Starting phenix.real_space_refine on Fri Feb 16 21:36:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zz6_11585/02_2024/6zz6_11585_updated.pdb" } resolution = 3.4 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: 6 Type Number sf(0) Gaussians P 74 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 10387 2.51 5 N 2820 2.21 5 O 3259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ASP 1076": "OD1" <-> "OD2" Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ASP 95": "OD1" <-> "OD2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C GLU 537": "OE1" <-> "OE2" Residue "D PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 455": "OE1" <-> "OE2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "D ASP 711": "OD1" <-> "OD2" Residue "D GLU 915": "OE1" <-> "OE2" Residue "D ASP 929": "OD1" <-> "OD2" Residue "D PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1144": "OE1" <-> "OE2" Residue "D GLU 1168": "OE1" <-> "OE2" Residue "D TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1398": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16597 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2871 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3368 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 639 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Chain: "D" Number of atoms: 8264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8264 Classifications: {'peptide': 1050} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 21, 'TRANS': 1028} Chain breaks: 19 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 677 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.44, per 1000 atoms: 0.57 Number of scatterers: 16597 At special positions: 0 Unit cell: (108.07, 124.12, 166.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 74 15.00 Mg 2 11.99 O 3259 8.00 N 2820 7.00 C 10387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 2.9 seconds 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 7 sheets defined 62.3% alpha, 6.3% beta 34 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 8.20 Creating SS restraints... Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.954A pdb=" N ALA A 159 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 1045 through 1083 removed outlier: 3.816A pdb=" N ILE A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A1070 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A1076 " --> pdb=" O SER A1072 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA A1077 " --> pdb=" O ASP A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1148 removed outlier: 4.109A pdb=" N TYR A1148 " --> pdb=" O ALA A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1178 Processing helix chain 'A' and resid 1192 through 1197 removed outlier: 3.752A pdb=" N GLU A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A1197 " --> pdb=" O THR A1193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1192 through 1197' Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.813A pdb=" N PHE B 42 " --> pdb=" O LYS B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.537A pdb=" N THR B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 172 through 227 removed outlier: 3.886A pdb=" N GLN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1059 removed outlier: 4.007A pdb=" N ARG B1008 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B1021 " --> pdb=" O SER B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1145 Processing helix chain 'B' and resid 1162 through 1177 removed outlier: 4.302A pdb=" N LYS B1177 " --> pdb=" O LYS B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1214 through 1221 Processing helix chain 'C' and resid 70 through 102 removed outlier: 3.837A pdb=" N THR C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 521 through 537 Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 279 through 290 Processing helix chain 'D' and resid 305 through 321 Proline residue: D 310 - end of helix Processing helix chain 'D' and resid 339 through 351 Proline residue: D 346 - end of helix Processing helix chain 'D' and resid 357 through 372 removed outlier: 3.690A pdb=" N ALA D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS D 362 " --> pdb=" O ASN D 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 405 Processing helix chain 'D' and resid 410 through 423 removed outlier: 3.908A pdb=" N HIS D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 457 removed outlier: 3.744A pdb=" N SER D 452 " --> pdb=" O PHE D 448 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE D 457 " --> pdb=" O MET