Starting phenix.real_space_refine on Thu Mar 21 10:48:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8prv_17839/03_2024/8prv_17839_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.016 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 P 11 5.49 5 S 109 5.16 5 C 18968 2.51 5 N 4982 2.21 5 O 5744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A TYR 1706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A ASP 1875": "OD1" <-> "OD2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "G PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1708": "OD1" <-> "OD2" Residue "G PHE 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 12379 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1522} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1222 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16010 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'J8W:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'A5S': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'COA': 1, 'FMN': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.00, per 1000 atoms: 0.50 Number of scatterers: 29814 At special positions: 0 Unit cell: (183.57, 181.46, 178.295, 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) S 109 16.00 P 11 15.00 O 5744 8.00 N 4982 7.00 C 18968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.20 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.75 Conformation dependent library (CDL) restraints added in 6.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 29 sheets defined 44.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.01 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.543A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ALA A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 381 removed outlier: 3.647A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 405 through 422 removed outlier: 4.197A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.764A pdb=" N ARG A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 653 through 668 removed outlier: 3.630A pdb=" N LEU A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 4.149A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 removed outlier: 4.829A pdb=" N ILE A 883 " --> pdb=" O ALA A 880 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.803A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 969 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.779A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.488A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.221A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 No H-bonds generated for 'chain 'A' and resid 1195 through 1198' Processing helix chain 'A' and resid 1202 through 1207 Processing helix chain 'A' and resid 1210 through 1226 Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1274 through 1278 removed outlier: 3.586A pdb=" N SER A1278 " --> pdb=" O ILE A1274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1274 through 1278' Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.932A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A1287 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1289 " --> pdb=" O TRP A1286 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A1290 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1321 removed outlier: 5.305A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A1313 " --> pdb=" O GLU A1310 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A1318 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1320 " --> pdb=" O GLU A1317 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A1321 " --> pdb=" O THR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1345 Processing helix chain 'A' and resid 1352 through 1358 Processing helix chain 'A' and resid 1362 through 1365 Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1476 removed outlier: 3.570A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1509 Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.527A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1547 through 1563 removed outlier: 3.822A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 4.009A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.572A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A1597 " --> pdb=" O ASN A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 Processing helix chain 'A' and resid 1658 through 1660 No H-bonds generated for 'chain 'A' and resid 1658 through 1660' Processing helix chain 'A' and resid 1662 through 1664 No H-bonds generated for 'chain 'A' and resid 1662 through 1664' Processing helix chain 'A' and resid 1667 through 1694 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1747 through 1757 Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1790 removed outlier: 4.279A pdb=" N ARG A1789 " --> pdb=" O THR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1801 removed outlier: 3.535A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.502A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 225 through 236 