Starting phenix.real_space_refine on Thu Feb 15 08:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/02_2024/7elc_31180.pdb" } resolution = 3.1 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= 0.003 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 4 6.06 5 P 7 5.49 5 S 83 5.16 5 C 7458 2.51 5 N 2002 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 7": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 712": "OD1" <-> "OD2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A ASP 1147": "OD1" <-> "OD2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ASP 1220": "OD1" <-> "OD2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1315": "OD1" <-> "OD2" Residue "A TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1319": "OD1" <-> "OD2" Residue "A ASP 1329": "OD1" <-> "OD2" Residue "A ASP 1347": "OD1" <-> "OD2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A GLU 1461": "OE1" <-> "OE2" Residue "A ASP 1464": "OD1" <-> "OD2" Residue "A ASP 1470": "OD1" <-> "OD2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A ASP 1487": "OD1" <-> "OD2" Residue "A ASP 1488": "OD1" <-> "OD2" Residue "A ASP 1504": "OD1" <-> "OD2" Residue "A ASP 1524": "OD1" <-> "OD2" Residue "A TYR 1533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1540": "OE1" <-> "OE2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A GLU 1642": "OE1" <-> "OE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1692": "OE1" <-> "OE2" Residue "A GLU 1695": "OE1" <-> "OE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ARG 1742": "NH1" <-> "NH2" Residue "A GLU 1750": "OE1" <-> "OE2" Residue "A PHE 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A PHE 1772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1796": "NH1" <-> "NH2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11754 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11193 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 39, 'TRANS': 1369} Chain breaks: 15 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2014 SG CYS A 284 50.115 66.499 25.945 1.00 39.04 S ATOM 2038 SG CYS A 287 53.363 66.957 23.538 1.00 38.92 S ATOM 3378 SG CYS A 470 49.797 68.522 22.607 1.00 67.43 S ATOM 9952 SG CYS A1650 39.911 15.154 42.832 1.00 76.77 S ATOM 9965 SG CYS A1652 36.471 15.298 43.227 1.00 78.38 S ATOM 9984 SG CYS A1655 39.918 18.510 43.735 1.00 66.72 S ATOM 10056 SG CYS A1664 38.079 16.333 45.513 1.00 59.44 S ATOM 11254 SG CYS B 39 23.348 77.702 52.665 1.00 45.38 S ATOM 11275 SG CYS B 42 25.973 79.094 51.654 1.00 44.44 S ATOM 11409 SG CYS B 58 21.496 79.659 50.588 1.00 59.01 S ATOM 11434 SG CYS B 61 23.404 77.092 49.258 1.00 58.68 S ATOM 11357 SG CYS B 52 16.244 70.508 55.345 1.00 68.57 S ATOM 11524 SG CYS B 72 18.943 69.558 53.533 1.00 53.78 S ATOM 11548 SG CYS B 75 18.152 67.872 56.362 1.00 52.91 S Time building chain proxies: 6.82, per 1000 atoms: 0.58 Number of scatterers: 11754 At special positions: 0 Unit cell: (119, 110, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Mn 1 24.99 S 83 16.00 P 7 15.00 O 2199 8.00 N 2002 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " Number of angles added : 18 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 52.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 4.014A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.751A pdb=" N ALA A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.763A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.930A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.860A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.536A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.750A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.688A pdb=" N ASP A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.550A pdb=" N LYS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.872A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 501 removed outlier: 3.525A pdb=" N GLN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 579 through 583 removed outlier: 4.392A pdb=" N PHE A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.777A pdb=" N LEU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.519A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.722A pdb=" N VAL