D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 476 through 505 Processing helix chain 'D' and resid 511 through 523 removed outlier: 4.370A pdb=" N PHE D 517 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 547 removed outlier: 3.600A pdb=" N ARG D 543 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 Processing helix chain 'D' and resid 598 through 615 removed outlier: 4.215A pdb=" N PHE D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS D 603 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 604 " --> pdb=" O HIS D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 633 removed outlier: 3.789A pdb=" N LEU D 630 " --> pdb=" O TRP D 626 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 631 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 661 Processing helix chain 'D' and resid 679 through 687 removed outlier: 3.617A pdb=" N PHE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 687 " --> pdb=" O ASP D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 709 removed outlier: 4.224A pdb=" N TYR D 697 " --> pdb=" O LEU D 693 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASP D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) Proline residue: D 699 - end of helix removed outlier: 3.985A pdb=" N ALA D 709 " --> pdb=" O LEU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 729 removed outlier: 4.035A pdb=" N LYS D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 748 removed outlier: 3.827A pdb=" N THR D 742 " --> pdb=" O MET D 738 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN D 748 " --> pdb=" O HIS D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 764 Processing helix chain 'D' and resid 769 through 778 removed outlier: 5.448A pdb=" N GLN D 773 " --> pdb=" O GLU D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 800 Processing helix chain 'D' and resid 804 through 818 removed outlier: 3.552A pdb=" N ILE D 818 " --> pdb=" O ILE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 837 Processing helix chain 'D' and resid 839 through 844 removed outlier: 4.361A pdb=" N VAL D 844 " --> pdb=" O LYS D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 865 removed outlier: 4.290A pdb=" N SER D 856 " --> pdb=" O LYS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 882 Processing helix chain 'D' and resid 893 through 916 removed outlier: 4.373A pdb=" N LYS D 897 " --> pdb=" O GLU D 893 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE D 898 " --> pdb=" O ALA D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 941 Processing helix chain 'D' and resid 950 through 961 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 968 through 980 Processing helix chain 'D' and resid 988 through 1000 Processing helix chain 'D' and resid 1007 through 1021 removed outlier: 4.331A pdb=" N ASP D1011 " --> pdb=" O VAL D1007 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU D1012 " --> pdb=" O ARG D1008 " (cutoff:3.500A) Proline residue: D1015 - end of helix Processing helix chain 'D' and resid 1028 through 1048 Proline residue: D1043 - end of helix Processing helix chain 'D' and resid 1060 through 1074 Processing helix chain 'D' and resid 1093 through 1103 Processing helix chain 'D' and resid 1111 through 1127 Processing helix chain 'D' and resid 1129 through 1133 Processing helix chain 'D' and resid 1135 through 1146 Processing helix chain 'D' and resid 1152 through 1174 removed outlier: 3.627A pdb=" N ILE D1156 " --> pdb=" O ILE D1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 1204 through 1211 Processing helix chain 'D' and resid 1213 through 1221 removed outlier: 3.883A pdb=" N LEU D1221 " --> pdb=" O LEU D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 Processing helix chain 'D' and resid 1246 through 1258 removed outlier: 3.685A pdb=" N ILE D1250 " --> pdb=" O SER D1247 " (cutoff:3.500A) Proline residue: D1251 - end of helix Processing helix chain 'D' and resid 1262 through 1285 removed outlier: 7.915A pdb=" N THR D1281 " --> pdb=" O GLU D1277 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D1282 " --> pdb=" O LYS D1278 " (cutoff:3.500A) Processing helix chain 'D' and resid 1287 through 1301 Processing helix chain 'D' and resid 1313 through 1319 Processing helix chain 'D' and resid 1326 through 1341 Processing helix chain 'D' and resid 1356 through 1368 removed outlier: 3.702A pdb=" N ASN D1368 " --> pdb=" O THR D1364 " (cutoff:3.500A) Processing helix chain 'D' and resid 1374 through 1397 Processing helix chain 'D' and resid 1414 through 1433 Processing helix chain 'D' and resid 1449 through 1454 Processing helix chain 