Starting phenix.real_space_refine on Thu Feb 15 02:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6v_33028/02_2024/7x6v_33028.pdb" } resolution = 3.6 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.083 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 S 70 5.16 5 C 6941 2.51 5 N 1844 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A PHE 1090": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A ASP 1105": "OD1" <-> "OD2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1131": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1158": "OD1" <-> "OD2" Residue "A PHE 1161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ARG 1173": "NH1" <-> "NH2" Residue "A ASP 1182": "OD1" <-> "OD2" Residue "A TYR 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1261": "NH1" <-> "NH2" Residue "A ARG 1264": "NH1" <-> "NH2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A ARG 1313": "NH1" <-> "NH2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A ARG 1329": "NH1" <-> "NH2" Residue "A ARG 1330": "NH1" <-> "NH2" Residue "A GLU 1341": "OE1" <-> "OE2" Residue "A ARG 1432": "NH1" <-> "NH2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1464": "NH1" <-> "NH2" Residue "A TYR 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1474": "OE1" <-> "OE2" Residue "A ARG 1510": "NH1" <-> "NH2" Residue "A ASP 1521": "OD1" <-> "OD2" Residue "A GLU 1527": "OE1" <-> "OE2" Residue "A ASP 1534": "OD1" <-> "OD2" Residue "A PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1547": "NH1" <-> "NH2" Residue "A ARG 1624": "NH1" <-> "NH2" Residue "A GLU 1625": "OE1" <-> "OE2" Residue "A TYR 1654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1657": "OD1" <-> "OD2" Residue "A TYR 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1807": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10903 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 360 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 43} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 10540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1381, 10537 Classifications: {'peptide': 1381} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 47, 'TRANS': 1333} Chain breaks: 13 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 294 Conformer: "B" Number of residues, atoms: 1381, 10537 Classifications: {'peptide': 1381} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 47, 'TRANS': 1333} Chain breaks: 13 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 819 Unresolved non-hydrogen dihedrals: 511 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 294 bond proxies already assigned to first conformer: 10736 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36 SG CYS B 32 41.306 24.323 103.168 1.00 50.18 S ATOM 57 SG CYS B 35 37.933 24.447 101.079 1.00 49.75 S ATOM 188 SG CYS B 51 39.226 21.873 103.451 1.00 51.81 S ATOM 215 SG CYS B 54 39.869 22.028 100.449 1.00 49.13 S ATOM 140 SG CYS B 45 49.874 18.848 99.557 1.00 48.54 S ATOM 299 SG CYS B 65 47.958 18.767 96.163 1.00 54.85 S ATOM 320 SG CYS B 68 50.956 19.300 96.272 1.00 55.00 S Time building chain proxies: 11.37, per 1000 atoms: 1.04 Number of scatterers: 10903 At special positions: 0 Unit cell: (101.52, 112.32, 119.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 70 16.00 O 2045 8.00 N 1844 7.00 C 6941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.08 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 51 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 35 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 32 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 54 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 65 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 45 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 68 " Number of angles added : 9 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 13 sheets defined 51.