Starting phenix.real_space_refine on Sat Sep 28 12:56:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpk_22414/09_2024/7jpk_22414_neut.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 10 5.49 5 S 109 5.16 5 C 12134 2.51 5 N 2985 2.21 5 O 3349 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 9009 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 9 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 419 Unusual residues: {' CA': 1, '3PE': 8, 'C8U': 1, 'PC1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Time building chain proxies: 13.12, per 1000 atoms: 0.71 Number of scatterers: 18591 At special positions: 0 Unit cell: (143.706, 138.136, 157.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 109 16.00 P 10 15.00 F 3 9.00 O 3349 8.00 N 2985 7.00 C 12134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.9 seconds 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4272 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 18 sheets defined 53.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 53 through 70 removed outlier: 4.959A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.515A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.634A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.834A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.768A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.729A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 3.592A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.613A pdb=" N LEU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.595A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 removed outlier: 3.819A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 450 removed outlier: 4.355A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 467 removed outlier: 3.583A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 removed outlier: 3.694A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 Processing helix chain 'A' and resid 499 through 515 removed outlier: 3.936A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.517A pdb=" N ILE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.852A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 4.265A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 3.521A pdb=" N LEU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 581 removed outlier: 5.088A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.676A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 670 removed outlier: 4.069A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 651 " --> pdb=" O CYS A 647 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 818 removed outlier: 3.636A pdb=" N THR A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 842 removed outlier: 3.665A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.795A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 899 removed outlier: 3.576A pdb=" N ARG A 897 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 906 through 911 removed outlier: 4.314A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 926 removed outlier: 3.581A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.697A pdb=" N LEU A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1024 removed outlier: 3.516A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.665A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1072 removed outlier: 3.918A pdb=" N GLU A1070 " --> pdb=" O VAL A1066 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN A1071 " --> pdb=" O THR A1067 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1072 " --> pdb=" O PHE A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.877A pdb=" N LEU A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 4.564A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A1116 " --> pdb=" O TRP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1136 Processing helix chain 'A' and resid 1151 through 1173 Processing helix chain 'A' and resid 1176 through 1179 Processing helix chain 'A' and resid 1180 through 1205 Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 3.537A pdb=" N PHE A1238 " --> pdb=" O PHE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.582A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1246 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A1249 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1267 removed outlier: 3.652A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A1267 " --> pdb=" O SER A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1289 removed outlier: 3.779A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 Processing helix chain 'A' and resid 1324 through 