Starting phenix.real_space_refine on Thu Feb 15 18:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_31983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_31983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_31983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_31983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh1_31983/02_2024/7vh1_31983.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 96 5.16 5 C 8398 2.51 5 N 2202 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1591": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A PHE 1716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1741": "NH1" <-> "NH2" Residue "A ARG 1796": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13156 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1612, 12749 Classifications: {'peptide': 1612} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 46, 'TRANS': 1565} Chain breaks: 14 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 407 Unusual residues: {' ZN': 2} Classifications: {'peptide': 49, 'undetermined': 2} Link IDs: {'PTRANS': 2, 'TRANS': 46, None: 2} Not linked: pdbres="SER B 82 " pdbres=" ZN B 101 " Not linked: pdbres=" ZN B 101 " pdbres=" ZN B 102 " 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: 7.30, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.58 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 41 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " Number of angles added : 6 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3166 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 46.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 4.487A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 3.552A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 4.152A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 52 removed outlier: 4.144A pdb=" N SER A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.711A pdb=" N HIS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.413A pdb=" N ALA A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.534A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 3.757A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 4.042A pdb=" N LYS A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.524A pdb=" N GLU A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 removed outlier: 4.326A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.931A pdb=" N ILE A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.761A pdb=" N LYS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 removed outlier: 5.365A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 removed outlier: 3.566A pdb=" N ILE A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.867A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.542A pdb=" N MET A 478 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.608A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 574 through 578 removed outlier: 4.193A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 4.044A pdb=" N CYS A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 602 through 622 removed outlier: 3.768A pdb=" N ASP A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Proline residue: A 611 - end of helix removed outlier: 3.512A pdb=" N ARG A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.321A pdb=" N LEU A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 644 removed outlier: 3.588A pdb=" N MET A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.848A pdb=" N ARG A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.802A pdb=" N ARG A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.908A pdb=" N LEU A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 removed outlier: 3.744A pdb=" N GLU A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 3.690A pdb=" N LYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 760 removed outlier: 3.841A pdb=" N ILE A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.724A pdb=" N TYR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.646A pdb=" N LYS A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 852 " --> pdb=" O MET A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 Processing helix chain 'A' and resid 887 through 893 removed