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.787A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.693A pdb=" N PHE G 27 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.530A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.909A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.459A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 234 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 266 removed outlier: 3.655A pdb=" N TYR G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 284 removed outlier: 3.811A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 313 Processing helix chain 'G' and resid 321 through 326 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.913A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 383 through 396 removed outlier: 3.584A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 430 through 445 Proline residue: G 434 - end of helix removed outlier: 3.954A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS G 445 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 520 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 552 through 554 No H-bonds generated for 'chain 'G' and resid 552 through 554' Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 584 through 587 No H-bonds generated for 'chain 'G' and resid 584 through 587' Processing helix chain 'G' and resid 604 through 613 Processing helix chain 'G' and resid 627 through 638 Processing helix chain 'G' and resid 656 through 672 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 723 removed outlier: 3.694A pdb=" N HIS G 723 " --> pdb=" O ILE G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.269A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 781 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 788 removed outlier: 3.709A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 807 removed outlier: 4.399A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 829 through 836 removed outlier: 3.721A pdb=" N TRP G 832 " --> pdb=" O ASP G 829 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 880 through 897 removed outlier: 5.701A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 removed outlier: 3.663A pdb=" N GLU G 955 " --> pdb=" O LEU G 951 " (cutoff:3.500A) Processing helix chain 'G' and resid 970 through 974 removed outlier: 3.752A pdb=" N ASP G 974 " --> pdb=" O SER G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 986 removed outlier: 3.683A pdb=" N ALA G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1008 removed outlier: 3.504A pdb=" N GLN G1008 " --> pdb=" O LEU G1004 " (cutoff:3.500A) Processing helix chain 'G' and resid 1025 through 1030 Processing helix chain 'G' and resid 1035 through 1038 Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1061 No H-bonds generated for 'chain 'G' and resid 1059 through 1061' Processing helix chain 'G' and resid 1070 through 1089 Processing helix chain 'G' and resid 1094 through 1096 No H-bonds generated for 'chain 'G' and resid 1094 through 1096' Processing helix chain 'G' and resid 1135 through 1143 Processing helix chain 'G' and resid 1149 through 1155 Processing helix chain 'G' and resid 1169 through 1173 Processing helix chain 'G' and resid 1190 through 1192 No H-bonds generated for 'chain 'G' and resid 1190 through 1192' Processing helix chain 'G' and resid 1258 through 1270 removed outlier: 3.575A pdb=" N MET G1265 " --> pdb=" O ARG G1261 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1338 removed outlier: 4.194A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1419 through 1421 No H-bonds generated for 'chain 'G' and resid 1419 through 1421' Processing helix chain 'G' and resid 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1602 through 1604 No H-bonds generated for 'chain 'G' and resid 1602 through 1604' Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.656A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1725 through 1735 Processing helix chain 'G' and resid 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1794 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1818 Processing helix chain 'G' and resid 1824 through 1841 Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1868 through 1882 removed outlier: 3.522A pdb=" N THR G1882 " --> pdb=" O VAL G1878 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1920 removed outlier: 3.562A pdb=" N ASN G1915 " --> pdb=" O THR G1911 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G1916 " --> pdb=" O ASN G1912 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1925 through 1929 removed outlier: 3.570A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1925 through 1929' Processing helix chain 'G' and resid 1935 through 1952 removed outlier: 4.265A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G1949 " --> pdb=" O ASP G1945 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1983 through 1994 removed outlier: 3.906A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.788A pdb=" N LYS G1993 " --> pdb=" O SER G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1998 