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'A' and resid 2 through 16 removed outlier: 4.141A pdb=" N LEU A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.823A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.625A pdb=" N ILE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 4.030A pdb=" N SER A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 126 removed outlier: 4.550A pdb=" N ILE A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 153 through 174 removed outlier: 3.541A pdb=" N ASN A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.929A pdb=" N CYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.652A pdb=" N LEU A 249 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.609A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.751A pdb=" N LEU A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.553A pdb=" N GLU A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 442 through 447 removed outlier: 4.068A pdb=" N HIS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.595A pdb=" N THR A 498 " --> pdb=" O CYS A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 removed outlier: 3.710A pdb=" N LYS A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 577 removed outlier: 4.764A pdb=" N PHE A 577 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.801A pdb=" N ASP A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 602 through 620 removed outlier: 3.559A pdb=" N LEU A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 640 removed outlier: 3.741A pdb=" N VAL A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.614A pdb=" N ASP A 650 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 676 removed outlier: 4.202A pdb=" N TYR A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 697 removed outlier: 3.787A pdb=" N LYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 701 removed outlier: 3.738A pdb=" N ILE A 701 " --> pdb=" O CYS A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 698 through 701' Processing helix chain 'A' and resid 708 through 727 removed outlier: 4.396A pdb=" N LYS A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.669A pdb=" N GLN A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 removed outlier: 3.694A pdb=" N THR A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 866 through 872 removed outlier: 4.368A pdb=" N VAL A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.595A pdb=" N LEU A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1148 removed outlier: 3.907A pdb=" N ARG A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A1138 " --> pdb=" O MET A1134 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A1139 " --> pdb=" O PHE A1135 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1173 removed outlier: 3.737A pdb=" N PHE A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1200 removed outlier: 3.653A pdb=" N PHE A1195 " --> pdb=" O CYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1226 removed outlier: 4.435A pdb=" N THR A1219 " --> pdb=" O ASP A1215 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR A1222 " --> pdb=" O SER A1218 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A1223 " --> pdb=" O THR A1219 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS A1226 " --> pdb=" O THR A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 3.527A pdb=" N ILE A1262 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG A1264 " --> pdb=" O GLU A1260 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1311 removed outlier: 3.612A pdb=" N ASN A1303 " --> pdb=" O GLU A1299 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A1304 " --> pdb=" O ARG A1300 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A1307 " --> pdb=" O ASN A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1338 removed outlier: 3.793A pdb=" N LEU A1334 " --> pdb=" O ARG A1330 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A1335 " --> pdb=" O LEU A1331 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A1336 " --> pdb=" O SER A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1356 removed outlier: 3.819A pdb=" N SER A1350 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A1353 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1395 