'D' and resid 1467 through 1474 removed outlier: 3.619A pdb=" N GLU D1474 " --> pdb=" O LEU D1470 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 18 through 22 removed outlier: 3.557A pdb=" N ARG A 3 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 97 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 7 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A 95 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU A 9 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N TYR A 93 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 119 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.518A pdb=" N ALA A1200 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A1185 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 31 " --> pdb=" O PHE A1185 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1187 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1096 through 1101 Processing sheet with id= D, first strand: chain 'B' and resid 18 through 20 Processing sheet with id= E, first strand: chain 'B' and resid 1207 through 1212 removed outlier: 4.171A pdb=" N PHE B1197 " --> pdb=" O VAL B1212 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B1196 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE B1181 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 30 " --> pdb=" O PHE B1181 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N CYS B1183 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1067 through 1070 removed outlier: 3.783A pdb=" N GLY B1106 " --> pdb=" O HIS B1070 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 541 through 544 891 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 7.78 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: 4816 1.34 - 1.46: 2754 1.46 - 1.58: 9186 1.58 - 1.70: 144 1.70 - 1.82: 89 Bond restraints: 16989 Sorted by residual: bond pdb=" C4 ATP A2000 " pdb=" C5 ATP A2000 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C4 ATP B2000 " pdb=" C5 ATP B2000 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C5 ATP A2000 " pdb=" C6 ATP A2000 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP B2000 " pdb=" C6 ATP B2000 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" C8 ATP B2000 " pdb=" N7 ATP B2000 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.16e+01 ... (remaining 16984 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.84: 668 106.84 - 114.14: 10047 114.14 - 121.45: 8885 121.45 - 128.75: 3467 128.75 - 136.06: 130 Bond angle restraints: 23197 Sorted by residual: angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 120.68 19.19 1.00e+00 1.00e+00 3.68e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 119.34 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 121.32 15.51 1.00e+00 1.00e+00 2.40e+02 angle pdb=" C5 ATP A2000 " pdb=" C4 ATP A2000 " pdb=" N3 ATP A2000 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.04e+01 ... (remaining 23192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.02: 9498 27.02 - 54.03: 670 54.03 - 81.05: 95 81.05 - 108.06: 7 108.06 - 135.08: 1 Dihedral angle restraints: 10271 sinusoidal: 4621 harmonic: 5650 Sorted by residual: dihedral pdb=" CA ASP A1219 " pdb=" C ASP A1219 " pdb=" N LEU A1220 " pdb=" CA LEU A1220 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA HIS D1025 " pdb=" C HIS D1025 " pdb=" N ASP D1026 " pdb=" CA ASP D1026 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ARG D 618 " pdb=" C ARG D 618 " pdb=" N ARG D 619 " pdb=" CA ARG D 619 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 10268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2469 0.065 - 0.129: 212 0.129 - 0.194: 22 0.194 - 0.258: 2 0.258 - 0.323: 1 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CB ILE D 474 " pdb=" CA ILE D 474 " pdb=" CG1 ILE D 474 " pdb=" CG2 ILE D 474 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ILE A 110 " pdb=" N ILE A 110 " pdb=" C ILE A 110 " pdb=" CB ILE A 110 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LYS A 63 " pdb=" N LYS A 63 " pdb=" C LYS A 63 " pdb=" CB LYS A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 2703 not shown) Planarity restraints: 2674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 121 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ARG B 121 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG B 121 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 122 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 527 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO D 528 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 528 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 