through 2000 No H-bonds generated for 'chain 'G' and resid 1998 through 2000' Processing helix chain 'G' and resid 2023 through 2032 Processing helix chain 'G' and resid 2036 through 2043 Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.722A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.494A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.158A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= G, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= H, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= I, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= J, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.457A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 3.671A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1768 through 1775 removed outlier: 3.776A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.684A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.823A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N GLY G 272 " --> pdb=" O PRO G 458 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR G 460 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.078A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 620 removed outlier: 7.000A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= T, first strand: chain 'G' and resid 1181 through 1185 removed outlier: 3.504A pdb=" N THR G1196 " --> pdb=" O GLU G1183 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 4.002A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 3.612A pdb=" N SER G1482 " --> pdb=" O THR G1473 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.679A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.825A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= Z, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.524A pdb=" N GLU G1749 " --> pdb=" O PHE G1738 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 6.642A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 1378 through 1384 removed outlier: 6.858A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 7.029A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3249 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: 13.18 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.63: 30241 1.63 - 2.24: 199 2.24 - 2.85: 0 2.85 - 3.47: 0 3.47 - 4.08: 2 Bond restraints: 30442 Sorted by residual: bond pdb=" AP1 COA G2103 " pdb="AO5* COA G2103 " ideal model delta sigma weight residual 1.610 4.081 -2.471 2.00e-02 2.50e+03 1.53e+04 bond pdb=" AO6 COA G2103 " pdb=" AP2 COA G2103 " ideal model delta sigma weight residual 1.610 3.571 -1.961 2.00e-02 2.50e+03 9.62e+03 bond pdb=" CG ASP G1845 " pdb=" OD1 ASP G1845 " ideal model delta sigma weight residual 1.249 1.557 -0.308 1.90e-02 2.77e+03 2.63e+02 bond pdb=" CG ASP G1845 " pdb=" OD2 ASP G1845 " ideal model delta sigma weight residual 1.249 1.012 0.237 1.90e-02 2.77e+03 1.56e+02 bond pdb=" PC9 COA G2103 " pdb=" PO9 COA G2103 " ideal model delta sigma weight residual 1.410 1.231 0.179 2.00e-02 2.50e+03 7.98e+01 ... (remaining 30437 not shown) Histogram of bond angle deviations from ideal: 3.82 - 30.54: 1 30.54 - 57.26: 1 57.26 - 83.98: 1 83.98 - 110.71: 8426 110.71 - 137.43: 32833 Bond angle restraints: 41262 Sorted by residual: angle pdb=" AO3 COA G2103 " pdb=" AP1 COA G2103 " pdb="AO5* COA G2103 " ideal model delta sigma weight residual 102.60 3.82 98.78 3.00e+00 1.11e-01 1.08e+03 angle pdb=" AO3 COA G2103 " pdb=" AP2 COA G2103 " pdb=" AO6 COA G2103 " ideal model delta sigma weight residual 102.60 36.58 66.02 3.00e+00 1.11e-01 4.84e+02 angle pdb=" AO4 COA G2103 " pdb=" AP2 COA G2103 " pdb=" AO6 COA G2103 " ideal model delta sigma weight residual 108.20 73.92 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" AP1 COA G2103 " pdb="AO5* COA G2103 " pdb="AC5* COA G2103 " ideal model delta sigma weight residual 120.50 91.94 28.56 3.00e+00 1.11e-01 9.06e+01 angle pdb=" CB ASP G1845 " pdb=" CG ASP G1845 " pdb=" OD1 ASP G1845 " ideal model delta sigma weight residual 118.40 98.01 20.39 2.30e+00 1.89e-01 7.86e+01 ... (remaining 41257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 17901 33.20 - 66.41: 473 66.41 - 99.61: 54 99.61 - 132.81: 6 132.81 - 166.01: 3 Dihedral angle restraints: 18437 sinusoidal: 7514 harmonic: 10923 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 0.34 -86.34 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" AO3 COA G2103 " pdb=" AO6 COA G2103 " pdb=" AP2 COA G2103 " pdb="PC12 COA G2103 " ideal model delta sinusoidal sigma weight residual -81.62 64.95 -146.57 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" AP2 COA G2103 " pdb=" AO6 COA G2103 " pdb="PC12 COA G2103 " pdb="PC11 COA G2103 " ideal model delta sinusoidal sigma weight residual 121.06 -115.56 -123.39 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 18434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2041 0.058 - 0.117: 1631 0.117 - 0.175: 747 0.175 - 0.234: 182 0.234 - 0.292: 28 Chirality restraints: 4629 Sorted by residual: chirality pdb=" CA J8W G1808 " pdb=" N J8W G1808 " pdb=" C J8W G1808 " pdb=" CB