removed outlier: 3.616A pdb=" N PHE A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A1392 " --> pdb=" O THR A1388 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1393 " --> pdb=" O LYS A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1420 removed outlier: 4.284A pdb=" N GLU A1408 " --> pdb=" O HIS A1404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A1410 " --> pdb=" O LEU A1406 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A1411 " --> pdb=" O CYS A1407 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A1420 " --> pdb=" O GLN A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1441 removed outlier: 3.919A pdb=" N SER A1429 " --> pdb=" O SER A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1476 removed outlier: 3.735A pdb=" N ARG A1467 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A1468 " --> pdb=" O ARG A1464 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A1474 " --> pdb=" O ARG A1470 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.515A pdb=" N LYS A1481 " --> pdb=" O ASN A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1501 through 1508 Processing helix chain 'A' and resid 1514 through 1524 removed outlier: 3.822A pdb=" N LEU A1523 " --> pdb=" O LEU A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1534 removed outlier: 4.398A pdb=" N LEU A1532 " --> pdb=" O ASP A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1576 Processing helix chain 'A' and resid 1606 through 1614 removed outlier: 4.484A pdb=" N LYS A1612 " --> pdb=" O ILE A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1639 removed outlier: 3.796A pdb=" N LEU A1632 " --> pdb=" O TYR A1628 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A1635 " --> pdb=" O LYS A1631 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A1636 " --> pdb=" O LEU A1632 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1660 Processing helix chain 'A' and resid 1675 through 1690 removed outlier: 3.906A pdb=" N ILE A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1682 " --> pdb=" O ASP A1678 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A1689 " --> pdb=" O SER A1685 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1690 " --> pdb=" O ASN A1686 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1696 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1752 Processing helix chain 'A' and resid 1774 through 1785 removed outlier: 3.582A pdb=" N SER A1785 " --> pdb=" O ILE A1781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.804A pdb=" N TYR B 70 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.425A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA7, first strand: chain 'A' and resid 551 through 553 removed outlier: 3.956A pdb=" N ARG A 551 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 567 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 565 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1115 Processing sheet with id=AA9, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 4.587A pdb=" N PHE A1359 " --> pdb=" O SER A1184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1229 through 1230 Processing sheet with id=AB2, first strand: chain 'A' and resid 1315 through 1316 removed outlier: 4.148A pdb=" N GLU A1315 " --> pdb=" O LEU A1326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1536 through 1538 Processing sheet with id=AB4, first strand: chain 'A' and resid 1619 through 1620 removed outlier: 3.807A pdb=" N VAL A1619 " --> pdb=" O LEU A1627 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1167 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: 3.31 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 57 1.22 - 1.37: 3966 1.37 - 1.52: 4055 1.52 - 1.66: 2937 1.66 - 1.81: 99 Bond restraints: 11114 Sorted by residual: bond pdb=" C ALA A1371 " pdb=" O ALA A1371 " ideal model delta sigma weight residual 1.234 1.078 0.155 1.20e-02 6.94e+03 1.68e+02 bond pdb=" C HIS B 53 " pdb=" N CYS B 54 " ideal model delta sigma weight residual 1.332 1.500 -0.167 1.40e-02 5.10e+03 1.43e+02 bond pdb=" C CYS B 54 " pdb=" N LEU B 55 " ideal model delta sigma weight residual 1.334 1.498 -0.163 1.43e-02 4.89e+03 1.30e+02 bond pdb=" C ASP A1182 " pdb=" O ASP A1182 " ideal model delta sigma weight residual 1.235 1.106 0.129 1.26e-02 6.30e+03 1.05e+02 bond pdb=" C ASP A1322 " pdb=" O ASP A1322 " ideal model delta sigma weight residual 1.234 1.133 0.101 1.07e-02 8.73e+03 8.87e+01 ... (remaining 11109 not shown) Histogram of bond angle deviations from ideal: 82.56 - 94.30: 8 94.30 - 106.03: 290 106.03 - 117.76: 7810 117.76 - 129.50: 6859 129.50 - 141.23: 77 Bond angle restraints: 15044 Sorted by residual: angle pdb=" O HIS B 53 " pdb=" C HIS B 53 " pdb=" N CYS B 54 " ideal model delta sigma weight residual 122.59 82.56 40.03 1.33e+00 5.65e-01 9.06e+02 angle pdb=" N ASP B 40 " pdb=" CA ASP B 40 " pdb=" C ASP B 40 " ideal model delta sigma weight residual 113.02 140.87 -27.85 1.49e+00 4.50e-01 3.49e+02 angle pdb=" N PHE A1369 " pdb=" CA PHE A1369 " pdb=" C PHE A1369 " ideal model delta sigma weight residual 113.89 133.24 -19.35 1.58e+00 4.01e-01 1.50e+02 angle pdb=" O SER A1787 " pdb=" C SER A1787 " pdb=" N LEU A1788 " ideal model delta sigma weight residual 122.10 138.39 -16.29 1.34e+00 5.57e-01 1.48e+02 angle pdb=" N ASN A 473 " pdb=" CA ASN A 473 " pdb=" C ASN A 473 " ideal model delta sigma weight residual 109.76 90.03 19.73 1.64e+00 3.72e-01 1.45e+02 ... (remaining 15039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5972 18.00 - 36.01: 617 36.01 - 54.01: 97 54.01 - 72.01: 17 72.01 - 90.02: 7 Dihedral angle restraints: 6710 sinusoidal: 2506 harmonic: 4204 Sorted by residual: dihedral pdb=" C ILE A 484 " pdb=" N ILE A 484 " pdb=" CA ILE A 484 " pdb=" CB ILE A 484 " ideal model delta harmonic sigma weight residual -122.00 -151.70 29.70 0 2.50e+00 1.60e-01 1.41e+02 dihedral pdb=" C THR A1480 " pdb=" N THR A1480 " pdb=" CA THR A1480 " pdb=" CB THR A1480 " ideal model delta harmonic sigma weight residual -122.00 -149.18 27.18 0 2.50e+00 1.60e-01 1.18e+02 dihedral pdb=" N ASP B 40 " pdb=" C ASP B 40 " pdb=" CA ASP B 40 " pdb=" CB ASP B 40 " ideal model delta harmonic sigma weight residual 122.80 148.90 -26.10 0 2.50e+00 1.60e-01 1.09e+02 ... (remaining 6707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1661 0.286 - 0.572: 34 0.572 - 0.857: 10 0.857 - 1.143: 4 1.143 - 1.429: 2 Chirality restraints: 1711 Sorted by residual: chirality pdb=" CA ASP B 40 " pdb=" N ASP B 40 " pdb=" C ASP B 40 " pdb=" CB ASP B 40 " both_signs ideal model delta sigma weight residual False 2.51 1.08 1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 1.27 1.16 2.00e-01 2.50e+01 3.37e+01 chirality pdb=" CA THR A1480 " pdb=" N THR A1480 " pdb=" C THR A1480 " pdb=" CB THR A1480 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.13 2.00e-01 2.50e+01 3.21e+01 ... (remaining 1708 not shown) Planarity restraints: 1943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 53 " -0.149 2.00e-02 2.50e+03 2.28e-01 5.19e+02 pdb=" C HIS B 53 " 0.392 2.00e-02 2.50e+03 pdb=" O HIS B 53 " -0.153 2.00e-02 2.50e+03 pdb=" N CYS B 54 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1497 " -0.038 2.00e-02 2.50e+03 7.50e-02 5.63e+01 pdb=" C GLY A1497 " 0.130 2.00e-02 2.50e+03 pdb=" O GLY A1497 " -0.048 2.00e-02 2.50e+03 pdb=" N GLU A1498 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " -0.036 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C THR A 478 " 0.127 2.00e-02 2.50e+03 pdb=" O THR A 478 " -0.048 2.00e-02 2.50e+03 pdb=" N GLU A 479 " -0.043 2.00e-02 2.50e+03 ... (remaining 1940 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 9 2.14 - 2.83: 3816 2.83 - 3.52: 14731 3.52 - 4.21: 22472 4.21 - 4.90: 39006 Nonbonded interactions: 80034 Sorted by model distance: nonbonded pdb=" CE1 HIS A 305 " pdb=" ND2 ASN A 473 " model vdw 1.450 3.340 nonbonded pdb=" O LEU A1334 " pdb=" O ASP A1338 " model vdw 1.640 3.040 nonbonded pdb=" NE2 HIS A 305 " pdb=" ND2 ASN A 473 " model vdw 1.689 3.200 nonbonded pdb=" OD1 ASP A1182 " pdb="MN MN A2301 " model vdw 1.955 2.320 nonbonded pdb=" OE1 GLU A1372 " pdb="MN MN A2301 " model vdw 1.956 2.320 ... (remaining 80029 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=0.11 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: 2.400 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 41.220 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 : 0.011 0.167 11114 Z= 0.676 Angle : 1.516 40.026 15044 Z= 0.899 Chirality : 0.116 1.429 1711 Planarity : 0.009 0.228 1943 Dihedral : 14.934 90.016 3964 Min Nonbonded Distance : 1.450 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.65 % Favored : 84.35 % Rotamer: Outliers : 0.62 % Allowed : 0.80 % Favored : 98.58 % Cbeta Deviations : 2.48 % 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: -3.94 (0.20), residues: 1400 helix: -1.53 (0.19), residues: 681 sheet: -2.69 (0.58), residues: 79 loop : -3.92 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 36 HIS 0.009 0.002 HIS A 561 PHE 0.042 0.003 PHE A 299 TYR 0.022 0.003 TYR A1803 ARG 0.010 0.001 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 MET cc_start: 0.8722 (mmm) cc_final: 0.8456 (tpt) REVERT: A 1654 TYR cc_start: 0.5580 (m-80) cc_final: 0.2678 (m-80) REVERT: A 1775 LEU cc_start: 0.8765 (tp) cc_final: 0.8555 (tp) REVERT: A 1807 PHE cc_start: 0.7801 (t80) cc_final: 0.7207 (m-80) outliers start: 7 outliers final: 3 residues processed: 206 average time/residue: 0.2119 time to fit residues: 61.6690 Evaluate side-chains 132 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain A residue 1372 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 ASN A 305 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1492 HIS ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11114 Z= 0.201 Angle : 0.787 10.681 15044 Z= 0.401 Chirality : 0.047 0.335 1711 Planarity : 0.005 0.065 1943 Dihedral : 6.524 46.388 1517 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.15 % Favored : 88.71 % Rotamer: Outliers : 1.42 % Allowed : 9.24 % Favored : 89.34 % 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: -3.27 (0.21), residues: 1400 helix: -0.97 (0.19), residues: 682 sheet: -2.04 (0.71), residues: 61 loop : -3.62 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1223 HIS 0.013 0.001 HIS A1492 PHE 0.035 0.002 PHE A1390 TYR 0.028 0.002 TYR A 745 ARG 0.008 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 ILE cc_start: 0.8172 (pt) cc_final: 0.7913 (pt) REVERT: A 233 ASP cc_start: 0.7653 (m-30) cc_final: 0.7376 (m-30) REVERT: A 544 GLN cc_start: 0.5588 (tm-30) cc_final: 0.5297 (tt0) REVERT: A 1498 GLU cc_start: 0.6094 (tp30) cc_final: 0.5669 (mp0) REVERT: A 1654 TYR cc_start: 0.5000 (m-80) cc_final: 0.2412 (m-80) outliers start: 16 outliers final: 9 residues processed: 160 average time/residue: 0.1983 time to fit residues: 47.4452 Evaluate side-chains 135 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1777 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1686 ASN ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11114 Z= 0.221 Angle : 0.723 9.483 15044 Z= 0.370 Chirality : 0.045 0.337 1711 Planarity : 0.005 0.068 1943 Dihedral : 5.910 30.424 1513 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.94 % Favored : 86.92 % Rotamer: Outliers : 1.69 % Allowed : 11.81 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.95 (0.21), residues: 1400 helix: -0.66 (0.20), residues: 680 sheet: -1.89 (0.66), residues: 70 loop : -3.51 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1223 HIS 0.030 0.002 HIS A1492 PHE 0.043 0.002 PHE A 720 TYR 0.012 0.001 TYR A1654 ARG 0.007 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.342 Fit side-chains REVERT: A 205 ILE cc_start: 0.8283 (pt) cc_final: 0.8039 (pt) REVERT: A 323 MET cc_start: 0.6506 (mmm) cc_final: 0.6036 (tpp) REVERT: A 1134 MET cc_start: 0.7848 (tpp) cc_final: 0.7523 (tpp) REVERT: A 1294 TYR cc_start: 0.8845 (t80) cc_final: 0.8544 (t80) REVERT: A 1498 GLU cc_start: 0.6118 (tp30) cc_final: 0.5811 (mp0) REVERT: A 1576 ASN cc_start: 0.8853 (t0) cc_final: 0.8436 (t0) outliers start: 19 outliers final: 14 residues processed: 142 average time/residue: 0.1980 time to fit