528 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 11 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C PHE B 11 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 11 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 12 " 0.010 2.00e-02 2.50e+03 ... (remaining 2671 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 134 2.61 - 3.18: 14523 3.18 - 3.76: 26611 3.76 - 4.33: 34698 4.33 - 4.90: 56597 Nonbonded interactions: 132563 Sorted by model distance: nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb=" OG SER A 40 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLN A 151 " pdb="MG MG A2001 " model vdw 2.068 2.170 nonbonded pdb=" OG SER A1130 " pdb=" O1B ATP B2000 " model vdw 2.104 2.440 ... (remaining 132558 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: 1.580 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: 7.500 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 52.910 Find NCS groups from input model: 0.450 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 0.083 16989 Z= 0.193 Angle : 0.648 20.387 23197 Z= 0.442 Chirality : 0.039 0.323 2706 Planarity : 0.003 0.052 2674 Dihedral : 17.084 135.081 6575 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.61 % Allowed : 0.12 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.20), residues: 1858 helix: 2.56 (0.15), residues: 1213 sheet: 0.76 (0.44), residues: 163 loop : -1.40 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 837 HIS 0.005 0.001 HIS D 744 PHE 0.023 0.001 PHE B 47 TYR 0.016 0.001 TYR D1094 ARG 0.005 0.000 ARG D 792 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 1.843 Fit side-chains REVERT: A 1196 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 1003 LYS cc_start: 0.5831 (ptmm) cc_final: 0.5572 (pttm) REVERT: C 102 MET cc_start: 0.5157 (tpp) cc_final: 0.4332 (ttm) REVERT: D 607 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 780 ASN cc_start: 0.7485 (t0) cc_final: 0.7060 (t0) REVERT: D 993 ASP cc_start: 0.7108 (m-30) cc_final: 0.6887 (m-30) outliers start: 10 outliers final: 2 residues processed: 245 average time/residue: 0.2834 time to fit residues: 105.2941 Evaluate side-chains 162 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain D residue 890 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 0.0370 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16989 Z= 0.234 Angle : 0.559 8.558 23197 Z= 0.300 Chirality : 0.040 0.211 2706 Planarity : 0.004 0.045 2674 Dihedral : 17.082 136.395 2920 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.33 % Allowed : 7.76 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.20), residues: 1858 helix: 2.50 (0.15), residues: 1216 sheet: 0.79 (0.44), residues: 163 loop : -1.53 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 626 HIS 0.008 0.001 HIS D 744 PHE 0.019 0.002 PHE B1150 TYR 0.030 0.002 TYR B 116 ARG 0.006 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.972 Fit side-chains REVERT: A 177 GLN cc_start: 0.5447 (OUTLIER) cc_final: 0.4553 (pm20) REVERT: A 1078 ILE cc_start: 0.8331 (mt) cc_final: 0.8074 (mm) REVERT: D 607 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6982 (tm-30) outliers start: 22 outliers final: 15 residues processed: 195 average time/residue: 0.2892 time to fit residues: 86.7104 Evaluate side-chains 185 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1288 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 ASN A1146 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 765 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16989 Z= 0.225 Angle : 0.547 8.477 23197 Z= 0.297 Chirality : 0.039 0.205 2706 Planarity : 0.004 0.044 2674 Dihedral : 17.978 139.802 2918 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.37 % Allowed : 9.58 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1858 helix: 2.51 (0.15), residues: 1207 sheet: 0.63 (0.43), residues: 166 loop : -1.58 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 626 HIS 0.007 0.001 HIS D 744 PHE 0.035 0.002 PHE D 624 TYR 0.029 0.002 TYR B 116 ARG 0.009 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.908 Fit side-chains REVERT: B 128 ILE cc_start: 0.7567 (mt) cc_final: 0.7363 (mm) REVERT: B 210 MET cc_start: 0.7781 (tpp) cc_final: 0.7544 (ttm) outliers start: 39 outliers final: 25 residues processed: 209 average time/residue: 0.2651 time to fit residues: 86.9954 Evaluate side-chains 181 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A1096 ASN A1146 ASN A1167 ASN A1178 HIS B 28 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16989 Z= 0.320 Angle : 0.597 8.417 