A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.894A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 4.227A pdb=" N MET A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1248 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 4.381A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.522A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.580A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1514 through 1520 Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 4.247A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.522A pdb=" N LEU A1668 " --> pdb=" O ASN A1665 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1665 through 1669' Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.575A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1698 Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1774 through 1783 removed outlier: 3.549A pdb=" N ALA A1778 " --> pdb=" O ASP A1774 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1780 " --> pdb=" O CYS A1776 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A1783 " --> pdb=" O LEU A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'B' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.011A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.290A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.633A pdb=" N CYS A 528 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 553 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 572 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 555 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 570 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 557 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 735 through 736 removed outlier: 6.941A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 553 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3765 1.34 - 1.46: 2121 1.46 - 1.58: 5955 1.58 - 1.70: 13 1.70 - 1.82: 116 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP A1470 " pdb=" CB ASP A1470 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.09e-01 bond pdb=" CB ASP A1470 " pdb=" CG ASP A1470 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.68e-01 bond pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 1.550 1.542 0.009 1.03e-02 9.43e+03 7.20e-01 bond pdb=" C ARG A 691 " pdb=" O ARG A 691 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 7.18e-01 bond pdb=" CB VAL A 358 " pdb=" CG1 VAL A 358 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.23e-01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 288 106.87 - 113.65: 6746 113.65 - 120.42: 4558 120.42 - 127.19: 4462 127.19 - 133.96: 112 Bond angle restraints: 16166 Sorted by residual: angle pdb=" N GLU A 427 " pdb=" CA GLU A 427 " pdb=" C GLU A 427 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.90e+01 angle pdb=" C CYS B 42 " pdb=" N TRP B 43 " pdb=" CA TRP B 43 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.73e+00 angle pdb=" CA TRP B 43 " pdb=" CB TRP B 43 " pdb=" CG TRP B 43 " ideal model delta sigma weight residual 113.60 118.98 -5.38 1.90e+00 2.77e-01 8.02e+00 angle pdb=" CA GLU A 427 " pdb=" C GLU A 427 " pdb=" N ILE A 428 " ideal model delta sigma weight residual 119.26 116.16 3.10 1.14e+00 7.69e-01 7.40e+00 angle pdb=" CA LEU A 435 " pdb=" CB LEU A 435 " pdb=" CG LEU A 435 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.26e+00 ... (remaining 16161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6539 17.97 - 35.94: 559 35.94 - 53.91: 139 53.91 - 71.87: 35 71.87 - 89.84: 12 Dihedral angle restraints: 7284 sinusoidal: 3032 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 60 " pdb=" CB CYS A 60 " ideal model delta sinusoidal sigma weight residual -86.00 -39.30 -46.70 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CA SER A1432 " pdb=" C SER A1432 " pdb=" N THR A1433 " pdb=" CA THR A1433 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS A1364 " pdb=" C LYS A1364 " pdb=" N LEU A1365 " pdb=" CA LEU A1365 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1183 0.031 - 0.062: 468 0.062 - 0.092: 135 0.092 - 0.123: 66 0.123 - 0.154: 6 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CB ILE A1510 " pdb=" CA ILE A1510 " pdb=" CG1 ILE A1510 " pdb=" CG2 ILE A1510 