residues: 42.6950 Evaluate side-chains 131 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN A 561 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN A1492 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11114 Z= 0.328 Angle : 0.773 11.288 15044 Z= 0.396 Chirality : 0.046 0.175 1711 Planarity : 0.005 0.074 1943 Dihedral : 6.132 30.024 1512 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.65 % Favored : 86.20 % Rotamer: Outliers : 2.22 % Allowed : 13.94 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.03 (0.21), residues: 1400 helix: -0.80 (0.19), residues: 691 sheet: -2.44 (0.60), residues: 80 loop : -3.44 (0.22), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1223 HIS 0.010 0.002 HIS A1492 PHE 0.030 0.002 PHE A 690 TYR 0.018 0.002 TYR A 274 ARG 0.006 0.001 ARG A1464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.339 Fit side-chains REVERT: A 205 ILE cc_start: 0.8669 (pt) cc_final: 0.8444 (pt) REVERT: A 233 ASP cc_start: 0.7978 (m-30) cc_final: 0.7322 (t0) REVERT: A 464 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5054 (ppp) REVERT: A 1134 MET cc_start: 0.7792 (tpp) cc_final: 0.7357 (tpp) REVERT: A 1328 ASP cc_start: 0.7067 (t0) cc_final: 0.6757 (t0) REVERT: A 1338 ASP cc_start: 0.6979 (t70) cc_final: 0.6468 (t0) REVERT: A 1576 ASN cc_start: 0.8999 (t0) cc_final: 0.8594 (t0) REVERT: A 1808 SER cc_start: 0.8351 (t) cc_final: 0.7948 (t) outliers start: 25 outliers final: 17 residues processed: 136 average time/residue: 0.1630 time to fit residues: 34.6013 Evaluate side-chains 125 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1452 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 0.0030 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 70 optimal weight: 0.0030 chunk 123 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 334 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11114 Z= 0.159 Angle : 0.668 8.728 15044 Z= 0.340 Chirality : 0.042 0.182 1711 Planarity : 0.004 0.068 1943 Dihedral : 5.607 28.275 1512 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.92 % Rotamer: Outliers : 1.07 % Allowed : 16.52 % Favored : 82.42 % 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: -2.65 (0.22), residues: 1400 helix: -0.39 (0.20), residues: 690 sheet: -2.35 (0.60), residues: 80 loop : -3.34 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1537 HIS 0.016 0.001 HIS A 561 PHE 0.022 0.001 PHE A 720 TYR 0.038 0.001 TYR A1179 ARG 0.004 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.369 Fit side-chains REVERT: A 200 MET cc_start: 0.7581 (ttp) cc_final: 0.7205 (pmm) REVERT: A 233 ASP cc_start: 0.7948 (m-30) cc_final: 0.7268 (t0) REVERT: A 1294 TYR cc_start: 0.8902 (t80) cc_final: 0.8601 (t80) REVERT: A 1328 ASP cc_start: 0.6786 (t0) cc_final: 0.6502 (t70) REVERT: A 1338 ASP cc_start: 0.6881 (t70) cc_final: 0.6378 (t0) REVERT: A 1452 THR cc_start: 0.8639 (m) cc_final: 0.8312 (m) REVERT: A 1576 ASN cc_start: 0.8948 (t0) cc_final: 0.8565 (t0) REVERT: A 1808 SER cc_start: 0.8343 (t) cc_final: 0.7958 (t) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.1959 time to fit residues: 37.1733 Evaluate side-chains 110 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.8556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11114 Z= 0.176 Angle : 0.653 8.844 15044 Z= 0.332 Chirality : 0.042 0.178 1711 Planarity : 0.004 0.072 1943 Dihedral : 5.412 27.809 1512 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.94 % Favored : 87.92 % Rotamer: Outliers : 0.98 % Allowed : 17.76 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.44 (0.22), residues: 1400 helix: -0.25 (0.20), residues: 696 sheet: -1.78 (0.64), residues: 72 loop : -3.30 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1537 HIS 0.012 0.001 HIS A 561 PHE 0.022 0.001 PHE A 720 TYR 0.030 0.001 TYR A1179 ARG 0.004 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.950 Fit side-chains REVERT: A 200 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7046 (pmm) REVERT: A 229 MET cc_start: 0.7937 (ttm) cc_final: 0.7404 (ttm) REVERT: A 233 ASP cc_start: 