outlier: 3.778A pdb=" N SER A 891 " --> pdb=" O GLN A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 920 removed outlier: 3.845A pdb=" N SER A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 907 " --> pdb=" O GLU A 903 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 970 Processing helix chain 'A' and resid 982 through 988 removed outlier: 3.610A pdb=" N ALA A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1024 through 1035 removed outlier: 3.892A pdb=" N GLY A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1085 removed outlier: 4.080A pdb=" N TYR A1085 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.905A pdb=" N ASN A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A1094 " --> pdb=" O LEU A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1135 through 1155 removed outlier: 3.738A pdb=" N LEU A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A1145 " --> pdb=" O MET A1141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1179 removed outlier: 3.916A pdb=" N PHE A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 removed outlier: 3.742A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1227 through 1233 removed outlier: 3.731A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 3.575A pdb=" N ILE A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1244 through 1249' Processing helix chain 'A' and resid 1265 through 1271 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.250A pdb=" N GLU A1307 " --> pdb=" O GLY A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 4.050A pdb=" N ILE A1355 " --> pdb=" O TRP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1366 No H-bonds generated for 'chain 'A' and resid 1364 through 1366' Processing helix chain 'A' and resid 1395 through 1404 removed outlier: 4.517A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A1400 " --> pdb=" O LEU A1396 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A1401 " --> pdb=" O THR A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1427 removed outlier: 3.513A pdb=" N THR A1418 " --> pdb=" O GLN A1414 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A1419 " --> pdb=" O LEU A1415 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP A1420 " --> pdb=" O SER A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1449 removed outlier: 4.436A pdb=" N LYS A1441 " --> pdb=" O ALA A1437 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A1444 " --> pdb=" O SER A1440 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A1447 " --> pdb=" O VAL A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 4.108A pdb=" N GLN A1478 " --> pdb=" O GLY A1474 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A1484 " --> pdb=" O LYS A1480 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1506 removed outlier: 4.321A pdb=" N ASP A1504 " --> pdb=" O LYS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1535 removed outlier: 3.643A pdb=" N GLN A1532 " --> pdb=" O THR A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 4.244A pdb=" N VAL A1541 " --> pdb=" O SER A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 4.184A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1587 " --> pdb=" O LYS A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1617 removed outlier: 3.658A pdb=" N SER A1616 " --> pdb=" O SER A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1618 through 1623 Processing helix chain 'A' and resid 1640 through 1645 Processing helix chain 'A' and resid 1654 through 1658 removed outlier: 3.535A pdb=" N LEU A1657 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1658 " --> pdb=" O CYS A1655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1654 through 1658' Processing helix chain 'A' and resid 1665 through 1669 Processing helix chain 'A' and resid 1677 through 1693 removed outlier: 4.292A pdb=" N ASP A1681 " --> pdb=" O PRO A1677 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1739 Processing helix chain 'A' and resid 1743 through 1750 Processing helix chain 'A' and resid 1777 through 1782 removed outlier: 3.684A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1792 Processing helix chain 'A' and resid 1806 through 1808 No H-bonds generated for 'chain 'A' and resid 1806 through 