1332 removed outlier: 3.644A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1382 removed outlier: 3.742A pdb=" N SER A1363 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 3.788A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1429 removed outlier: 3.627A pdb=" N LEU A1426 " --> pdb=" O VAL A1423 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1429 " --> pdb=" O LEU A1426 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 27 removed outlier: 4.167A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.526A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 136 through 163 removed outlier: 3.586A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 204 removed outlier: 3.632A pdb=" N CYS E 184 " --> pdb=" O TRP E 180 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 53 removed outlier: 3.862A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 76 through 96 removed outlier: 3.569A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 110 removed outlier: 3.726A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 3.876A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 239 through 242 Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.719A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.516A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.830A pdb=" N LYS F 272 " --> pdb=" O GLY F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 325 Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'F' and resid 371 through 379 Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.567A pdb=" N ASN F 408 " --> pdb=" O MET F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'F' and resid 420 through 426 Processing helix chain 'F' and resid 427 through 433 removed outlier: 4.046A pdb=" N VAL F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.502A pdb=" N LYS F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 562 through 566 removed outlier: 3.530A pdb=" N ALA F 566 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 582 removed outlier: 3.627A pdb=" N GLU F 575 " --> pdb=" O ASP F 571 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 650 Processing helix chain 'F' and resid 651 through 654 removed outlier: 7.226A pdb=" N ASP F 654 " --> pdb=" O LEU F 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 651 through 654' Processing helix chain 'F' and resid 655 through 660 removed outlier: 3.630A pdb=" N SER F 659 " --> pdb=" O ASN F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 693 Processing helix chain 'F' and resid 701 through 722 Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.743A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.556A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 removed outlier: 3.878A pdb=" N LYS F 830 " --> pdb=" O GLU F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.520A pdb=" N MET F 886 " --> pdb=" O ASP F 882 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.542A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 34 through 36 removed outlier: 3.559A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 48 through 50 removed outlier: 4.034A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA7, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.031A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.711A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.711A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'F' and resid 300 through 302 removed outlier: 6.787A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N TYR F 411 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 523 through 525 removed outlier: 6.080A pdb=" N ALA F 516 " --> pdb=" O LEU F 524 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 540 through 541 removed outlier: 3.564A pdb=" N ILE F 541 " --> pdb=" O GLY F 910 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.926A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.926A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB8, first strand: chain 'F' and resid 862 through 864 removed outlier: 6.610A pdb=" N ILE F 855 " --> pdb=" O LEU F 863 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU F1016 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 895 through 907 removed outlier: 4.331A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2483 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: 6.54 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2941 1.30 - 1.43: 5125 1.43 - 1.56: 10751 1.56 - 1.69: 20 1.69 - 1.82: 168 Bond restraints: 19005 Sorted by residual: bond pdb=" N09 C8U A1911 " pdb=" O10 C8U A1911 " ideal model delta sigma weight residual 1.220 1.400 -0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C05 C8U A1911 " pdb=" C06 C8U A1911 " ideal model delta sigma weight residual 1.364 1.530 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C02 C8U A1911 " pdb=" C03 C8U A1911 " ideal model delta sigma weight residual 1.351 1.514 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.78e+01 ... (remaining 19000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 24786 2.00 - 3.99: 723 3.99 - 5.99: 129 5.99 - 7.99: 20 7.99 - 9.99: 29 Bond angle restraints: 25687 Sorted by residual: angle pdb=" N ASN A 649 " pdb=" CA ASN A 649 " pdb=" C ASN A 649 " ideal model delta sigma weight residual 111.03 103.57 7.46 1.11e+00 8.12e-01 4.51e+01 angle pdb=" N ALA A 665 " pdb=" CA ALA A 665 " pdb=" C ALA A 665 " ideal model delta sigma weight residual 111.07 105.36 5.71 1.07e+00 8.73e-01 2.85e+01 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 112.98 108.02 4.96 1.25e+00 6.40e-01 1.58e+01 angle pdb=" C PHE A 112 " pdb=" N HIS A 113 " pdb=" CA HIS A 113 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" O ASN A 649 " pdb=" C ASN A 649 " pdb=" N TYR A 650 " ideal model delta sigma weight residual 122.03 125.92 -3.89 1.08e+00 8.57e-01 1.29e+01 ... (remaining 25682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.51: 9980 22.51 - 45.01: 1114 45.01 - 67.52: 318 67.52 - 90.02: 40 90.02 - 112.53: 1 Dihedral angle restraints: 11453 sinusoidal: 4837 harmonic: 6616 Sorted by residual: dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual -86.00 -142.82 56.82 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CA THR F 628 " pdb=" C THR F 628 " pdb=" N TYR F 629 " pdb=" CA TYR F 629 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 46.72 46.28 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 11450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2514 0.068 - 0.137: 317 0.137 - 0.205: 15 0.205 - 0.273: 1 0.273 - 0.342: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA VAL A 661 " pdb=" N VAL A 661 " pdb=" C VAL A 661 " pdb=" CB VAL A 661 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU F 257 " pdb=" CB LEU F 257 " pdb=" CD1 LEU F 257 " pdb=" CD2 LEU F 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 2845 not shown) Planarity restraints: 3203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 648 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLY A 648 " -0.056 2.00e-02 2.50e+03 pdb=" O GLY A 648 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 649 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 656 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C PHE A 656 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 656 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 657 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 654 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ASN A 654 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 654 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 655 " 0.016 2.00e-02 2.50e+03 ... (remaining 3200 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 204 2.62 - 3.19: 16159 3.19 - 3.76: 27463 3.76 - 4.33: 40755 4.33 - 4.90: 66256 Nonbonded interactions: 150837 Sorted by model distance: nonbonded pdb=" OD2 ASP F 711 " pdb=" OG1 THR F 739 " model vdw 2.047 3.040 nonbonded pdb=" O ILE A 931 " pdb=" CG2 THR A 935 " model vdw 2.113 3.460 nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.125 3.040 nonbonded pdb=" O TYR F 647 " pdb=" OG1 THR F 650 " model vdw 2.142 3.040 nonbonded pdb=" O GLU F 184 " pdb=" OG1 THR F 188 " model vdw 2.150 3.040 ... (remaining 150832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.060 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.320 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.007 0.180 19005 Z= 0.489 Angle : 0.856 9.987 25687 Z= 0.446 Chirality : 0.046 0.342 2848 Planarity : 0.005 0.059 3203 Dihedral : 19.601 112.530 7142 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 8.84 % Allowed : 24.15 % Favored : 67.