23197 Z= 0.321 Chirality : 0.041 0.193 2706 Planarity : 0.004 0.050 2674 Dihedral : 18.045 137.649 2918 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.34 % Allowed : 11.34 % Favored : 85.32 % 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: 1.67 (0.20), residues: 1858 helix: 2.25 (0.15), residues: 1210 sheet: 0.52 (0.42), residues: 165 loop : -1.76 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 626 HIS 0.007 0.001 HIS D 744 PHE 0.016 0.002 PHE A1195 TYR 0.035 0.002 TYR B 116 ARG 0.006 0.000 ARG B 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 2.075 Fit side-chains REVERT: A 42 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7314 (ttm) REVERT: A 191 LYS cc_start: 0.8079 (tttp) cc_final: 0.7793 (mmtm) REVERT: A 1146 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7376 (t0) REVERT: B 2 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6661 (t80) REVERT: B 106 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6898 (ttt90) REVERT: B 198 LYS cc_start: 0.7296 (pptt) cc_final: 0.6654 (pttp) REVERT: B 200 MET cc_start: 0.6126 (tpt) cc_final: 0.5916 (tpp) REVERT: B 1190 MET cc_start: 0.7430 (pmm) cc_final: 0.6613 (ptm) REVERT: D 960 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6028 (tpp) REVERT: D 970 TYR cc_start: 0.6912 (t80) cc_final: 0.6669 (t80) REVERT: D 1062 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7092 (mt0) REVERT: D 1396 MET cc_start: 0.6572 (mmm) cc_final: 0.6287 (mmm) outliers start: 55 outliers final: 32 residues processed: 206 average time/residue: 0.2889 time to fit residues: 90.8720 Evaluate side-chains 181 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 HIS Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 960 MET Chi-restraints excluded: chain D residue 1062 GLN Chi-restraints excluded: chain D residue 1107 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 170 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1146 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16989 Z= 0.233 Angle : 0.542 7.681 23197 Z= 0.295 Chirality : 0.039 0.168 2706 Planarity : 0.003 0.047 2674 Dihedral : 18.083 139.398 2918 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.27 % Allowed : 12.86 % Favored : 83.87 % 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: 1.74 (0.20), residues: 1858 helix: 2.34 (0.15), residues: 1209 sheet: 0.43 (0.42), residues: 165 loop : -1.79 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 626 HIS 0.007 0.001 HIS A1115 PHE 0.017 0.002 PHE D 412 TYR 0.022 0.001 TYR B 116 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 1.851 Fit side-chains REVERT: A 42 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7228 (ttm) REVERT: A 191 LYS cc_start: 0.8111 (tttp) cc_final: 0.7813 (mmtm) REVERT: B 198 LYS cc_start: 0.7339 (pptt) cc_final: 0.6764 (pttp) REVERT: B 1190 MET cc_start: 0.7199 (pmm) cc_final: 0.6660 (ptm) REVERT: C 102 MET cc_start: 0.5804 (tpp) cc_final: 0.4792 (ttm) REVERT: D 970 TYR cc_start: 0.7094 (t80) cc_final: 0.6859 (t80) outliers start: 54 outliers final: 37 residues processed: 199 average time/residue: 0.2763 time to fit residues: 85.9642 Evaluate side-chains 175 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1288 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 15 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16989 Z= 0.285 Angle : 0.577 7.972 23197 Z= 0.312 Chirality : 0.040 0.197 2706 Planarity : 0.004 0.049 2674 Dihedral : 18.216 138.985 2918 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.00 % Allowed : 12.67 % Favored : 83.32 % 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: 1.55 (0.20), residues: 1858 helix: 2.19 (0.15), residues: 1210 sheet: 0.28 (0.42), residues: 165 loop : -1.84 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 626 HIS 0.007 0.001 HIS D 744 PHE 0.015 0.002 PHE A1195 TYR 0.024 0.002 TYR B 116 ARG 0.004 0.000 ARG B1008 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 158 time to evaluate : 1.937 Fit side-chains REVERT: A 42 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7340 (ttm) REVERT: A 177 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.5030 (pm20) REVERT: A 191 LYS cc_start: 0.8142 (tttp) cc_final: 0.7836 (mmtm) REVERT: B 2 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6649 (t80) REVERT: B 106 ARG cc_start: 0.7115 (ttt90) cc_final: 0.6890 (ttt90) REVERT: B 1190 MET cc_start: 0.7106 (pmm) cc_final: 0.6823 (ptm) REVERT: D 1229 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8686 (mm) REVERT: D 1396 MET cc_start: 0.6406 (mmm) cc_final: 0.6162 (mmm) outliers start: 66 