1808' Processing helix chain 'B' and resid 58 through 67 removed outlier: 4.141A pdb=" N GLN B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 67 " --> pdb=" O GLN B 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.687A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 removed outlier: 7.422A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 3.547A pdb=" N TYR A 545 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 543 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 533 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 558 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 647 removed outlier: 3.730A pdb=" N GLY A1376 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N CYS A1185 " --> pdb=" O THR A1333 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1333 " --> pdb=" O CYS A1185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A1332 " --> pdb=" O TYR A1325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1549 through 1550 Processing sheet with id=AA7, first strand: chain 'A' and resid 1630 through 1631 removed outlier: 3.502A pdb=" N VAL A1630 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1718 394 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 5.02 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: 96.61 - 104.13: 152 104.13 - 111.64: 5677 111.64 - 119.16: 5402 119.16 - 126.68: 6673 126.68 - 134.20: 149 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 2.440 nonbonded pdb=" O LEU A 497 " pdb=" OG SER A 500 " model vdw 2.222 2.440 nonbonded pdb=" OG SER A1098 " pdb=" OG SER A1101 " model vdw 2.273 2.440 nonbonded pdb=" OE1 GLU A1307 " pdb=" OG SER A1324 " model vdw 2.276 2.440 nonbonded pdb=" O SER A1327 " pdb=" OG SER A1327 " model vdw 2.290 2.440 ... (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 ========== 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: 0.310 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: 2.000 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.940 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.770 ------------------------------------------------------------------------------- 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 : 0.009 0.100 13384 Z= 0.610 Angle : 1.320 15.592 18053 Z= 0.708 Chirality : 0.070 0.377 2075 Planarity : 0.008 0.066 2279 Dihedral : 12.238 76.148 4974 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.91 % Favored : 87.85 % Rotamer: Outliers : 0.74 % Allowed : 6.72 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.15), residues: 1629 helix: -3.54 (0.12), residues: 718 sheet: -3.89 (0.47), residues: 78 loop : -3.52 (0.18), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP A1717 HIS 0.011 0.004 HIS A1283 PHE 0.037 0.005 PHE A1457 TYR 0.035 0.004 TYR A 695 ARG 0.009 0.002 ARG A1741 *********************** 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 fitting. rotamer outliers: 11 poor density : 277 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.7390 (m90) cc_final: 0.7066 (m90) REVERT: A 510 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5466 (pp) REVERT: A 850 GLU cc_start: 0.8123 (tt0) cc_final: 0.7809 (tm-30) REVERT: A 870 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8810 (tm) REVERT: A 910 TYR cc_start: 0.8108 (t80) cc_final: 0.7668 (t80) REVERT: A 1019 TYR cc_start: 0.5559 (t80) cc_final: 0.5321 (t80) REVERT: A 1028 PHE cc_start: 0.8793 (t80) cc_final: 0.8589 (t80) REVERT: A 1029 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8547 (mtmm) REVERT: A 1132 TYR cc_start: 0.7698 (m-10) cc_final: 0.7423 (m-80) REVERT: A 1207 MET cc_start: 0.8940 (mmt) cc_final: 0.8707 (mmm) REVERT: A 1285 MET cc_start: 0.6901 (ttm) cc_final: 0.6635 (mtp) REVERT: A 1308 GLN cc_start: 0.8668 (mm110) cc_final: 0.8432 (mm-40) REVERT: A 1495 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7982 (mtp180) REVERT: A 1496 ASN cc_start: 0.6155 (m-40) cc_final: 0.5908 (m-40) REVERT: A 1623 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8599 (ttpp) REVERT: A 1715 PHE cc_start: 0.6972 (t80) cc_final: 0.6293 (t80) REVERT: B 47 THR cc_start: 0.8682 (p) cc_final: 0.8203 (t) outliers start: 11 outliers final: 3 residues processed: 286 average time/residue: 0.2978 time to fit residues: 