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ASP A1470 " pdb=" N ASP A1470 " pdb=" C ASP A1470 " pdb=" CB ASP A1470 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1855 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1280 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A1281 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A1281 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1281 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1753 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A1754 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1754 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1754 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 710 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 711 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 711 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 711 " 0.017 5.00e-02 4.00e+02 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 969 2.74 - 3.28: 12104 3.28 - 3.82: 19734 3.82 - 4.36: 24062 4.36 - 4.90: 40471 Nonbonded interactions: 97340 Sorted by model distance: nonbonded pdb=" OD1 ASP A 769 " pdb=" OG1 THR A 772 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 538 " pdb=" OD1 ASN A 562 " model vdw 2.235 2.440 nonbonded pdb=" O ASP A 370 " pdb=" OG SER A 374 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASP A1420 " pdb=" NH1 ARG A1476 " model vdw 2.237 2.520 nonbonded pdb=" O LYS A1191 " pdb=" OG1 THR A1195 " model vdw 2.250 2.440 ... (remaining 97335 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.690 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.003 0.027 11970 Z= 0.182 Angle : 0.548 9.427 16166 Z= 0.305 Chirality : 0.039 0.154 1858 Planarity : 0.003 0.035 2014 Dihedral : 15.027 89.844 4506 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 2.73 % Allowed : 9.64 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.20), residues: 1424 helix: -0.84 (0.17), residues: 733 sheet: -2.89 (0.39), residues: 104 loop : -3.40 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1680 HIS 0.003 0.001 HIS A 647 PHE 0.018 0.001 PHE A 533 TYR 0.009 0.001 TYR A 534 ARG 0.002 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 232 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 357 MET cc_start: 0.8158 (tpp) cc_final: 0.7516 (mmt) REVERT: A 766 ASP cc_start: 0.7883 (p0) cc_final: 0.7635 (p0) REVERT: A 1143 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6681 (tpp80) REVERT: A 1272 GLN cc_start: 0.7779 (mt0) cc_final: 0.7479 (mt0) REVERT: A 1391 GLU cc_start: 0.7493 (pt0) cc_final: 0.7147 (pm20) REVERT: A 1414 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 1527 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 1625 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7547 (mmp) REVERT: B 65 MET cc_start: 0.8039 (mtm) cc_final: 0.7761 (mtm) REVERT: B 68 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6129 (p0) outliers start: 36 outliers final: 23 residues processed: 250 average time/residue: 0.2923 time to fit residues: 99.4546 Evaluate side-chains 199 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.0050 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 125 ASN A 148 ASN A 185 GLN A 189 HIS A 348 ASN A 359 ASN A 442 ASN A 522 ASN A 546 GLN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1206 GLN A1231 HIS A1275 GLN A1279 GLN A1283 HIS A1331 GLN A1463 GLN A1496 ASN A1551 ASN A1712 ASN A1726 GLN A1734 ASN ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN A1791 HIS B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 68 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.214 Angle : 0.564 10.278 16166 Z= 0.283 Chirality : 0.041 0.166 1858 Planarity : 0.004 0.037 2014 Dihedral : 9.985 75.406 1720 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.48 % Favored : 90.45 % Rotamer: Outliers : 3.95 % Allowed : 13.81 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.22), residues: 1424 helix: 0.06 (0.18), residues: 758 sheet: -2.43 (0.47), residues: 94 loop : -3.05 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1549 HIS 0.003 0.001 HIS A1735 PHE 0.024 0.001 PHE A1511 TYR 0.011 0.001 TYR A 572 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8215 (tpp) cc_final: 