Starting phenix.real_space_refine on Sat Dec 9 10:12:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hvh_35043/12_2023/8hvh_35043.pdb" } resolution = 3.07 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= 0.001 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6963 2.51 5 N 1794 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1002": "OD1" <-> "OD2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1134": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1168": "NH1" <-> "NH2" Residue "A PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1459": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10704 Classifications: {'peptide': 1364} Link IDs: {'PTRANS': 59, 'TRANS': 1304} Chain breaks: 2 Time building chain proxies: 5.93, per 1000 atoms: 0.55 Number of scatterers: 10704 At special positions: 0 Unit cell: (72.76, 113.42, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1891 8.00 N 1794 7.00 C 6963 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 6 sheets defined 62.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.573A pdb=" N TRP A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Proline residue: A 41 - end of helix removed outlier: 4.139A pdb=" N TRP A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.938A pdb=" N LEU A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.605A pdb=" N LEU A 72 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 93 removed outlier: 4.070A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.992A pdb=" N PHE A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.935A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.629A pdb=" N ILE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 154 through 159 removed outlier: 5.428A pdb=" N LEU A 157 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.550A pdb=" N LEU A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 223 through 233 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.814A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 4.048A pdb=" N GLN A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 4.069A pdb=" N GLY A 349 " --> pdb=" O PRO A 345 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.636A pdb=" N HIS A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.817A pdb=" N LEU A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.381A pdb=" N PHE A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.994A pdb=" N ALA A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.921A pdb=" N MET A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 474 through 497 removed outlier: 3.832A pdb=" N LYS A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.566A pdb=" N ILE A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.771A pdb=" N THR A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 556 " --> pdb=" O TRP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 583 removed outlier: 3.642A pdb=" N SER A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 584 through 595 removed outlier: 3.668A pdb=" N LEU A 588 " --> pdb=" O MET A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.504A pdb=" N LYS A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 removed outlier: 3.697A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 716 through 727 removed outlier: 3.662A pdb=" N GLN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 removed outlier: 4.297A pdb=" N MET A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 736' Processing helix chain 'A' and resid 752 through 768 Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 834 through 841 Processing helix chain 'A' and resid 843 through 849 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.868A pdb=" N PHE A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 977 through 996 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 3.659A pdb=" N TYR A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A1018 " --> pdb=" O VAL A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 3.878A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.692A pdb=" N PHE A1060 " --> pdb=" O PRO A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1072 removed outlier: 3.538A pdb=" N ILE A1068 " --> pdb=" O PRO A1064 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1069 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A1070 " --> pdb=" O GLY A1066 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N CYS A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A1072 " --> pdb=" O ILE A1068 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1064 through 1072' Processing helix chain 'A' and resid 1073 through 1082 removed outlier: 3.639A pdb=" N TYR A1077 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A1078 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.615A pdb=" N ILE A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1107 " --> pdb=" O VAL A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1116 through 1153 removed outlier: 3.775A pdb=" N TYR A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1131 " --> pdb=" O ARG A1127 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1132 " --> pdb=" O PHE A1128 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN A1135 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Proline residue: A1146 - end of helix removed outlier: 3.982A pdb=" N GLU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1164 Processing helix chain 'A' and resid 1166 through 1186 removed outlier: 3.625A pdb=" N PHE A1170 " --> pdb=" O ARG A1166 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A1180 " --> pdb=" O THR A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1200 removed outlier: 3.702A pdb=" N GLY A1198 " --> pdb=" O TRP A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 4.006A pdb=" N VAL A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A1211 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1224 through 1232 Processing helix chain 'A' and resid 1233 through 1236 Processing helix chain 'A' and resid 1237 through 1254 removed outlier: 3.524A pdb=" N ASN