118.7533 Evaluate side-chains 147 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 131 GLN A 149 ASN A 512 ASN A 522 ASN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1088 ASN A1111 ASN A1206 GLN A1297 ASN A1405 HIS ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 ASN A1586 GLN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13384 Z= 0.180 Angle : 0.684 9.873 18053 Z= 0.353 Chirality : 0.043 0.195 2075 Planarity : 0.005 0.066 2279 Dihedral : 6.494 35.339 1770 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.18), residues: 1629 helix: -2.20 (0.17), residues: 713 sheet: -3.21 (0.43), residues: 90 loop : -3.08 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 245 HIS 0.005 0.001 HIS A1812 PHE 0.017 0.002 PHE A 223 TYR 0.017 0.001 TYR A 214 ARG 0.004 0.001 ARG A 106 *********************** 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 221 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8788 (mp) cc_final: 0.8578 (mt) REVERT: A 402 LEU cc_start: 0.8964 (pp) cc_final: 0.8739 (mm) REVERT: A 501 MET cc_start: 0.6395 (mmt) cc_final: 0.6098 (mmt) REVERT: A 565 MET cc_start: 0.5571 (tmm) cc_final: 0.5364 (tmm) REVERT: A 701 TYR cc_start: 0.7485 (m-80) cc_final: 0.7282 (m-80) REVERT: A 850 GLU cc_start: 0.8095 (tt0) cc_final: 0.7864 (tm-30) REVERT: A 1028 PHE cc_start: 0.8741 (t80) cc_final: 0.8421 (t80) REVERT: A 1122 LYS cc_start: 0.8813 (tttp) cc_final: 0.8547 (tppt) REVERT: A 1207 MET cc_start: 0.8935 (mmt) cc_final: 0.8715 (mmm) REVERT: A 1271 HIS cc_start: 0.7038 (m-70) cc_final: 0.6758 (m-70) REVERT: A 1274 MET cc_start: 0.5781 (mmt) cc_final: 0.5083 (mtt) REVERT: A 1285 MET cc_start: 0.7552 (ttm) cc_final: 0.7308 (mtp) REVERT: A 1290 MET cc_start: 0.6361 (ttt) cc_final: 0.5671 (tpt) REVERT: A 1308 GLN cc_start: 0.8626 (mm110) cc_final: 0.8224 (mm-40) REVERT: A 1419 ILE cc_start: 0.8650 (mt) cc_final: 0.8441 (mm) REVERT: A 1715 PHE cc_start: 0.6897 (t80) cc_final: 0.6618 (t80) REVERT: B 47 THR cc_start: 0.8626 (p) cc_final: 0.8214 (t) outliers start: 2 outliers final: 1 residues processed: 221 average time/residue: 0.2571 time to fit residues: 83.2451 Evaluate side-chains 141 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.0020 chunk 151 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1111 ASN A1128 ASN ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1496 ASN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13384 Z= 0.150 Angle : 0.628 9.758 18053 Z= 0.321 Chirality : 0.042 0.191 2075 Planarity : 0.004 0.050 2279 Dihedral : 5.712 31.518 1770 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.19), residues: 1629 helix: -1.53 (0.18), residues: 715 sheet: -2.39 (0.51), residues: 87 loop : -2.80 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1192 HIS 0.003 0.001 HIS A1812 PHE 0.013 0.001 PHE A 852 TYR 0.014 0.001 TYR A 782 ARG 0.004 0.000 ARG A1543 *********************** 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 192 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6697 (m110) cc_final: 0.6033 (t0) REVERT: A 218 LEU cc_start: 0.8618 (mp) cc_final: 0.8366 (mt) REVERT: A 402 LEU cc_start: 0.8958 (pp) cc_final: 0.8731 (mm) REVERT: A 458 MET cc_start: 0.7707 (tpp) cc_final: 0.6740 (tpp) REVERT: A 850 GLU cc_start: 0.8178 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 860 LEU cc_start: 0.8443 (tp) cc_final: 0.8085 (tp) REVERT: A 1026 MET cc_start: 0.6546 (mmt) cc_final: 0.6266 (mmm) REVERT: A 1028 PHE cc_start: 0.8598 (t80) cc_final: 0.8363 (t80) REVERT: A 1207 MET cc_start: 0.8883 (mmt) cc_final: 0.8614 (mmm) REVERT: A 1271 HIS cc_start: 0.6989 (m-70) cc_final: 0.6674 (m-70) REVERT: A 1274 MET cc_start: 0.5746 (mmt) cc_final: 0.5020 (mtt) REVERT: A 1623 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8592 (ttpp) REVERT: B 47 THR cc_start: 0.8584 (p) cc_final: 0.8146 (t) REVERT: B 77 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8355 (mmmt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2522 time to fit residues: 71.9127 Evaluate side-chains 135 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.0570 chunk 43 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 335 ASN A 704 HIS A1111 ASN ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13384 