J8W G1808 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL G1616 " pdb=" N VAL G1616 " pdb=" C VAL G1616 " pdb=" CB VAL G1616 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4626 not shown) Planarity restraints: 5305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP G1845 " -0.075 2.00e-02 2.50e+03 1.55e-01 2.40e+02 pdb=" CG ASP G1845 " 0.263 2.00e-02 2.50e+03 pdb=" OD1 ASP G1845 " -0.050 2.00e-02 2.50e+03 pdb=" OD2 ASP G1845 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1* FMN G2101 " -0.006 2.00e-02 2.50e+03 2.41e-02 2.76e+01 pdb=" C10 FMN G2101 " 0.009 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.026 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.021 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.038 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.043 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.003 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.037 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.014 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.024 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.037 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.044 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.011 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.063 2.00e-02 2.50e+03 3.23e-02 2.09e+01 pdb=" CG TYR A1529 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.033 2.00e-02 2.50e+03 ... (remaining 5302 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 3 2.27 - 2.93: 11084 2.93 - 3.58: 41993 3.58 - 4.24: 70868 4.24 - 4.90: 122131 Nonbonded interactions: 246079 Sorted by model distance: nonbonded pdb=" AP2 COA G2103 " pdb="AO5* COA G2103 " model vdw 1.611 2.720 nonbonded pdb=" AO6 COA G2103 " pdb=" AP1 COA G2103 " model vdw 1.612 2.720 nonbonded pdb=" OD1 ASP A 376 " pdb=" NH1 ARG B 276 " model vdw 2.228 2.520 nonbonded pdb=" O ALA G1813 " pdb=" OG SER G1817 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.296 2.440 ... (remaining 246074 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 individual isotropic 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.000 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 77.990 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.023 2.471 30442 Z= 1.617 Angle : 2.001 98.780 41262 Z= 1.388 Chirality : 0.091 0.292 4629 Planarity : 0.007 0.155 5305 Dihedral : 15.599 166.012 11400 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 0.22 % Allowed : 3.33 % Favored : 96.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.56 % 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: -3.14 (0.11), residues: 3764 helix: -2.66 (0.09), residues: 1650 sheet: -1.90 (0.19), residues: 511 loop : -1.22 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.010 TRP G 732 HIS 0.016 0.004 HIS G1568 PHE 0.054 0.007 PHE G 799 TYR 0.063 0.008 TYR A1529 ARG 0.040 0.001 ARG G1849 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 152 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 3.425 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9096 (mtt) cc_final: 0.8864 (mtt) REVERT: A 352 MET cc_start: 0.8699 (ttp) cc_final: 0.8480 (ttm) REVERT: A 1066 ASN cc_start: 0.7930 (m-40) cc_final: 0.7384 (m-40) REVERT: A 1692 MET cc_start: 0.9131 (ttt) cc_final: 0.8916 (ttt) REVERT: A 1840 VAL cc_start: 0.7749 (p) cc_final: 0.7425 (m) REVERT: G 46 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6991 (mp0) REVERT: G 132 MET cc_start: 0.7992 (mmp) cc_final: 0.7646 (mmp) REVERT: G 300 ILE cc_start: 0.8780 (mm) cc_final: 0.8553 (mt) REVERT: G 447 ASN cc_start: 0.8688 (m-40) cc_final: 0.8084 (p0) REVERT: G 599 PRO cc_start: 0.8882 (OUTLIER) cc_final: 0.8589 (Cg_endo) REVERT: G 794 MET cc_start: 0.9264 (mtt) cc_final: 0.9054 (mtt) REVERT: G 1265 MET cc_start: 0.9084 (tmm) cc_final: 0.8514 (tmm) REVERT: G 1838 MET cc_start: 0.8968 (mtt) cc_final: 0.8668 (mtt) REVERT: G 1939 HIS cc_start: 0.7983 (t-90) cc_final: 0.7550 (t70) REVERT: G 1964 PHE cc_start: 0.7420 (m-80) cc_final: 0.7062 (m-80) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 1.5836 time to fit residues: 282.1606 Evaluate side-chains 116 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain G residue 599 PRO Chi-restraints excluded: chain G residue 709 SER Chi-restraints excluded: chain G residue 1586 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 0.0000 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 411 GLN A 475 GLN A 527 GLN A1380 GLN A1852 HIS B 271 ASN B 292 GLN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN G 102 HIS G 110 GLN G 181 HIS G 245 GLN G 440 ASN G 718 ASN G 747 HIS G 760 HIS G 993 GLN G1055 HIS G1178 GLN G1217 ASN G1355 ASN G1432 GLN G1633 ASN G1851 ASN G1912 ASN G1983 ASN G2020 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30442 Z= 0.270 Angle : 0.554 7.531 41262 Z= 0.291 Chirality : 0.043 0.202 4629 Planarity : 0.004 0.042 5305 Dihedral : 9.236 174.237 4212 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.77 % Allowed : 6.16 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -0.53 (0.13), residues: 3764 helix: 0.08 (0.12), residues: 1666 sheet: -1.16 (0.21), residues: 491 loop : -0.35 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.019 0.002 PHE A1111 TYR 0.022 0.002 TYR G1553 ARG 0.004 0.000 ARG A1680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 138 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 3.