outliers final: 48 residues processed: 200 average time/residue: 0.2667 time to fit residues: 82.7814 Evaluate side-chains 191 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 HIS Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 828 MET Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 189 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 117 optimal weight: 0.0470 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1146 ASN D 458 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16989 Z= 0.213 Angle : 0.537 7.800 23197 Z= 0.293 Chirality : 0.038 0.210 2706 Planarity : 0.003 0.043 2674 Dihedral : 18.139 139.844 2918 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.46 % Allowed : 14.07 % Favored : 82.47 % 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: 1.73 (0.20), residues: 1858 helix: 2.34 (0.15), residues: 1213 sheet: 0.21 (0.42), residues: 165 loop : -1.76 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 PHE 0.019 0.001 PHE D 412 TYR 0.020 0.001 TYR D 611 ARG 0.003 0.000 ARG B1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 157 time to evaluate : 2.086 Fit side-chains REVERT: A 42 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7225 (ttm) REVERT: A 177 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5087 (pm20) REVERT: A 191 LYS cc_start: 0.8146 (tttp) cc_final: 0.7844 (mmtm) REVERT: C 102 MET cc_start: 0.5839 (tpp) cc_final: 0.5037 (ttm) REVERT: C 531 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7882 (tp) REVERT: D 960 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6044 (tpp) REVERT: D 1229 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8660 (mm) outliers start: 57 outliers final: 41 residues processed: 197 average time/residue: 0.2708 time to fit residues: 82.5980 Evaluate side-chains 190 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain B residue 1203 GLU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 828 MET Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 960 MET Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1146 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN D 458 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16989 Z= 0.251 Angle : 0.565 8.407 23197 Z= 0.305 Chirality : 0.039 0.230 2706 Planarity : 0.004 0.045 2674 Dihedral : 18.184 139.336 2918 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.70 % Allowed : 14.07 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.20), residues: 1858 helix: 2.27 (0.15), residues: 1218 sheet: 0.23 (0.42), residues: 165 loop : -1.91 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 626 HIS 0.007 0.001 HIS D 744 PHE 0.015 0.001 PHE A1195 TYR 0.018 0.002 TYR B 116 ARG 0.007 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 142 time to evaluate : 1.860 Fit side-chains REVERT: A 42 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7299 (ttm) REVERT: A 177 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5242 (pm20) REVERT: A 191 LYS cc_start: 0.8152 (tttp) cc_final: 0.7858 (mmtm) REVERT: B 2 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6421 (t80) REVERT: C 102 MET cc_start: 0.5869 (tpp) cc_final: 0.5088 (ttm) REVERT: C 531 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7901 (tp) REVERT: D 458 ASN cc_start: 0.4156 (p0) cc_final: 0.3951 (p0) REVERT: D 579 SER cc_start: 0.8057 (m) cc_final: 0.7773 (t) REVERT: D 960 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6042 (tpp) REVERT: D 1229 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 1396 MET cc_start: 0.6640 (mmm) cc_final: 0.6314 (mmm) outliers start: 61 outliers final: 44 residues processed: 187 average time/residue: 0.2715 time to fit residues: 79.2023 Evaluate side-chains 190 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 140 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 828 MET Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 960 MET Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1385 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 3.9990 chunk 165 optimal weight: 0.0470 chunk 176 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 167 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 ASN D 439 GLN D 456 ASN ** D 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16989 Z= 0.177 Angle : 0.532 14.064 23197 Z= 0.287 Chirality : 0.038 0.251 2706 Planarity : 0.003 0.042 2674 Dihedral : 18.046 139.501 2918 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.21 % Allowed : 14.80 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.20), residues: 1858 helix: 2.42 (0.15), residues: 1218 sheet: 0.16 (0.42), residues: 