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % 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: -3.85 (0.15), residues: 2222 helix: -2.22 (0.13), residues: 1076 sheet: -1.61 (0.30), residues: 244 loop : -3.14 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1016 HIS 0.006 0.001 HIS A 113 PHE 0.022 0.002 PHE F 157 TYR 0.023 0.002 TYR F 629 ARG 0.004 0.000 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 255 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6774 (pt0) REVERT: A 524 ILE cc_start: 0.8138 (mt) cc_final: 0.7923 (mp) REVERT: A 538 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5762 (tt) REVERT: A 905 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 926 ARG cc_start: 0.6467 (mtt90) cc_final: 0.5917 (mtp85) REVERT: A 967 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 1004 MET cc_start: 0.8651 (mtm) cc_final: 0.8263 (mtp) REVERT: A 1091 TYR cc_start: 0.7744 (t80) cc_final: 0.7430 (t80) REVERT: A 1125 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7072 (t80) REVERT: A 1129 MET cc_start: 0.8091 (mtp) cc_final: 0.7762 (mtt) REVERT: A 1199 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7364 (mt) REVERT: A 1234 PHE cc_start: 0.8714 (p90) cc_final: 0.8385 (p90) REVERT: A 1239 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8388 (ptt180) REVERT: A 1385 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7392 (p0) REVERT: F 404 MET cc_start: 0.9011 (mtt) cc_final: 0.8610 (mtt) REVERT: F 501 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7570 (mtm110) REVERT: F 505 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7693 (ppt-90) REVERT: F 717 GLU cc_start: 0.7943 (tt0) cc_final: 0.7685 (tt0) REVERT: F 1020 MET cc_start: 0.8295 (ttp) cc_final: 0.8076 (ttm) outliers start: 176 outliers final: 100 residues processed: 402 average time/residue: 0.9609 time to fit residues: 450.9735 Evaluate side-chains 322 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 214 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1321 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 659 SER Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain F residue 711 ASP Chi-restraints excluded: chain F residue 715 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 907 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 183 GLN A 453 HIS A 464 GLN A 490 GLN A 554 ASN A 599 ASN A 829 ASN ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A 999 ASN A1071 GLN A1087 GLN A1108 GLN A1138 GLN E 31 HIS E 38 HIS E 209 GLN F 56 GLN F 145 GLN F 156 ASN F 165 HIS F 169 HIS F 186 ASN F 233 ASN F 308 HIS ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS F 424 ASN F 470 ASN F 484 GLN F 511 ASN F 542 ASN F 644 GLN F 655 ASN F 679 ASN F 685 ASN F 701 ASN F 728 ASN F 806 GLN F 888 HIS F 891 ASN F1007 HIS F1065 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19005 Z= 0.203 Angle : 0.612 8.665 25687 Z= 0.315 Chirality : 0.043 0.279 2848 Planarity : 0.005 0.065 3203 Dihedral : 15.327 103.313 3058 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.28 % Allowed : 26.15 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.39 (0.16), residues: 2222 helix: -0.80 (0.15), residues: 1108 sheet: -1.09 (0.31), residues: 241 loop : -2.71 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.004 0.001 HIS E 31 PHE 0.014 0.001 PHE A 801 TYR 0.023 0.001 TYR F 629 ARG 0.004 0.000 ARG F 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 233 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3057 (OUTLIER) cc_final: 0.2844 (m90) REVERT: A 187 ASN cc_start: 0.6746 (t0) cc_final: 0.6281 (p0) REVERT: A 190 PHE cc_start: 0.7572 (t80) cc_final: 0.6587 (m-80) REVERT: A 479 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.3142 (tpt) REVERT: A 491 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.5094 (t80) REVERT: A 535 LEU cc_start: 0.8378 (mp) cc_final: 0.8162 (mt) REVERT: A 538 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5692 (tt) REVERT: A 547 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5245 (p0) REVERT: A 897 ARG cc_start: 0.7052 (mpt-90) cc_final: 0.6650 (mpt-90) REVERT: A 926 ARG cc_start: 0.6359 (mtt90) cc_final: 0.5518 (mtp85) REVERT: A 1125 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 1199 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7603 (mt) REVERT: A 1384 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6090 (m-80) REVERT: A 1385 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7604 (p0) REVERT: F 205 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8453 (tt) REVERT: F 404 MET cc_start: 0.8898 (mtt) cc_final: 0.8458 (mtt) REVERT: F 501 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7517 (mtm110) REVERT: F 649 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: F 717 GLU cc_start: 0.7852 (tt0) cc_final: 0.7648 (tt0) REVERT: F 851 MET cc_start: 0.7255 (ptp) cc_final: 0.7048 (ptp) REVERT: F 1020 MET cc_start: 0.8374 (ttp) cc_final: 0.8126 (ttm) outliers start: 125 outliers final: 51 residues processed: 331 average time/residue: 1.0360 time to fit residues: 398.6660 Evaluate side-chains 265 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 203 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 649 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 753 