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8800 (ttp) cc_final: 0.8572 (ttm) REVERT: A 1066 ASN cc_start: 0.7941 (m-40) cc_final: 0.7369 (m-40) REVERT: G 794 MET cc_start: 0.9196 (mtt) cc_final: 0.8952 (mtp) REVERT: G 1939 HIS cc_start: 0.8014 (t-90) cc_final: 0.7559 (t70) REVERT: G 1964 PHE cc_start: 0.7421 (m-80) cc_final: 0.7196 (m-80) outliers start: 25 outliers final: 12 residues processed: 132 average time/residue: 1.4657 time to fit residues: 230.9665 Evaluate side-chains 120 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1845 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1000 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN G 446 ASN G 495 GLN G 500 HIS G 752 GLN G1088 GLN G1529 GLN G1581 HIS G1619 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30442 Z= 0.344 Angle : 0.555 9.266 41262 Z= 0.288 Chirality : 0.045 0.200 4629 Planarity : 0.004 0.053 5305 Dihedral : 8.914 178.016 4206 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.02 % Allowed : 7.95 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.17 (0.13), residues: 3764 helix: 0.82 (0.13), residues: 1669 sheet: -0.87 (0.21), residues: 481 loop : -0.17 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 661 HIS 0.009 0.001 HIS A1689 PHE 0.023 0.002 PHE A1376 TYR 0.024 0.002 TYR G1553 ARG 0.004 0.001 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 144 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8736 (ttp) cc_final: 0.8505 (ttm) REVERT: A 1066 ASN cc_start: 0.7838 (m-40) cc_final: 0.7259 (m-40) REVERT: G 794 MET cc_start: 0.9170 (mtt) cc_final: 0.8942 (mtp) REVERT: G 1854 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: G 1939 HIS cc_start: 0.7973 (t-90) cc_final: 0.7557 (t-170) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 1.4219 time to fit residues: 235.8675 Evaluate side-chains 127 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 364 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A1794 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30442 Z= 0.302 Angle : 0.525 9.083 41262 Z= 0.272 Chirality : 0.044 0.191 4629 Planarity : 0.004 0.055 5305 Dihedral : 8.709 179.592 4205 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 8.93 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.39 (0.14), residues: 3764 helix: 1.02 (0.13), residues: 1671 sheet: -0.74 (0.22), residues: 481 loop : -0.09 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.019 0.002 PHE A1376 TYR 0.022 0.002 TYR G1553 ARG 0.004 0.000 ARG A1680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 151 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 107 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: A 352 MET cc_start: 0.8753 (ttp) cc_final: 0.8514 (ttm) REVERT: A 1066 ASN cc_start: 0.7851 (m-40) cc_final: 0.7283 (m-40) REVERT: A 1507 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: B 232 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7781 (tp) REVERT: G 794 MET cc_start: 0.9155 (mtt) cc_final: 0.8922 (mtp) REVERT: G 843 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9031 (mt) REVERT: G 1854 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8132 (mmm) REVERT: G 1939 HIS cc_start: 0.7977 (t-90) cc_final: 0.7612 (t-170) outliers start: 44 outliers final: 26 residues processed: 143 average time/residue: 1.3264 time to fit residues: 230.1560 Evaluate side-chains 138 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 40.0000 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN G 715 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30442 Z= 0.295 Angle : 0.520 9.064 41262 Z= 0.268 Chirality : 0.044 0.190 4629 Planarity : 0.004 0.056 5305 Dihedral : 8.571 177.684 4205 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.57 % Allowed : 9.67 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.48 (0.14), residues: 3764 helix: 1.09 (0.13), residues: 1679 sheet: -0.66 (0.22), residues: 483 loop : -0.05 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.019 0.002 PHE A1376 TYR 0.021 0.002 TYR G1553 ARG 0.003 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 162 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 3.