0.7643 (mmt) REVERT: A 381 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6536 (tt) REVERT: A 1143 ARG cc_start: 0.7278 (tmm-80) cc_final: 0.6716 (tpp80) REVERT: A 1272 GLN cc_start: 0.7825 (mt0) cc_final: 0.7625 (mt0) REVERT: A 1391 GLU cc_start: 0.7363 (pt0) cc_final: 0.6990 (pm20) REVERT: A 1462 ASP cc_start: 0.6479 (t0) cc_final: 0.6269 (t0) REVERT: A 1527 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8020 (tp) REVERT: B 65 MET cc_start: 0.7945 (mtm) cc_final: 0.7672 (mtm) REVERT: B 70 GLU cc_start: 0.7300 (tp30) cc_final: 0.6520 (tp30) outliers start: 52 outliers final: 36 residues processed: 228 average time/residue: 0.2437 time to fit residues: 79.7480 Evaluate side-chains 206 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 359 ASN A 476 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 GLN A1726 GLN ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11970 Z= 0.180 Angle : 0.551 12.065 16166 Z= 0.274 Chirality : 0.040 0.162 1858 Planarity : 0.003 0.040 2014 Dihedral : 9.584 73.439 1714 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.31 % Rotamer: Outliers : 3.79 % Allowed : 16.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1424 helix: 0.47 (0.19), residues: 757 sheet: -2.18 (0.49), residues: 95 loop : -2.91 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1549 HIS 0.012 0.001 HIS A 189 PHE 0.021 0.001 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.6823 (tpt) cc_final: 0.6616 (tpt) REVERT: A 142 ASP cc_start: 0.6310 (t0) cc_final: 0.5547 (p0) REVERT: A 144 ARG cc_start: 0.6690 (mtm-85) cc_final: 0.5357 (mmp-170) REVERT: A 166 GLU cc_start: 0.4298 (OUTLIER) cc_final: 0.4028 (mp0) REVERT: A 357 MET cc_start: 0.8236 (tpp) cc_final: 0.7644 (mmt) REVERT: A 381 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6563 (tt) REVERT: A 736 VAL cc_start: 0.8238 (t) cc_final: 0.8015 (t) REVERT: A 1143 ARG cc_start: 0.7264 (tmm-80) cc_final: 0.6693 (tpp80) REVERT: A 1268 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6158 (tp30) REVERT: A 1272 GLN cc_start: 0.7995 (mt0) cc_final: 0.7674 (mt0) REVERT: A 1391 GLU cc_start: 0.7341 (pt0) cc_final: 0.6955 (pm20) REVERT: A 1527 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 68 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.6183 (p0) REVERT: B 70 GLU cc_start: 0.7306 (tp30) cc_final: 0.6520 (tp30) outliers start: 50 outliers final: 38 residues processed: 222 average time/residue: 0.2470 time to fit residues: 78.9580 Evaluate side-chains 220 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 149 ASN A 189 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11970 Z= 0.193 Angle : 0.557 12.606 16166 Z= 0.277 Chirality : 0.040 0.188 1858 Planarity : 0.003 0.040 2014 Dihedral : 9.472 73.192 1713 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.31 % Rotamer: Outliers : 4.40 % Allowed : 17.45 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1424 helix: 0.67 (0.19), residues: 764 sheet: -2.03 (0.51), residues: 94 loop : -2.83 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 43 HIS 0.002 0.001 HIS A 647 PHE 0.022 0.001 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 183 time to evaluate : 1.348 Fit side-chains REVERT: A 120 MET cc_start: 0.6700 (tpt) cc_final: 0.6474 (tpt) REVERT: A 144 ARG cc_start: 0.6717 (mtm-85) cc_final: 0.5444 (mmp-170) REVERT: A 166 GLU cc_start: 0.4192 (OUTLIER) cc_final: 0.3891 (mp0) REVERT: A 357 MET cc_start: 0.8256 (tpp) cc_final: 0.7673 (mmt) REVERT: A 381 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6628 (tt) REVERT: A 736 VAL cc_start: 0.8236 (t) cc_final: 0.8009 (t) REVERT: A 1143 ARG cc_start: 0.7261 (tmm-80) cc_final: 0.6677 (tpp80) REVERT: A 1268 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5908 (mm-30) REVERT: A 1272 GLN cc_start: 0.8036 (mt0) cc_final: 0.7784 (mt0) REVERT: A 1391 GLU cc_start: 0.7192 (pt0) cc_final: 0.6866 (pm20) REVERT: A 1527 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 1657 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8012 (pt) REVERT: B 68 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6307 (p0) REVERT: B 70 GLU cc_start: 0.7342 (tp30) cc_final: 0.6572 (tp30) outliers start: 58 outliers final: 42 residues processed: 