Z= 0.173 Angle : 0.613 9.677 18053 Z= 0.313 Chirality : 0.042 0.194 2075 Planarity : 0.003 0.046 2279 Dihedral : 5.384 32.089 1770 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1629 helix: -1.19 (0.19), residues: 722 sheet: -1.98 (0.53), residues: 90 loop : -2.67 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1549 HIS 0.004 0.001 HIS A1812 PHE 0.021 0.001 PHE A1772 TYR 0.015 0.001 TYR A 782 ARG 0.003 0.000 ARG A1543 *********************** 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 180 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6580 (m110) cc_final: 0.5993 (t0) REVERT: A 151 PHE cc_start: 0.7208 (m-80) cc_final: 0.6336 (t80) REVERT: A 218 LEU cc_start: 0.8551 (mp) cc_final: 0.7820 (tp) REVERT: A 445 ILE cc_start: 0.8881 (mm) cc_final: 0.8554 (tp) REVERT: A 850 GLU cc_start: 0.8257 (tt0) cc_final: 0.7848 (tm-30) REVERT: A 1026 MET cc_start: 0.6657 (mmt) cc_final: 0.6310 (mmm) REVERT: A 1028 PHE cc_start: 0.8703 (t80) cc_final: 0.8503 (t80) REVERT: A 1030 TYR cc_start: 0.7847 (m-80) cc_final: 0.7330 (m-80) REVERT: A 1207 MET cc_start: 0.8853 (mmt) cc_final: 0.8603 (mmm) REVERT: A 1274 MET cc_start: 0.5706 (mmt) cc_final: 0.4946 (mtt) REVERT: A 1623 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8651 (ttpp) REVERT: B 47 THR cc_start: 0.8587 (p) cc_final: 0.8040 (t) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2640 time to fit residues: 72.3587 Evaluate side-chains 131 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 472 HIS A 754 ASN A1111 ASN ** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1712 ASN A1713 GLN A1714 ASN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13384 Z= 0.383 Angle : 0.798 9.996 18053 Z= 0.410 Chirality : 0.048 0.189 2075 Planarity : 0.004 0.053 2279 Dihedral : 6.042 29.288 1770 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.19), residues: 1629 helix: -1.31 (0.18), residues: 737 sheet: -2.31 (0.53), residues: 96 loop : -2.74 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1192 HIS 0.006 0.002 HIS A1283 PHE 0.020 0.002 PHE A1457 TYR 0.027 0.002 TYR A 695 ARG 0.007 0.001 ARG A 553 *********************** 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 150 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6565 (m110) cc_final: 0.6254 (t0) REVERT: A 151 PHE cc_start: 0.6778 (m-80) cc_final: 0.6091 (t80) REVERT: A 458 MET cc_start: 0.8008 (tpp) cc_final: 0.7480 (tpt) REVERT: A 565 MET cc_start: 0.6456 (tmm) cc_final: 0.6199 (tmm) REVERT: A 850 GLU cc_start: 0.8211 (tt0) cc_final: 0.7865 (tm-30) REVERT: A 973 ASP cc_start: 0.8298 (t70) cc_final: 0.7878 (m-30) REVERT: A 1028 PHE cc_start: 0.8742 (t80) cc_final: 0.8451 (t80) REVERT: A 1030 TYR cc_start: 0.8277 (m-80) cc_final: 0.7641 (m-80) REVERT: A 1271 HIS cc_start: 0.6546 (m-70) cc_final: 0.5915 (m-70) REVERT: A 1274 MET cc_start: 0.5408 (mmt) cc_final: 0.5068 (mtt) REVERT: A 1623 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8678 (ttpp) REVERT: A 1696 TRP cc_start: 0.6364 (p-90) cc_final: 0.6013 (p-90) REVERT: B 47 THR cc_start: 0.8742 (p) cc_final: 0.8118 (t) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2420 time to fit residues: 54.1558 Evaluate side-chains 111 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 94 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 531 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1308 GLN ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1713 GLN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13384 Z= 0.156 Angle : 0.628 9.438 18053 Z= 0.317 Chirality : 0.042 0.240 2075 Planarity : 0.003 0.044 2279 Dihedral : 5.369 29.749 1770 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.20), residues: 1629 helix: -0.74 (0.19), residues: 727 sheet: -2.26 (0.51), residues: 96 loop : -2.53 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1549 HIS 0.004 0.001 HIS A1189 PHE 0.012 0.001 PHE A 852 TYR 0.015 0.001 TYR A 450 ARG 0.005 0.000 ARG A1742 *********************** 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 173 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6472 (m110) cc_final: 0.5739 (t0) REVERT: A 151 PHE cc_start: 0.6886 (m-80) cc_final: 0.6195 (t80) REVERT: A 218 LEU cc_start: 0.8407 (mm) cc_final: 