0.8013 (m-30) cc_final: 0.7397 (t0) REVERT: A 464 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5031 (ppp) REVERT: A 1332 SER cc_start: 0.8906 (t) cc_final: 0.8359 (p) REVERT: A 1338 ASP cc_start: 0.6920 (t70) cc_final: 0.6487 (t0) REVERT: A 1452 THR cc_start: 0.8529 (m) cc_final: 0.8254 (m) REVERT: A 1576 ASN cc_start: 0.8924 (t0) cc_final: 0.8566 (t0) REVERT: A 1808 SER cc_start: 0.8341 (t) cc_final: 0.7965 (t) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1902 time to fit residues: 33.4043 Evaluate side-chains 113 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 382 HIS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1791 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.0060 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 83 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1661 HIS ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11114 Z= 0.156 Angle : 0.627 9.188 15044 Z= 0.319 Chirality : 0.041 0.179 1711 Planarity : 0.004 0.070 1943 Dihedral : 5.142 27.399 1512 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.01 % Favored : 89.85 % Rotamer: Outliers : 1.15 % Allowed : 18.12 % Favored : 80.73 % 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: -2.22 (0.22), residues: 1400 helix: 0.02 (0.20), residues: 693 sheet: -2.25 (0.59), residues: 82 loop : -3.21 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1537 HIS 0.008 0.001 HIS A 561 PHE 0.020 0.001 PHE A 720 TYR 0.027 0.001 TYR A 183 ARG 0.004 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.455 Fit side-chains REVERT: A 200 MET cc_start: 0.7346 (ttp) cc_final: 0.7019 (pmm) REVERT: A 229 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7359 (ttm) REVERT: A 233 ASP cc_start: 0.7975 (m-30) cc_final: 0.7361 (t0) REVERT: A 464 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5225 (ppp) REVERT: A 745 TYR cc_start: 0.6465 (m-10) cc_final: 0.6017 (m-10) REVERT: A 1294 TYR cc_start: 0.8887 (t80) cc_final: 0.8598 (t80) REVERT: A 1332 SER cc_start: 0.8771 (t) cc_final: 0.8390 (p) REVERT: A 1338 ASP cc_start: 0.6933 (t70) cc_final: 0.6470 (t0) REVERT: A 1452 THR cc_start: 0.8208 (m) cc_final: 0.7951 (m) REVERT: A 1576 ASN cc_start: 0.8891 (t0) cc_final: 0.8568 (t0) outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 0.1851 time to fit residues: 35.1654 Evaluate side-chains 117 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1777 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 26 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11114 Z= 0.158 Angle : 0.629 11.185 15044 Z= 0.318 Chirality : 0.041 0.180 1711 Planarity : 0.004 0.072 1943 Dihedral : 4.979 26.990 1512 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.51 % Favored : 89.35 % Rotamer: Outliers : 0.89 % Allowed : 18.74 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.22), residues: 1400 helix: 0.21 (0.20), residues: 694 sheet: -2.19 (0.59), residues: 82 loop : -3.15 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1223 HIS 0.011 0.001 HIS A 561 PHE 0.020 0.001 PHE A 720 TYR 0.022 0.001 TYR A1179 ARG 0.006 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.224 Fit side-chains REVERT: A 104 PHE cc_start: 0.7793 (p90) cc_final: 0.7573 (p90) REVERT: A 200 MET cc_start: 0.7471 (ttp) cc_final: 0.7088 (pmm) REVERT: A 229 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: A 233 ASP cc_start: 0.7996 (m-30) cc_final: 0.7389 (t0) REVERT: A 464 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5315 (ppp) REVERT: A 1181 MET cc_start: 0.7005 (ptt) cc_final: 0.6763 (ptt) REVERT: A 1294 TYR cc_start: 0.8873 (t80) cc_final: 0.8575 (t80) REVERT: A 1332 SER cc_start: 0.8795 (t) cc_final: 0.8327 (p) REVERT: A 1338 ASP cc_start: 0.7005 (t70) cc_final: 0.6563 (t0) REVERT: A 1450 LEU cc_start: 0.7235 (tp) cc_final: 0.6754 (mp) REVERT: A 1576 ASN cc_start: 0.8857 (t0) cc_final: 0.8573 (t0) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.2027 time to fit residues: 35.9615 Evaluate side-chains 111 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1777 