229 average time/residue: 0.2411 time to fit residues: 79.7347 Evaluate side-chains 225 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 189 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 628 ASN A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN A1666 ASN A1743 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11970 Z= 0.222 Angle : 0.570 12.702 16166 Z= 0.286 Chirality : 0.041 0.199 1858 Planarity : 0.004 0.039 2014 Dihedral : 9.447 73.960 1708 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.25 % Favored : 89.68 % Rotamer: Outliers : 4.48 % Allowed : 17.98 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1424 helix: 0.75 (0.19), residues: 765 sheet: -1.91 (0.51), residues: 92 loop : -2.74 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 43 HIS 0.014 0.001 HIS A 189 PHE 0.024 0.001 PHE A1105 TYR 0.015 0.001 TYR A 534 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 1.414 Fit side-chains REVERT: A 120 MET cc_start: 0.6662 (tpt) cc_final: 0.6413 (tpt) REVERT: A 142 ASP cc_start: 0.6303 (t0) cc_final: 0.5464 (p0) REVERT: A 166 GLU cc_start: 0.4350 (OUTLIER) cc_final: 0.4012 (mp0) REVERT: A 357 MET cc_start: 0.8277 (tpp) cc_final: 0.7621 (mmt) REVERT: A 376 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7349 (mmt-90) REVERT: A 381 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6643 (tt) REVERT: A 595 MET cc_start: 0.8708 (mmm) cc_final: 0.8315 (mtt) REVERT: A 743 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7478 (mtmm) REVERT: A 1143 ARG cc_start: 0.7256 (tmm-80) cc_final: 0.6676 (tpp80) REVERT: A 1268 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5938 (mm-30) REVERT: A 1272 GLN cc_start: 0.7932 (mt0) cc_final: 0.7687 (mt0) REVERT: A 1391 GLU cc_start: 0.7199 (pt0) cc_final: 0.6868 (pm20) REVERT: A 1462 ASP cc_start: 0.6477 (t0) cc_final: 0.6268 (t0) REVERT: A 1657 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8075 (pt) REVERT: B 68 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6410 (p0) REVERT: B 70 GLU cc_start: 0.7361 (tp30) cc_final: 0.6531 (tp30) outliers start: 59 outliers final: 45 residues processed: 224 average time/residue: 0.2402 time to fit residues: 77.4814 Evaluate side-chains 228 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 177 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 189 HIS A 359 ASN A 425 HIS A 438 GLN A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11970 Z= 0.251 Angle : 0.587 12.769 16166 Z= 0.293 Chirality : 0.042 0.217 1858 Planarity : 0.004 0.038 2014 Dihedral : 9.468 75.459 1706 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.11 % Favored : 89.82 % Rotamer: Outliers : 4.78 % Allowed : 19.04 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1424 helix: 0.73 (0.19), residues: 767 sheet: -1.88 (0.51), residues: 92 loop : -2.63 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 43 HIS 0.008 0.001 HIS A 189 PHE 0.021 0.002 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.005 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 1.275 Fit side-chains REVERT: A 166 GLU cc_start: 0.4469 (OUTLIER) cc_final: 0.4103 (mp0) REVERT: A 376 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7265 (mmt-90) REVERT: A 381 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6666 (tt) REVERT: A 595 MET cc_start: 0.8709 (mmm) cc_final: 0.8405 (mtt) REVERT: A 743 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7536 (mtmm) REVERT: A 1143 ARG cc_start: 0.7267 (tmm-80) cc_final: 0.6702 (tpp80) REVERT: A 1268 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5867 (mm-30) REVERT: A 1272 GLN cc_start: 0.7948 (mt0) cc_final: 0.7715 (mt0) REVERT: A 1462 ASP cc_start: 0.6566 (t0) cc_final: 0.6357 (t0) REVERT: A 1657 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8066 (pt) REVERT: B 68 ASN cc_start: 0.6864 (OUTLIER) cc_final: 0.6449 (p0) REVERT: B 70 GLU cc_start: 0.7355 (tp30) cc_final: 0.6534 (tp30) outliers start: 63 outliers final: 51 residues processed: 216 average time/residue: 0.2430 time to fit residues: 76.1076 Evaluate side-chains 222 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 165 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.0040 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11970 