A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP A1242 " --> pdb=" O PHE A1238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A1251 " --> pdb=" O MET A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1264 removed outlier: 3.711A pdb=" N GLU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1334 removed outlier: 3.559A pdb=" N THR A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1357 removed outlier: 3.531A pdb=" N ILE A1357 " --> pdb=" O VAL A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1413 through 1417 Processing helix chain 'A' and resid 1427 through 1443 Processing helix chain 'A' and resid 1457 through 1472 Processing helix chain 'A' and resid 1483 through 1488 removed outlier: 4.037A pdb=" N ILE A1487 " --> pdb=" O ARG A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1513 Processing helix chain 'A' and resid 1515 through 1523 Processing sheet with id=AA1, first strand: chain 'A' and resid 616 through 617 removed outlier: 4.336A pdb=" N ALA A 626 " --> pdb=" O PRO A 652 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 628 " --> pdb=" O GLN A 650 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN A 650 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS A 630 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP A 648 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY A 632 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 removed outlier: 3.740A pdb=" N GLU A 682 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR A 635 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS A 680 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 691 through 694 removed outlier: 6.255A pdb=" N PHE A 772 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 808 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 657 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU A 656 " --> pdb=" O PHE A 820 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE A 822 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 658 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 824 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 660 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 821 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET A 832 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 823 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.631A pdb=" N CYS A 703 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1306 through 1313 removed outlier: 6.063A pdb=" N ARG A1307 " --> pdb=" O VAL A1296 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL A1296 " --> pdb=" O ARG A1307 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A1311 " --> pdb=" O ARG A1292 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ARG A1292 " --> pdb=" O LEU A1311 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A1313 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU A1290 " --> pdb=" O VAL A1313 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A1294 " --> pdb=" O LYS A1344 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A1344 " --> pdb=" O TYR A1294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1366 through 1369 removed outlier: 6.802A pdb=" N THR A1367 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASP A1450 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A1369 " --> pdb=" O ASP A1450 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU A1447 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A1480 " --> pdb=" O LEU A1447 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1449 " --> pdb=" O ILE A1480 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS A1318 " --> pdb=" O ARG A1492 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A1494 " --> pdb=" O LYS A1318 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY A1320 " --> pdb=" O LEU A1494 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU A1496 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A1322 " --> pdb=" O LEU A1496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A1503 " --> pdb=" O VAL A1495 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP A1497 " --> pdb=" O VAL A1501 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 4.40 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: 3295 1.34 - 1.45: 1733 1.45 - 1.57: 5835 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10953 Sorted by residual: bond pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 1.524 1.464 0.059 2.25e-02 1.98e+03 6.92e+00 bond pdb=" CG LEU A 243 " pdb=" CD2 LEU A 243 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CG1 ILE A1190 " pdb=" CD1 ILE A1190 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" C SER A 216 " pdb=" O SER A 216 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.62e-02 3.81e+03 1.64e+00 bond pdb=" CG LEU A1250 " pdb=" CD1 LEU A1250 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 10948 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.03: 161 104.03 - 111.54: 4994 111.54 - 119.04: 3931 119.04 - 126.55: 5623 126.55 - 134.05: 187 Bond angle restraints: 14896 Sorted by residual: angle pdb=" N ILE A 498 " pdb=" CA ILE A 498 " pdb=" C ILE A 498 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" N VAL A 111 " pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 113.53 109.08 4.45 9.80e-01 1.04e+00 2.07e+01 angle pdb=" C ILE A 385 " pdb=" N MET A 386 " pdb=" CA MET A 386 " ideal model delta sigma weight residual 122.31 115.30 7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" N VAL A1014 " pdb=" CA VAL A1014 " pdb=" C VAL A1014 " ideal model delta sigma weight residual 112.98 108.91 4.07 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N PRO A 103 " pdb=" CD PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 103.20 98.48 4.72 1.50e+00 4.44e-01 9.91e+00 ... (remaining 14891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5833 17.85 - 35.70: 554 35.70 - 53.55: 81 53.55 - 71.40: 20 71.40 - 89.25: 8 Dihedral angle restraints: 6496 sinusoidal: 2534 harmonic: 3962 Sorted by residual: dihedral pdb=" CA TYR A1186 " pdb=" C TYR A1186 " pdb=" N PRO A1187 " pdb=" CA