0.7947 (tp) REVERT: A 458 MET cc_start: 0.7870 (tpp) cc_final: 0.7615 (tpp) REVERT: A 850 GLU cc_start: 0.8220 (tt0) cc_final: 0.7815 (tm-30) REVERT: A 973 ASP cc_start: 0.8315 (t70) cc_final: 0.8021 (m-30) REVERT: A 1030 TYR cc_start: 0.8296 (m-80) cc_final: 0.7523 (m-80) REVERT: A 1271 HIS cc_start: 0.6706 (m-70) cc_final: 0.6025 (m-70) REVERT: A 1274 MET cc_start: 0.5223 (mmt) cc_final: 0.4953 (mtt) REVERT: A 1285 MET cc_start: 0.6038 (mtp) cc_final: 0.5728 (mtp) REVERT: A 1623 LYS cc_start: 0.9056 (ttmt) cc_final: 0.8565 (ttpp) REVERT: B 47 THR cc_start: 0.8766 (p) cc_final: 0.8233 (t) REVERT: B 77 LYS cc_start: 0.9096 (mmmm) cc_final: 0.8665 (mmtp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2300 time to fit residues: 60.7980 Evaluate side-chains 125 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ** A1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1713 GLN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13384 Z= 0.295 Angle : 0.721 9.833 18053 Z= 0.366 Chirality : 0.046 0.208 2075 Planarity : 0.004 0.042 2279 Dihedral : 5.616 28.137 1770 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.20), residues: 1629 helix: -0.82 (0.19), residues: 729 sheet: -2.39 (0.50), residues: 96 loop : -2.54 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1192 HIS 0.005 0.001 HIS A1283 PHE 0.015 0.002 PHE A1201 TYR 0.021 0.002 TYR A 695 ARG 0.005 0.001 ARG A 553 *********************** 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 149 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6394 (m110) cc_final: 0.6021 (t0) REVERT: A 160 MET cc_start: 0.5463 (mpp) cc_final: 0.5167 (mpp) REVERT: A 850 GLU cc_start: 0.8167 (tt0) cc_final: 0.7782 (tm-30) REVERT: A 973 ASP cc_start: 0.8361 (t70) cc_final: 0.7989 (m-30) REVERT: A 1030 TYR cc_start: 0.8284 (m-80) cc_final: 0.7423 (m-80) REVERT: A 1207 MET cc_start: 0.8609 (mmm) cc_final: 0.8318 (mmm) REVERT: A 1271 HIS cc_start: 0.6666 (m-70) cc_final: 0.5933 (m-70) REVERT: A 1274 MET cc_start: 0.5321 (mmt) cc_final: 0.4981 (mtt) REVERT: B 47 THR cc_start: 0.8830 (p) cc_final: 0.8234 (t) REVERT: B 77 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8651 (mmtp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2387 time to fit residues: 55.1690 Evaluate side-chains 114 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 48 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.0070 chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 531 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13384 Z= 0.141 Angle : 0.623 9.070 18053 Z= 0.311 Chirality : 0.042 0.198 2075 Planarity : 0.003 0.038 2279 Dihedral : 5.036 29.060 1770 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.21), residues: 1629 helix: -0.32 (0.20), residues: 718 sheet: -2.16 (0.50), residues: 96 loop : -2.32 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1549 HIS 0.004 0.001 HIS A1812 PHE 0.012 0.001 PHE A 246 TYR 0.014 0.001 TYR A1019 ARG 0.005 0.000 ARG A1543 *********************** 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 171 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6685 (m110) cc_final: 0.5817 (t0) REVERT: A 218 LEU cc_start: 0.8330 (mm) cc_final: 0.7943 (tp) REVERT: A 458 MET cc_start: 0.5686 (tpp) cc_final: 0.5146 (tpt) REVERT: A 850 GLU cc_start: 0.8099 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 973 ASP cc_start: 0.8178 (t70) cc_final: 0.7969 (m-30) REVERT: A 1030 TYR cc_start: 0.8298 (m-80) cc_final: 0.7551 (m-80) REVERT: A 1271 HIS cc_start: 0.7069 (m-70) cc_final: 0.6452 (m-70) REVERT: A 1274 MET cc_start: 0.5533 (mmt) cc_final: 0.4780 (mtt) REVERT: A 1285 MET cc_start: 0.6048 (mtp) cc_final: 0.5802 (mtp) REVERT: A 1438 ARG cc_start: 0.8289 (mtt180) cc_final: 0.7901 (mtp85) REVERT: B 47 THR cc_start: 0.8764 (p) cc_final: 0.8254 (t) REVERT: B 77 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8577 (mmtp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2405 time to fit residues: 61.6851 Evaluate side-chains 125 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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** ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13384 Z= 0.167 Angle : 0.629 8.765 18053 Z= 0.311 Chirality : 0.042 