Z= 0.191 Angle : 0.571 12.910 16166 Z= 0.286 Chirality : 0.041 0.193 1858 Planarity : 0.003 0.039 2014 Dihedral : 9.396 75.451 1705 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.55 % Favored : 90.38 % Rotamer: Outliers : 4.48 % Allowed : 19.65 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.23), residues: 1424 helix: 0.88 (0.19), residues: 765 sheet: -1.78 (0.51), residues: 94 loop : -2.56 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.013 0.001 HIS A 189 PHE 0.026 0.001 PHE A1511 TYR 0.008 0.001 TYR A 695 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 1.401 Fit side-chains REVERT: A 166 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.4104 (mp0) REVERT: A 381 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6569 (tt) REVERT: A 595 MET cc_start: 0.8690 (mmm) cc_final: 0.8408 (mtt) REVERT: A 713 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7199 (tpt90) REVERT: A 720 CYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7749 (t) REVERT: A 743 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7537 (mtmm) REVERT: A 1105 PHE cc_start: 0.8357 (p90) cc_final: 0.8151 (p90) REVERT: A 1143 ARG cc_start: 0.7276 (tmm-80) cc_final: 0.6676 (tpp80) REVERT: A 1268 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5956 (mm-30) REVERT: A 1272 GLN cc_start: 0.7941 (mt0) cc_final: 0.7706 (mt0) REVERT: A 1657 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8073 (pt) REVERT: B 68 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6354 (p0) REVERT: B 70 GLU cc_start: 0.7337 (tp30) cc_final: 0.6528 (tp30) outliers start: 59 outliers final: 47 residues processed: 220 average time/residue: 0.2382 time to fit residues: 76.4192 Evaluate side-chains 220 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 0.0010 chunk 126 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11970 Z= 0.192 Angle : 0.571 12.919 16166 Z= 0.285 Chirality : 0.041 0.190 1858 Planarity : 0.003 0.038 2014 Dihedral : 9.355 75.531 1705 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.34 % Favored : 90.59 % Rotamer: Outliers : 4.63 % Allowed : 20.26 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1424 helix: 0.93 (0.19), residues: 764 sheet: -1.80 (0.51), residues: 92 loop : -2.49 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.003 0.001 HIS A 425 PHE 0.027 0.001 PHE A1511 TYR 0.008 0.001 TYR A 695 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.251 Fit side-chains REVERT: A 166 GLU cc_start: 0.4396 (OUTLIER) cc_final: 0.4019 (mp0) REVERT: A 376 ARG cc_start: 0.7489 (mmt-90) cc_final: 0.7118 (mmt-90) REVERT: A 381 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6559 (tt) REVERT: A 595 MET cc_start: 0.8676 (mmm) cc_final: 0.8452 (mtt) REVERT: A 713 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7210 (tpt90) REVERT: A 743 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7546 (mtmm) REVERT: A 1138 THR cc_start: 0.8720 (t) cc_final: 0.8499 (t) REVERT: A 1143 ARG cc_start: 0.7274 (tmm-80) cc_final: 0.6688 (tpp80) REVERT: A 1268 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5962 (mm-30) REVERT: A 1272 GLN cc_start: 0.7924 (mt0) cc_final: 0.7680 (mt0) REVERT: A 1285 MET cc_start: 0.8637 (ttm) cc_final: 0.8383 (ttp) REVERT: A 1657 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8078 (pt) REVERT: B 68 ASN cc_start: 0.6772 (OUTLIER) cc_final: 0.6383 (p0) REVERT: B 70 GLU cc_start: 0.7346 (tp30) cc_final: 0.6529 (tp30) outliers start: 61 outliers final: 49 residues processed: 212 average time/residue: 0.2329 time to fit residues: 72.3377 Evaluate side-chains 218 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0670 chunk 121 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11970 Z= 0.191 Angle : 0.578 12.634 16166 Z= 0.287 Chirality : 0.041 0.200 1858 Planarity : 0.003 0.038 2014 Dihedral : 9.329 75.720 1705 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.55 % Favored : 90.38 % Rotamer: Outliers : 4.25 % Allowed : 20.41 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1424 helix: 0.97 (0.19), residues: 764 sheet: -1.81 (0.51), residues: 92 loop : -2.45 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.002 0.000 HIS A 58 PHE 0.033 0.001 PHE A1105 TYR 0.017 