165 loop : -1.86 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 PHE 0.021 0.001 PHE D 412 TYR 0.017 0.001 TYR D 970 ARG 0.006 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 150 time to evaluate : 2.023 Fit side-chains REVERT: A 42 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7215 (ttm) REVERT: A 177 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.5491 (pm20) REVERT: A 191 LYS cc_start: 0.8152 (tttp) cc_final: 0.7864 (mmtm) REVERT: C 102 MET cc_start: 0.5726 (tpp) cc_final: 0.5049 (ttm) REVERT: C 531 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7851 (tp) REVERT: D 456 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8318 (t0) REVERT: D 458 ASN cc_start: 0.4009 (OUTLIER) cc_final: 0.3749 (p0) REVERT: D 579 SER cc_start: 0.7988 (m) cc_final: 0.7704 (t) REVERT: D 960 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6053 (tpp) REVERT: D 1229 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8640 (mm) REVERT: D 1396 MET cc_start: 0.6645 (mmm) cc_final: 0.6314 (mmm) outliers start: 53 outliers final: 41 residues processed: 188 average time/residue: 0.2761 time to fit residues: 80.7755 Evaluate side-chains 193 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 456 ASN Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 960 MET Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1045 ILE Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1385 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 156 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 ASN D 439 GLN D 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16989 Z= 0.223 Angle : 0.560 16.007 23197 Z= 0.299 Chirality : 0.039 0.272 2706 Planarity : 0.003 0.044 2674 Dihedral : 18.001 139.199 2918 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.03 % Allowed : 15.04 % Favored : 81.93 % 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: 1.75 (0.20), residues: 1858 helix: 2.38 (0.15), residues: 1216 sheet: 0.20 (0.42), residues: 165 loop : -1.87 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 PHE 0.014 0.001 PHE A1195 TYR 0.019 0.001 TYR D 970 ARG 0.004 0.000 ARG B 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 145 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.7213 (ttt) cc_final: 0.6981 (ttt) REVERT: A 191 LYS cc_start: 0.8154 (tttp) cc_final: 0.7865 (mmtm) REVERT: C 102 MET cc_start: 0.5739 (tpp) cc_final: 0.5081 (ttm) REVERT: C 531 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7876 (tp) REVERT: D 458 ASN cc_start: 0.4069 (OUTLIER) cc_final: 0.3778 (p0) REVERT: D 579 SER cc_start: 0.8005 (m) cc_final: 0.7712 (t) REVERT: D 1229 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8640 (mm) REVERT: D 1396 MET cc_start: 0.6645 (mmm) cc_final: 0.6292 (mmm) outliers start: 50 outliers final: 43 residues processed: 182 average time/residue: 0.2939 time to fit residues: 82.5648 Evaluate side-chains 185 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1212 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 1001 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1188 THR Chi-restraints excluded: chain B residue 1193 VAL Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 456 ASN Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 460 TYR Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 713 ILE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 744 HIS Chi-restraints excluded: chain D residue 865 VAL Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1045 ILE Chi-restraints excluded: chain D residue 1092 THR Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1288 SER Chi-restraints excluded: chain D residue 1385 ASP Chi-restraints excluded: chain D residue 1422 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114977 restraints weight = 22366.188| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.95 r_work: 0.3273 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16989 Z= 0.214 Angle : 0.556 16.053 23197 Z= 0.297 Chirality : 0.038 0.267 2706 Planarity : 0.003 0.043 2674 Dihedral : 17.995 139.098 2918 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.21 % Allowed : 14.92 % Favored : 81.87 % 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: 1.73 (0.20), residues: 1858 helix: 2.37 (0.15), residues: 1217 sheet: 0.18 (0.43), residues: 165 loop : -1.87 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 626 HIS 0.007 0.001 HIS A1115 PHE 0.014 0.001 PHE A1195 TYR 0.019 0.001 TYR D 970 ARG 0.004 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.01 seconds wall clock time: 62 minutes 38.65 seconds (3758.65 seconds total)