0.190 2075 Planarity : 0.003 0.038 2279 Dihedral : 4.949 27.089 1770 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.21), residues: 1629 helix: -0.26 (0.20), residues: 730 sheet: -2.06 (0.52), residues: 96 loop : -2.32 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 155 HIS 0.005 0.001 HIS A1812 PHE 0.010 0.001 PHE A1037 TYR 0.013 0.001 TYR A 782 ARG 0.004 0.000 ARG A1543 *********************** 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 157 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ASN cc_start: 0.6650 (m110) cc_final: 0.5760 (t0) REVERT: A 218 LEU cc_start: 0.8421 (mm) cc_final: 0.8049 (tp) REVERT: A 458 MET cc_start: 0.6019 (tpp) cc_final: 0.4886 (tpt) REVERT: A 850 GLU cc_start: 0.8036 (tt0) cc_final: 0.7782 (tm-30) REVERT: A 973 ASP cc_start: 0.8143 (t70) cc_final: 0.7915 (m-30) REVERT: A 1026 MET cc_start: 0.7496 (mmm) cc_final: 0.7012 (mmp) REVERT: A 1030 TYR cc_start: 0.8304 (m-80) cc_final: 0.7552 (m-80) REVERT: A 1196 MET cc_start: 0.7036 (mtt) cc_final: 0.6586 (mtt) REVERT: A 1271 HIS cc_start: 0.6711 (m-70) cc_final: 0.6200 (m-70) REVERT: A 1274 MET cc_start: 0.5190 (mmt) cc_final: 0.4839 (mtt) REVERT: B 47 THR cc_start: 0.8819 (p) cc_final: 0.8261 (t) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2491 time to fit residues: 58.6205 Evaluate side-chains 122 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 131 optimal weight: 0.0670 chunk 13 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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 ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1714 ASN ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13384 Z= 0.202 Angle : 0.655 8.280 18053 Z= 0.327 Chirality : 0.043 0.190 2075 Planarity : 0.003 0.040 2279 Dihedral : 5.035 28.324 1770 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1629 helix: -0.32 (0.20), residues: 744 sheet: -2.10 (0.53), residues: 96 loop : -2.36 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 155 HIS 0.005 0.001 HIS A1812 PHE 0.011 0.001 PHE A 246 TYR 0.012 0.001 TYR A 782 ARG 0.004 0.000 ARG A1543 ********************** 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 fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 HIS cc_start: 0.6848 (m90) cc_final: 0.6637 (m90) REVERT: A 149 ASN cc_start: 0.6450 (m110) cc_final: 0.5695 (t0) REVERT: A 218 LEU cc_start: 0.8464 (mm) cc_final: 0.8100 (tp) REVERT: A 850 GLU cc_start: 0.8006 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 973 ASP cc_start: 0.8223 (t70) cc_final: 0.7998 (m-30) REVERT: A 1030 TYR cc_start: 0.8304 (m-80) cc_final: 0.7569 (m-80) REVERT: A 1196 MET cc_start: 0.7227 (mtt) cc_final: 0.6714 (mtm) REVERT: A 1271 HIS cc_start: 0.7160 (m-70) cc_final: 0.6493 (m-70) REVERT: A 1274 MET cc_start: 0.5109 (mmt) cc_final: 0.4769 (mtt) REVERT: A 1285 MET cc_start: 0.6173 (mtp) cc_final: 0.5561 (mtp) REVERT: B 47 THR cc_start: 0.8836 (p) cc_final: 0.8299 (t) REVERT: B 77 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8639 (mmtt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2477 time to fit residues: 60.3051 Evaluate side-chains 122 residues out of total 1525 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1734 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.121739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097790 restraints weight = 33763.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099045 restraints weight = 22872.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.100140 restraints weight = 16638.987| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13384 Z= 0.165 Angle : 0.641 10.542 18053 Z= 0.316 Chirality : 0.043 0.224 2075 Planarity : 0.003 0.037 2279 Dihedral : 4.926 26.549 1770 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.21), residues: 1629 helix: -0.25 (0.20), residues: 749 sheet: -1.97 (0.53), residues: 94 loop : -2.30 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 155 HIS 0.005 0.001 HIS A1812 PHE 0.010 0.001 PHE A 852 TYR 0.022 0.001 TYR A1312 ARG 0.004 0.000 ARG A1543 =============================================================================== Job complete usr+sys time: 2429.78 seconds wall clock time: 45 minutes 33.27 seconds (2733.27 seconds total)