOND : bond 0.00416 ( 3) SS BOND : angle 0.82326 ( 6) hydrogen bonds : bond 0.03170 ( 394) hydrogen bonds : angle 4.52826 ( 1122) metal coordination : bond 0.00797 ( 6) metal coordination : angle 5.21631 ( 6) *********************** 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 156 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.6731 (m90) cc_final: 0.6472 (m90) REVERT: A 149 ASN cc_start: 0.6474 (m110) cc_final: 0.5579 (t0) REVERT: A 458 MET cc_start: 0.6476 (tpp) cc_final: 0.4912 (tpt) REVERT: A 565 MET cc_start: 0.6506 (tmm) cc_final: 0.6263 (tmm) REVERT: A 850 GLU cc_start: 0.8333 (tt0) cc_final: 0.7992 (tm-30) REVERT: A 973 ASP cc_start: 0.8166 (t70) cc_final: 0.7917 (m-30) REVERT: A 1030 TYR cc_start: 0.8356 (m-80) cc_final: 0.7623 (m-80) REVERT: A 1188 ASP cc_start: 0.7875 (t70) cc_final: 0.7605 (t0) REVERT: A 1271 HIS cc_start: 0.7715 (m-70) cc_final: 0.7183 (m-70) REVERT: A 1274 MET cc_start: 0.5269 (mmt) cc_final: 0.4685 (mtt) REVERT: A 1308 GLN cc_start: 0.8719 (mm110) cc_final: 0.8375 (mm-40) REVERT: A 1623 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8696 (ttpp) REVERT: A 1657 LEU cc_start: 0.7939 (tp) cc_final: 0.7725 (tp) REVERT: B 47 THR cc_start: 0.8711 (p) cc_final: 0.8166 (t) REVERT: B 77 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8455 (mmmt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0985 time to fit residues: 23.9690 Evaluate side-chains 130 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.122146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098085 restraints weight = 33704.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099300 restraints weight = 22893.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100042 restraints weight = 16799.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100334 restraints weight = 15003.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100486 restraints weight = 14024.429| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13393 Z= 0.112 Angle : 0.649 8.999 18065 Z= 0.321 Chirality : 0.043 0.189 2075 Planarity : 0.003 0.047 2279 Dihedral : 5.009 28.137 1770 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.21), residues: 1629 helix: -0.18 (0.20), residues: 733 sheet: -1.97 (0.55), residues: 88 loop : -2.22 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.009 0.001 TYR A 529 PHE 0.012 0.001 PHE A 852 TRP 0.013 0.001 TRP A1549 HIS 0.005 0.001 HIS A1812 Details of bonding type rmsd covalent geometry : bond 0.00252 (13384) covalent geometry : angle 0.64392 (18053) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.90248 ( 6) hydrogen bonds : bond 0.02862 ( 394) hydrogen bonds : angle 4.30653 ( 1122) metal coordination : bond 0.00389 ( 6) metal coordination : angle 4.29833 ( 6) ********************** 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 159 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6420 (m110) cc_final: 0.5647 (t0) REVERT: A 174 MET cc_start: 0.8993 (ppp) cc_final: 0.8787 (ppp) REVERT: A 292 MET cc_start: 0.8034 (mmm) cc_final: 0.7826 (mmm) REVERT: A 355 LEU cc_start: 0.8943 (mp) cc_final: 0.8453 (tp) REVERT: A 458 MET cc_start: 0.6910 (tpp) cc_final: 0.5496 (tpt) REVERT: A 565 MET cc_start: 0.6670 (tmm) cc_final: 0.6401 (tmm) REVERT: A 850 GLU cc_start: 0.8336 (tt0) cc_final: 0.8000 (tm-30) REVERT: A 1026 MET cc_start: 0.7543 (mmm) cc_final: 0.7134 (mmm) REVERT: A 1030 TYR cc_start: 0.8289 (m-80) cc_final: 0.7646 (m-80) REVERT: A 1188 ASP cc_start: 0.7771 (t70) cc_final: 0.7430 (t0) REVERT: A 1271 HIS cc_start: 0.7384 (m-70) cc_final: 0.6949 (m-70) REVERT: A 1274 MET cc_start: 0.5133 (mmt) cc_final: 0.4574 (mtt) REVERT: A 1285 MET cc_start: 0.6355 (mtp) cc_final: 0.5969 (mtp) REVERT: A 1308 GLN cc_start: 0.8695 (mm110) cc_final: 0.8363 (mm-40) REVERT: A 1623 LYS cc_start: 0.9065 (ttmt) cc_final: 0.8514 (ttpp) REVERT: B 47 THR cc_start: 0.8730 (p) cc_final: 0.8235 (t) REVERT: B 77 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8482 (mmmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0967 time to fit residues: 23.8347 Evaluate side-chains 125 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.121794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097752 restraints weight = 33299.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098831 restraints weight = 22684.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099907 restraints weight = 16461.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099953 restraints weight = 15215.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100085 restraints weight = 13890.891| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13393 Z= 0.118 Angle : 0.652 8.974 18065 Z= 0.322 Chirality : 0.043 0.190 2075 Planarity : 0.003 0.043 2279 Dihedral : 4.957 26.978 1770 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.21), residues: 1629 helix: -0.12 (0.20), residues: 732 sheet: -1.91 (0.55), residues: 88 loop : -2.12 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.022 0.001 TYR A1312 PHE 0.011 0.001 PHE A 852 TRP 0.010 0.001 TRP A1549 HIS 0.005 0.001 HIS A1271 Details of bonding type rmsd covalent geometry : bond 0.00270 (13384) covalent geometry : angle 0.64663 (18053) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.60434 ( 6) hydrogen bonds : bond 0.02910 ( 394) hydrogen bonds : angle 4.32817 ( 1122) metal coordination : bond 0.00506 ( 6) metal coordination : angle 4.44117 ( 6) =============================================================================== Job complete usr+sys time: 1793.52 seconds wall clock time: 32 minutes 3.22 seconds (1923.22 seconds total)