GLU Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1061 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 202 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 599 ASN A 829 ASN A 930 ASN A1108 GLN E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 726 GLN F 806 GLN F1065 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19005 Z= 0.240 Angle : 0.612 11.171 25687 Z= 0.313 Chirality : 0.044 0.320 2848 Planarity : 0.005 0.060 3203 Dihedral : 14.304 84.812 2948 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.57 % Allowed : 27.46 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.17), residues: 2222 helix: -0.25 (0.15), residues: 1111 sheet: -0.87 (0.32), residues: 237 loop : -2.49 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1112 HIS 0.016 0.001 HIS A 113 PHE 0.019 0.001 PHE A 92 TYR 0.020 0.001 TYR F 629 ARG 0.004 0.000 ARG F 707 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 212 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2987 (OUTLIER) cc_final: 0.2695 (m90) REVERT: A 187 ASN cc_start: 0.6737 (t0) cc_final: 0.6255 (p0) REVERT: A 190 PHE cc_start: 0.7558 (t80) cc_final: 0.6535 (m-80) REVERT: A 449 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 491 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 538 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5716 (tt) REVERT: A 547 ASN cc_start: 0.5636 (OUTLIER) cc_final: 0.5154 (p0) REVERT: A 897 ARG cc_start: 0.7134 (mpt-90) cc_final: 0.6793 (mpt-90) REVERT: A 926 ARG cc_start: 0.6404 (mtt90) cc_final: 0.5562 (mtp85) REVERT: A 984 GLU cc_start: 0.7987 (pt0) cc_final: 0.7660 (pm20) REVERT: A 1124 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7237 (mmm) REVERT: A 1173 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5659 (tttt) REVERT: A 1199 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7641 (mt) REVERT: A 1384 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: A 1401 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6415 (mm-30) REVERT: E 142 MET cc_start: 0.6905 (mtm) cc_final: 0.6558 (ptp) REVERT: F 205 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8470 (tt) REVERT: F 404 MET cc_start: 0.8925 (mtt) cc_final: 0.8402 (mtt) REVERT: F 501 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7569 (mtm110) REVERT: F 717 GLU cc_start: 0.7877 (tt0) cc_final: 0.7672 (tt0) REVERT: F 851 MET cc_start: 0.7233 (ptp) cc_final: 0.7024 (ptp) outliers start: 111 outliers final: 58 residues processed: 295 average time/residue: 0.9965 time to fit residues: 342.1163 Evaluate side-chains 276 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 207 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN A1108 GLN E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 701 ASN F 726 GLN F 806 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19005 Z= 0.405 Angle : 0.685 13.048 25687 Z= 0.347 Chirality : 0.047 0.351 2848 Planarity : 0.005 0.060 3203 Dihedral : 14.159 86.071 2933 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.78 % Allowed : 26.76 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.17), residues: 2222 helix: -0.18 (0.15), residues: 1106 sheet: -0.82 (0.32), residues: 248 loop : -2.41 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1112 HIS 0.011 0.001 HIS A 113 PHE 0.019 0.002 PHE F 689 TYR 0.018 0.002 TYR F 767 ARG 0.004 0.000 ARG F 707 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 212 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2782 (OUTLIER) cc_final: 0.2381 (m90) REVERT: A 187 ASN cc_start: 0.6758 (t0) cc_final: 0.6247 (p0) REVERT: A 190 PHE cc_start: 0.7596 (t80) cc_final: 0.6533 (m-80) REVERT: A 479 MET cc_start: 0.6033 (pp-130) cc_final: 0.5067 (ppp) REVERT: A 491 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.4889 (t80) REVERT: A 538 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.5872 (tt) REVERT: A 540 LYS cc_start: 0.5811 (OUTLIER) cc_final: 0.5410 (tptp) REVERT: A 547 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.5239 (p0) REVERT: A 835 PHE cc_start: 0.7569 (m-10) cc_final: 0.7348 (m-10) REVERT: A 849 LEU cc_start: 0.3063 (OUTLIER) cc_final: 0.2466 (mt) REVERT: A 897 ARG cc_start: 0.7141 (mpt-90) cc_final: 0.6788 (mpt-90) REVERT: A 926 ARG cc_start: 0.6572 (mtt90) cc_final: 0.5632 (mtp85) REVERT: A 984 GLU cc_start: 0.7994 (pt0) cc_final: 0.7688 (pm20) REVERT: A 1124 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6554 (mpm) REVERT: A 1173 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5718 (tttt) REVERT: A 1199 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7695 (mt) REVERT: A 1401 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: E 8 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5581 (ttmm) REVERT: E 216 MET cc_start: 0.6930 (ttp) cc_final: 0.6662 (ttp) REVERT: F 404 MET cc_start: 0.8989 (mtt) cc_final: 0.8553 (mtt) REVERT: F 501 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7586 (mtm110) REVERT: F 717 GLU cc_start: 0.7996 (tt0) cc_final: 0.7775 (tt0) outliers start: 135 outliers final: 75 residues processed: 320 average time/residue: 0.9662 time to fit residues: 359.4020 Evaluate side-chains 292 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 206 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 80 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 641 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 819 ILE Chi-restraints excluded: chain F residue 823 SER Chi-restraints excluded: chain F residue 867 HIS Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 3 optimal weight: 0.0170 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 930 ASN A1108 GLN E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 701 ASN F 726 GLN F 806 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19005 Z= 0.163 Angle : 0.586 13.189 25687 Z= 0.294 Chirality : 0.042 0.226 2848 Planarity : 0.004 0.058 3203 Dihedral : 13.086 82.651 2933 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.42 % Allowed : 28.61 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.23 (0.17), residues: 2222 helix: 0.21 (0.16), residues: 1107 sheet: -0.65 (0.33), residues: 239 loop : -2.20 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1112 HIS 0.022 0.001 HIS A 113 PHE 0.024 0.001 PHE F 689 TYR 0.020 0.001 TYR F 629 ARG 0.004 0.000 ARG F 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 231 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6681 (t0) cc_final: 0.6404 (p0) REVERT: A 190 PHE cc_start: 0.7559 (t80) cc_final: 0.6551 (m-80) REVERT: A 479 MET cc_start: 0.6173 (pp-130) cc_final: 0.5502 (ppp) REVERT: A 481 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3770 (pp) REVERT: A 491 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.4807 (t80) REVERT: A 493 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4814 (mpt) REVERT: A 538 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6051 (tt) REVERT: A 540 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5578 (tptp) REVERT: A 547 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.5075 (p0) REVERT: A 835 PHE cc_start: 0.7656 (m-10) cc_final: 0.7419 (m-10) REVERT: A 849 LEU cc_start: 0.3389 (OUTLIER) cc_final: 0.2794 (mt) REVERT: A 897 ARG cc_start: 0.7180 (mpt-90) cc_final: 0.6840 (mpt-90) REVERT: A 984 GLU cc_start: 0.7896 (pt0) cc_final: 0.7637 (pm20) REVERT: A 1165 MET cc_start: 0.6754 (tmm) cc_final: 0.6227 (tmm) REVERT: A 1173 LYS cc_start: 0.6016 (OUTLIER) cc_final: 0.5668 (tttt) REVERT: A 1199 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7580 (mt) REVERT: A 1295 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 1384 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: E 131 LYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5550 (ttpt) REVERT: F 311 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: F 404 MET cc_start: 0.8813 (mtt) cc_final: 0.8290 (mtt) REVERT: F 717 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: F 1045 ASP cc_start: 0.8133 (t0) cc_final: 0.7798 (t70) outliers start: 108 outliers final: 51 residues processed: 313 average time/residue: 0.9859 time to fit residues: 358.5653 Evaluate side-chains 275 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 210 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 0.0030 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 113 optimal weight: 10.0000 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 930 ASN A1108 GLN E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 551 GLN F 644 GLN F 726 GLN F 806 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19005 Z= 0.154 Angle : 0.573 11.865 25687 Z= 0.288 Chirality : 0.042 0.291 2848 Planarity : 0.004 0.058 3203 Dihedral : 12.290 82.118 2926 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.22 % Allowed : 29.82 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.88 (0.18), residues: 2222 helix: 0.52 (0.16), residues: 1108 sheet: -0.59 (0.33), residues: 239 loop : -2.02 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 187 HIS 0.002 0.000 HIS A 113 PHE 0.023 0.001 PHE F 689 TYR 0.020 0.001 TYR F 629 ARG 0.009 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 236 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6803 (t0) cc_final: 0.6411 (p0) REVERT: A 190 PHE cc_start: 0.7519 (t80) cc_final: 