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: A 352 MET cc_start: 0.8746 (ttp) cc_final: 0.8504 (ttm) REVERT: A 1066 ASN cc_start: 0.7876 (m-40) cc_final: 0.7323 (m-40) REVERT: A 1507 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: B 232 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7779 (tp) REVERT: B 301 ASP cc_start: 0.5943 (t0) cc_final: 0.5573 (t0) REVERT: G 80 PHE cc_start: 0.7232 (m-80) cc_final: 0.7017 (m-80) REVERT: G 794 MET cc_start: 0.9154 (mtt) cc_final: 0.8913 (mtp) REVERT: G 1854 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: G 1939 HIS cc_start: 0.7985 (t-90) cc_final: 0.7724 (t-170) outliers start: 51 outliers final: 30 residues processed: 154 average time/residue: 1.3432 time to fit residues: 252.8020 Evaluate side-chains 144 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30442 Z= 0.266 Angle : 0.505 8.934 41262 Z= 0.261 Chirality : 0.043 0.183 4629 Planarity : 0.004 0.056 5305 Dihedral : 8.381 175.184 4205 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 10.44 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.58 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1678 sheet: -0.57 (0.22), residues: 478 loop : -0.01 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.019 0.002 PHE A 35 TYR 0.020 0.002 TYR G1553 ARG 0.003 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 157 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: A 352 MET cc_start: 0.8707 (ttp) cc_final: 0.8462 (ttm) REVERT: A 1066 ASN cc_start: 0.7889 (m-40) cc_final: 0.7356 (m-40) REVERT: A 1507 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: A 1792 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7809 (p) REVERT: B 232 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7784 (tp) REVERT: B 301 ASP cc_start: 0.6115 (t0) cc_final: 0.5729 (t0) REVERT: G 80 PHE cc_start: 0.7202 (m-80) cc_final: 0.6985 (m-80) REVERT: G 714 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8515 (p) REVERT: G 794 MET cc_start: 0.9151 (mtt) cc_final: 0.8912 (mtp) REVERT: G 1854 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: G 1939 HIS cc_start: 0.8030 (t-90) cc_final: 0.7712 (t70) outliers start: 46 outliers final: 27 residues processed: 151 average time/residue: 1.3862 time to fit residues: 252.6773 Evaluate side-chains 142 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1792 THR Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 307 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30442 Z= 0.273 Angle : 0.507 8.849 41262 Z= 0.262 Chirality : 0.043 0.186 4629 Planarity : 0.004 0.057 5305 Dihedral : 8.248 172.763 4205 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.88 % Allowed : 10.20 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.59 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1681 sheet: -0.55 (0.22), residues: 478 loop : -0.01 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.019 0.002 PHE A 35 TYR 0.020 0.002 TYR G1553 ARG 0.003 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 171 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 110 time to evaluate : 3.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: A 352 MET cc_start: 0.8720 (ttp) cc_final: 0.8476 (ttm) REVERT: A 1066 ASN cc_start: 0.7901 (m-40) cc_final: 0.7377 (m-40) REVERT: A 1507 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: B 232 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7779 (tp) REVERT: B 301 ASP cc_start: 0.6086 (t0) cc_final: 0.5694 (t0) REVERT: G 714 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8518 (p) REVERT: G 794 MET cc_start: 0.9154 (mtt) cc_final: 0.8901 (mtp) REVERT: G 1854 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: G 1939 HIS cc_start: 0.8096 (t-90) cc_final: 0.7748 (t70) outliers start: 61 outliers final: 35 residues processed: 163 average time/residue: 1.4008 time to fit residues: 279.7487 Evaluate side-chains 147 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 429 SER Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 2039 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 247 optimal weight: 30.0000 chunk 179 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30442 Z= 0.233 Angle : 0.490 9.274 41262 Z= 0.253 Chirality : 0.042 0.181 4629 Planarity : 0.004 0.057 5305 Dihedral : 8.072 169.403 4205 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.54 % Allowed : 10.66 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.68 (0.14), residues: 3764 helix: 1.25 (0.13), residues: 1682 sheet: -0.51 (0.22), residues: 478 loop : 0.03 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.019 0.001 PHE A 35 TYR 0.019 0.001 TYR G1553 ARG 0.003 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 157 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: A 352 MET cc_start: 0.8717 (ttp) cc_final: 0.8477 (ttm) REVERT: A 1066 ASN cc_start: 0.7895 (m-40) cc_final: 0.7363 (m-40) REVERT: A 1507 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: B 232 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7793 (tp) REVERT: G 714 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8508 (p) REVERT: G 794 MET cc_start: 0.9175 (mtt) cc_final: 0.8932 (mtp) REVERT: G 1433 MET cc_start: 0.8300 (mtp) cc_final: 0.8069 (ttm) REVERT: G 1854 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8154 (mmm) REVERT: G 1939 HIS cc_start: 0.8103 (t-90) cc_final: 0.7739 (t70) REVERT: G 1945 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7923 (t0) outliers start: 50 outliers final: 34 residues processed: 151 average time/residue: 1.4069 time to fit residues: 258.0253 Evaluate