0.001 TYR A 534 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 166 time to evaluate : 1.399 Fit side-chains REVERT: A 166 GLU cc_start: 0.4366 (OUTLIER) cc_final: 0.3990 (mp0) REVERT: A 376 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.7134 (mmt-90) REVERT: A 381 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6572 (tt) REVERT: A 595 MET cc_start: 0.8675 (mmm) cc_final: 0.8466 (mtt) REVERT: A 720 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 743 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7558 (mtmm) REVERT: A 1138 THR cc_start: 0.8800 (t) cc_final: 0.8561 (t) REVERT: A 1143 ARG cc_start: 0.7251 (tmm-80) cc_final: 0.6698 (tpp80) REVERT: A 1268 GLU cc_start: 0.6800 (mp0) cc_final: 0.5952 (mm-30) REVERT: A 1272 GLN cc_start: 0.8027 (mt0) cc_final: 0.7789 (mt0) REVERT: A 1657 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8032 (pt) REVERT: B 68 ASN cc_start: 0.6811 (OUTLIER) cc_final: 0.6443 (p0) outliers start: 56 outliers final: 47 residues processed: 207 average time/residue: 0.2353 time to fit residues: 71.0571 Evaluate side-chains 214 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11970 Z= 0.221 Angle : 0.589 12.625 16166 Z= 0.292 Chirality : 0.042 0.282 1858 Planarity : 0.004 0.039 2014 Dihedral : 9.215 76.241 1700 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.41 % Favored : 90.52 % Rotamer: Outliers : 4.17 % Allowed : 20.86 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1424 helix: 0.94 (0.19), residues: 764 sheet: -1.88 (0.51), residues: 90 loop : -2.44 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 PHE 0.033 0.002 PHE A1105 TYR 0.009 0.001 TYR A 534 ARG 0.004 0.000 ARG A 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 170 time to evaluate : 1.438 Fit side-chains REVERT: A 166 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.4062 (mp0) REVERT: A 376 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.7217 (mmt-90) REVERT: A 381 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6559 (tt) REVERT: A 595 MET cc_start: 0.8682 (mmm) cc_final: 0.8464 (mtt) REVERT: A 743 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7366 (mmtt) REVERT: A 1138 THR cc_start: 0.8742 (t) cc_final: 0.8496 (t) REVERT: A 1143 ARG cc_start: 0.7238 (tmm-80) cc_final: 0.6698 (tpp80) REVERT: A 1268 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5963 (mm-30) REVERT: A 1272 GLN cc_start: 0.7906 (mt0) cc_final: 0.7691 (mt0) REVERT: A 1657 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8074 (pt) REVERT: B 68 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6537 (p0) REVERT: B 70 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7105 (tp30) outliers start: 55 outliers final: 46 residues processed: 210 average time/residue: 0.2267 time to fit residues: 69.7886 Evaluate side-chains 218 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 166 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1106 THR Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1411 THR Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1557 ASP Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1702 LYS Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 117 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 425 HIS A 737 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.177812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140589 restraints weight = 13310.579| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.06 r_work: 0.3415 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11970 Z= 0.178 Angle : 0.581 12.446 16166 Z= 0.286 Chirality : 0.041 0.263 1858 Planarity : 0.003 0.039 2014 Dihedral : 9.168 76.125 1700 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.34 % Favored : 90.59 % Rotamer: Outliers : 4.02 % Allowed : 21.47 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1424 helix: 1.00 (0.19), residues: 764 sheet: -1.94 (0.54), residues: 82 loop : -2.41 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1717 HIS 0.002 0.000 HIS A1405 PHE 0.034 0.001 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.004 0.000 ARG A 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.12 seconds wall clock time: 52 minutes 25.26 seconds (3145.26 seconds total)