PRO A1187 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLN A 436 " pdb=" C GLN A 436 " pdb=" N ILE A 437 " pdb=" CA ILE A 437 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLU A 209 " pdb=" C GLU A 209 " pdb=" N THR A 210 " pdb=" CA THR A 210 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 6493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1119 0.041 - 0.082: 479 0.082 - 0.123: 119 0.123 - 0.164: 18 0.164 - 0.204: 2 Chirality restraints: 1737 Sorted by residual: chirality pdb=" CG LEU A 137 " pdb=" CB LEU A 137 " pdb=" CD1 LEU A 137 " pdb=" CD2 LEU A 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE A 196 " pdb=" N PHE A 196 " pdb=" C PHE A 196 " pdb=" CB PHE A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA ASN A1165 " pdb=" N ASN A1165 " pdb=" C ASN A1165 " pdb=" CB ASN A1165 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1734 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 328 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 329 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1116 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A1117 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1117 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 542 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 543 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.025 5.00e-02 4.00e+02 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 167 2.67 - 3.22: 10778 3.22 - 3.78: 16458 3.78 - 4.34: 23189 4.34 - 4.90: 37230 Nonbonded interactions: 87822 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU A 126 " model vdw 2.107 2.440 nonbonded pdb=" O SER A 216 " pdb=" OG SER A 216 " model vdw 2.243 2.440 nonbonded pdb=" O ALA A 764 " pdb=" OG SER A 767 " model vdw 2.247 2.440 nonbonded pdb=" O ASP A1461 " pdb=" NE2 GLN A1465 " model vdw 2.274 2.520 nonbonded pdb=" O THR A1108 " pdb=" OG1 THR A1108 " model vdw 2.279 2.440 ... (remaining 87817 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: 0.840 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: 4.150 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.320 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.005 0.059 10953 Z= 0.356 Angle : 0.761 9.572 14896 Z= 0.416 Chirality : 0.046 0.204 1737 Planarity : 0.005 0.066 1862 Dihedral : 14.435 89.249 3936 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -3.04 (0.21), residues: 1358 helix: -2.01 (0.17), residues: 841 sheet: -0.22 (0.63), residues: 74 loop : -1.97 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 347 HIS 0.006 0.001 HIS A 372 PHE 0.029 0.002 PHE A 311 TYR 0.018 0.002 TYR A 504 ARG 0.010 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2347 time to fit residues: 92.8230 Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 496 ASN ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 GLN A1092 ASN A1181 ASN A1182 GLN A1204 ASN A1418 GLN A1465 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10953 Z= 0.296 Angle : 0.731 9.611 14896 Z= 0.371 Chirality : 0.046 0.167 1737 Planarity : 0.005 0.050 1862 Dihedral : 5.690 23.724 1468 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.74 % Allowed : 11.73 % Favored : 85.53 % 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: -2.28 (0.22), residues: 1358 helix: -1.35 (0.17), residues: 865 sheet: 0.12 (0.61), residues: 74 loop : -1.81 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 222 HIS 0.004 0.001 HIS A 372 PHE 0.026 0.002 PHE A 196 TYR 0.030 0.002 TYR A1122 ARG 0.006 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 27 residues processed: 206 average time/residue: 0.2046 time to fit residues: 63.3514 Evaluate side-chains 179 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.478 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1237 time to fit residues: 7.5076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 519 GLN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 702 ASN A 810 HIS ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 ASN A1204 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10953 Z= 0.182 Angle : 0.626 8.972 14896 Z= 0.314 Chirality : 0.042 0.165 1737 Planarity : 0.004 0.042 1862 Dihedral : 5.204 23.878 1468 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.28 % Allowed : 15.07 % Favored : 83.65 % 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: -1.68 (0.22), residues: 1358 helix: -0.86 (0.18), residues: 864 sheet: -0.21 (0.62), residues: 68 loop : -1.49 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.002 0.001 HIS A1360 PHE 0.031 0.001 PHE A1024 TYR 0.028 0.001 TYR A1122 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 183 average time/residue: 0.2003 time to fit residues: 55.1049 Evaluate side-chains 156 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1046 time to fit residues: 2.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 828 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN A1253 ASN A1465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10953 Z= 0.343 Angle : 0.693 9.781 14896 Z= 0.345 Chirality : 0.046 0.142 1737 Planarity : 0.004 0.038 1862 Dihedral : 5.231 24.306 1468 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.83 % Allowed : 17.47 % Favored : 79.71 % 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: -1.66 (0.22), residues: 1358 helix: -0.86 (0.17), residues: 859 sheet: -0.39 (0.59), residues: 73 loop : -1.40 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 995 HIS 0.006 0.001 HIS A 372 PHE 0.025 0.002 PHE A 196 TYR 0.018 0.002 TYR A 766 ARG 0.007 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 28 residues processed: 188 average time/residue: 0.1976 time to fit residues: 56.3594 Evaluate side-chains 172 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1053 time to fit residues: 6.9935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.0770 chunk 1 optimal weight: 0.1980 chunk 97 optimal weight: 0.0670 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 117 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10953 Z= 0.153 Angle : 0.596 11.256 14896 Z= 0.294 Chirality : 0.041 0.148 1737 Planarity : 0.004 0.035 1862 Dihedral : 4.827 23.221 1468 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.28 % Allowed : 18.58 % Favored : 80.14 % 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: -1.07 (0.23), residues: 1358 helix: -0.41 (0.18), residues: 853 sheet: 0.11 (0.59), residues: 81 loop : -1.23 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.002 0.001 HIS A1360 PHE 0.034 0.001 PHE A1024 TYR 0.013 0.001 TYR A 766 ARG 0.004 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 176 average time/residue: 0.1853 time to fit residues: 50.8006 Evaluate side-chains 150 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1274 time to fit residues: 3.3691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.3980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN A1471 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10953 Z= 0.181 Angle : 0.604 9.693 14896 Z= 0.293 Chirality : 0.042 0.147 1737 Planarity : 0.004 0.034 1862 Dihedral : 4.681 23.284 1468 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 20.55 % Favored : 77.83 % 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: -0.83 (0.23), residues: 1358 helix: -0.19 (0.18), residues: 842 sheet: 0.10 (0.59), residues: 81 loop : -1.16 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.001 HIS A1360 PHE 0.028 0.001 PHE A1024 TYR 0.014 0.001 TYR A 766 ARG 0.004 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.222 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 169 average time/residue: 0.2073 time to fit residues: 52.7471 Evaluate side-chains 157 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1082 time to fit residues: 3.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 0.0040 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10953 Z= 0.165 Angle : 0.594 10.348 14896 Z= 0.287 Chirality : 0.041 0.138 1737 Planarity : 0.003 0.033 1862 Dihedral : 4.560 22.765 1468 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.11 % Allowed : 20.80 % Favored : 78.08 % 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: -0.65 (0.23), residues: 1358 helix: -0.02 (0.18), residues: 852 sheet: 0.16 (0.59), residues: 81 loop : -1.18 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.003 0.000 HIS A1360 PHE 0.025 0.001 PHE A1024 TYR 0.012 0.001 TYR A 766 ARG 0.003 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.420 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 166 average time/residue: 0.1783 time to fit residues: 46.7313 Evaluate side-chains 155 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1068 time to fit residues: 3.5375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10953 Z= 0.157 Angle : 0.588 10.172 14896 Z= 0.283 Chirality : 0.041 0.135 1737 Planarity : 0.003 0.032 1862 Dihedral : 4.441 22.447 1468 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.60 % Allowed : 21.66 % Favored : 77.74 % 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: -0.42 (0.23), residues: 1358 helix: 0.14 (0.18), residues: 850 sheet: 0.40 (0.60), residues: 76 loop : -1.04 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 347 HIS 0.002 0.000 HIS A1360 PHE 0.023 0.001 PHE A1024 TYR 0.011 0.001 TYR A 766 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.244 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 160 average time/residue: 0.1744 time to fit residues: 43.5528 Evaluate side-chains 153 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1193 time to fit residues: 1.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10953 Z= 0.207 Angle : 0.599 9.876 14896 Z= 0.291 Chirality : 0.042 0.153 1737 Planarity : 0.004 0.032 1862 Dihedral : 4.472 22.909 1468 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.94 % Allowed : 22.43 % Favored : 76.63 % 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: -0.44 (0.23), residues: 1358 helix: 0.14 (0.18), residues: 862 sheet: 0.44 (0.60), residues: 76 loop : -1.13 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.003 0.001 HIS A 372 PHE 0.022 0.001 PHE A1024 TYR 0.011 0.001 TYR A 766 ARG 0.003 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 160 average time/residue: 0.1907 time to fit residues: 47.3185 Evaluate side-chains 151 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1124 time to fit residues: 2.7693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10953 Z= 0.213 Angle : 0.609 9.928 14896 Z= 0.294 Chirality : 0.043 0.173 1737 Planarity : 0.004 0.031 1862 Dihedral : 4.519 23.410 1468 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.43 % Allowed : 22.52 % Favored : 77.05 % 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: -0.43 (0.23), residues: 1358 helix: 0.11 (0.18), residues: 858 sheet: 0.50 (0.61), residues: 75 loop : -1.04 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.004 0.001 HIS A1360 PHE 0.022 0.001 PHE A1024 TYR 0.011 0.001 TYR A 766 ARG 0.006 0.000 ARG A1168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 1.196 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 150 average time/residue: 0.1830 time to fit residues: 43.6200 Evaluate side-chains 143 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1062 time to fit residues: 1.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113751 restraints weight = 15567.594| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.86 r_work: 0.3291 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10953 Z= 0.243 Angle : 0.618 9.804 14896 Z= 0.301 Chirality : 0.044 0.177 1737 Planarity : 0.004 0.032 1862 Dihedral : 4.576 23.352 1468 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.51 % Allowed : 23.37 % Favored : 76.11 % 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: -0.49 (0.23), residues: 1358 helix: 0.08 (0.18), residues: 864 sheet: 0.48 (0.60), residues: 75 loop : -1.11 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.004 0.001 HIS A1360 PHE 0.023 0.001 PHE A1024 TYR 0.012 0.001 TYR A 766 ARG 0.006 0.000 ARG A1168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.35 seconds wall clock time: 44 minutes 28.87 seconds (2668.87 seconds total)