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 8.9990 chunk 127 optimal weight: 0.0270 chunk 131 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11114 Z= 0.185 Angle : 0.634 9.205 15044 Z= 0.323 Chirality : 0.042 0.236 1711 Planarity : 0.004 0.072 1943 Dihedral : 4.994 26.776 1512 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.08 % Favored : 88.71 % Rotamer: Outliers : 0.71 % Allowed : 19.09 % Favored : 80.20 % 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: -1.90 (0.23), residues: 1400 helix: 0.27 (0.20), residues: 695 sheet: -2.17 (0.59), residues: 82 loop : -3.03 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.009 0.001 HIS A 561 PHE 0.020 0.001 PHE A 720 TYR 0.022 0.001 TYR A1179 ARG 0.006 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.293 Fit side-chains REVERT: A 233 ASP cc_start: 0.8083 (m-30) cc_final: 0.7389 (t0) REVERT: A 464 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5026 (ppp) REVERT: A 1181 MET cc_start: 0.7084 (ptt) cc_final: 0.6858 (ptt) REVERT: A 1332 SER cc_start: 0.8815 (t) cc_final: 0.8346 (p) REVERT: A 1338 ASP cc_start: 0.7007 (t70) cc_final: 0.6634 (t0) REVERT: A 1576 ASN cc_start: 0.8856 (t0) cc_final: 0.8611 (t0) outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.1792 time to fit residues: 31.3332 Evaluate side-chains 113 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 130 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN A1208 GLN ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11114 Z= 0.153 Angle : 0.629 12.191 15044 Z= 0.316 Chirality : 0.041 0.175 1711 Planarity : 0.004 0.071 1943 Dihedral : 4.873 26.759 1512 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.86 % Favored : 89.92 % Rotamer: Outliers : 0.62 % Allowed : 18.56 % Favored : 80.82 % 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: -1.76 (0.23), residues: 1400 helix: 0.40 (0.21), residues: 695 sheet: -2.06 (0.58), residues: 82 loop : -3.00 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.010 0.001 HIS A 561 PHE 0.020 0.001 PHE A 112 TYR 0.021 0.001 TYR A1179 ARG 0.006 0.000 ARG A 867 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.917 Fit side-chains REVERT: A 104 PHE cc_start: 0.7802 (p90) cc_final: 0.7601 (p90) REVERT: A 233 ASP cc_start: 0.8066 (m-30) cc_final: 0.7519 (t0) REVERT: A 464 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.5198 (ppp) REVERT: A 1181 MET cc_start: 0.7047 (ptt) cc_final: 0.6844 (ptt) REVERT: A 1264 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7993 (tpp-160) REVERT: A 1332 SER cc_start: 0.8766 (t) cc_final: 0.8306 (p) REVERT: A 1338 ASP cc_start: 0.6871 (t70) cc_final: 0.6497 (t0) REVERT: A 1450 LEU cc_start: 0.7359 (tp) cc_final: 0.6943 (mp) REVERT: A 1576 ASN cc_start: 0.8792 (t0) cc_final: 0.8572 (t0) outliers start: 7 outliers final: 5 residues processed: 113 average time/residue: 0.1928 time to fit residues: 32.5803 Evaluate side-chains 113 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS ** A1087 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.190854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.140706 restraints weight = 17968.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138925 restraints weight = 11839.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140491 restraints weight = 10040.911| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11114 Z= 0.266 Angle : 0.688 9.740 15044 Z= 0.350 Chirality : 0.044 0.175 1711 Planarity : 0.004 0.075 1943 Dihedral : 5.284 26.685 1512 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.22 % Favored : 86.56 % Rotamer: Outliers : 0.89 % Allowed : 18.56 % Favored : 80.55 % 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 (0.23), residues: 1400 helix: 0.10 (0.20), residues: 689 sheet: -2.55 (0.55), residues: 89 loop : -3.02 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1186 HIS 0.008 0.001 HIS A 561 PHE 0.024 0.002 PHE A 690 TYR 0.023 0.002 TYR A1179 ARG 0.008 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.00 seconds wall clock time: 51 minutes 40.26 seconds (3100.26 seconds total)