side-chains 145 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 429 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1945 ASP Chi-restraints excluded: chain G residue 2039 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 317 optimal weight: 0.0670 chunk 338 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30442 Z= 0.267 Angle : 0.506 8.767 41262 Z= 0.260 Chirality : 0.043 0.186 4629 Planarity : 0.004 0.057 5305 Dihedral : 8.034 168.499 4205 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.51 % Allowed : 10.81 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.65 (0.14), residues: 3764 helix: 1.22 (0.13), residues: 1682 sheet: -0.52 (0.22), residues: 478 loop : 0.03 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.025 0.002 PHE G 80 TYR 0.020 0.002 TYR G1553 ARG 0.003 0.000 ARG A 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 155 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 106 time to evaluate : 3.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: A 352 MET cc_start: 0.8713 (ttp) cc_final: 0.8473 (ttm) REVERT: A 1066 ASN cc_start: 0.7905 (m-40) cc_final: 0.7374 (m-40) REVERT: A 1507 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: B 232 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7772 (tp) REVERT: G 714 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8506 (p) REVERT: G 794 MET cc_start: 0.9185 (mtt) cc_final: 0.8944 (mtp) REVERT: G 1854 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8160 (mmm) REVERT: G 1939 HIS cc_start: 0.8100 (t-90) cc_final: 0.7761 (t70) REVERT: G 1945 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (t0) outliers start: 49 outliers final: 36 residues processed: 149 average time/residue: 1.2849 time to fit residues: 233.8513 Evaluate side-chains 148 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 429 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1840 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1945 ASP Chi-restraints excluded: chain G residue 2039 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 375 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1790 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30442 Z= 0.225 Angle : 0.488 10.230 41262 Z= 0.251 Chirality : 0.042 0.178 4629 Planarity : 0.003 0.057 5305 Dihedral : 7.876 166.249 4205 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.29 % Allowed : 11.09 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.73 (0.14), residues: 3764 helix: 1.30 (0.13), residues: 1681 sheet: -0.49 (0.22), residues: 478 loop : 0.06 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.019 0.001 PHE A 35 TYR 0.018 0.001 TYR G1553 ARG 0.002 0.000 ARG G1834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 149 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 3.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: A 352 MET cc_start: 0.8711 (ttp) cc_final: 0.8489 (ttm) REVERT: A 1066 ASN cc_start: 0.7908 (m-40) cc_final: 0.7398 (m-40) REVERT: A 1507 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: B 232 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7771 (tp) REVERT: G 714 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8499 (p) REVERT: G 794 MET cc_start: 0.9171 (mtt) cc_final: 0.8931 (mtp) REVERT: G 1433 MET cc_start: 0.8282 (mtp) cc_final: 0.8081 (ttm) REVERT: G 1854 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: G 1939 HIS cc_start: 0.8103 (t-90) cc_final: 0.7759 (t70) REVERT: G 1945 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7936 (t0) outliers start: 42 outliers final: 33 residues processed: 144 average time/residue: 1.3316 time to fit residues: 234.0346 Evaluate side-chains 144 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 105 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 920 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1728 SER Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 166 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 429 SER Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1177 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1549 THR Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1854 MET Chi-restraints excluded: chain G residue 1945 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046700 restraints weight = 98119.926| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.02 r_work: 0.2767 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30442 Z= 0.248 Angle : 0.503 11.776 41262 Z= 0.257 Chirality : 0.043 0.181 4629 Planarity : 0.004 0.056 5305 Dihedral : 7.848 166.260 4205 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.54 % Allowed : 11.00 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.70 (0.14), residues: 3764 helix: 1.26 (0.13), residues: 1681 sheet: -0.49 (0.22), residues: 478 loop : 0.06 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.019 0.001 PHE A 35 TYR 0.022 0.001 TYR G2030 ARG 0.003 0.000 ARG G1834 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6768.61 seconds wall clock time: 123 minutes 25.23 seconds (7405.23 seconds total)