0.6499 (m-80) REVERT: A 479 MET cc_start: 0.6147 (pp-130) cc_final: 0.5895 (pp-130) REVERT: A 491 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4881 (t80) REVERT: A 493 MET cc_start: 0.5273 (OUTLIER) cc_final: 0.5001 (mpt) REVERT: A 540 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5529 (tptp) REVERT: A 547 ASN cc_start: 0.5538 (OUTLIER) cc_final: 0.5128 (p0) REVERT: A 849 LEU cc_start: 0.3288 (OUTLIER) cc_final: 0.2716 (mt) REVERT: A 883 MET cc_start: 0.4754 (tmm) cc_final: 0.4481 (tmm) REVERT: A 897 ARG cc_start: 0.7143 (mpt-90) cc_final: 0.6808 (mpt-90) REVERT: A 984 GLU cc_start: 0.7920 (pt0) cc_final: 0.7676 (pm20) REVERT: A 1165 MET cc_start: 0.6896 (tmm) cc_final: 0.6156 (tmm) REVERT: A 1173 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5614 (tttt) REVERT: A 1234 PHE cc_start: 0.8669 (p90) cc_final: 0.8449 (p90) REVERT: A 1295 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 1334 TYR cc_start: 0.6436 (t80) cc_final: 0.6115 (t80) REVERT: E 59 LYS cc_start: 0.3774 (OUTLIER) cc_final: 0.2653 (pttt) REVERT: E 106 SER cc_start: 0.6168 (OUTLIER) cc_final: 0.5890 (p) REVERT: E 158 MET cc_start: 0.7093 (tpp) cc_final: 0.6863 (tpp) REVERT: F 404 MET cc_start: 0.8790 (mtt) cc_final: 0.8273 (mtt) REVERT: F 717 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: F 1045 ASP cc_start: 0.8063 (t0) cc_final: 0.7688 (t70) outliers start: 84 outliers final: 43 residues processed: 304 average time/residue: 0.9831 time to fit residues: 348.3693 Evaluate side-chains 270 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19005 Z= 0.165 Angle : 0.577 14.208 25687 Z= 0.289 Chirality : 0.042 0.243 2848 Planarity : 0.004 0.058 3203 Dihedral : 11.903 80.280 2912 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.71 % Allowed : 30.92 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.72 (0.18), residues: 2222 helix: 0.66 (0.16), residues: 1108 sheet: -0.56 (0.32), residues: 243 loop : -1.96 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1112 HIS 0.002 0.001 HIS A 113 PHE 0.023 0.001 PHE F 689 TYR 0.018 0.001 TYR F 629 ARG 0.012 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 220 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6803 (t0) cc_final: 0.6418 (p0) REVERT: A 190 PHE cc_start: 0.7470 (t80) cc_final: 0.6404 (m-80) REVERT: A 449 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (tt) REVERT: A 479 MET cc_start: 0.6426 (pp-130) cc_final: 0.5620 (ppp) REVERT: A 491 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4831 (t80) REVERT: A 493 MET cc_start: 0.5353 (OUTLIER) cc_final: 0.5045 (mpt) REVERT: A 519 MET cc_start: 0.6245 (mtp) cc_final: 0.5355 (ppp) REVERT: A 540 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5496 (tptp) REVERT: A 547 ASN cc_start: 0.5601 (OUTLIER) cc_final: 0.5217 (p0) REVERT: A 849 LEU cc_start: 0.3266 (OUTLIER) cc_final: 0.2704 (mt) REVERT: A 883 MET cc_start: 0.4782 (tmm) cc_final: 0.4528 (tmm) REVERT: A 897 ARG cc_start: 0.7174 (mpt-90) cc_final: 0.6800 (mpt-90) REVERT: A 1031 MET cc_start: 0.8448 (mmm) cc_final: 0.8144 (mtp) REVERT: A 1165 MET cc_start: 0.6890 (tmm) cc_final: 0.6184 (tmm) REVERT: A 1234 PHE cc_start: 0.8669 (p90) cc_final: 0.8447 (p90) REVERT: A 1295 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8550 (t) REVERT: A 1334 TYR cc_start: 0.6492 (t80) cc_final: 0.6200 (t80) REVERT: A 1383 ASN cc_start: 0.8306 (m110) cc_final: 0.8007 (m110) REVERT: E 59 LYS cc_start: 0.3754 (OUTLIER) cc_final: 0.2605 (ptmm) REVERT: E 118 LEU cc_start: 0.7495 (mm) cc_final: 0.7294 (mm) REVERT: E 158 MET cc_start: 0.7094 (tpp) cc_final: 0.6851 (tpp) REVERT: F 404 MET cc_start: 0.8765 (mtt) cc_final: 0.8178 (mtt) REVERT: F 557 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7053 (mm-30) REVERT: F 681 GLU cc_start: 0.4982 (mp0) cc_final: 0.4501 (mm-30) REVERT: F 717 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: F 1045 ASP cc_start: 0.8034 (t0) cc_final: 0.7697 (t70) outliers start: 74 outliers final: 45 residues processed: 275 average time/residue: 1.0149 time to fit residues: 323.1530 Evaluate side-chains 268 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 214 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN F 726 GLN F 806 GLN F 866 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19005 Z= 0.179 Angle : 0.585 16.012 25687 Z= 0.293 Chirality : 0.042 0.225 2848 Planarity : 0.004 0.058 3203 Dihedral : 11.597 79.423 2912 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.92 % Allowed : 31.12 % Favored : 64.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.60 (0.18), residues: 2222 helix: 0.76 (0.16), residues: 1115 sheet: -0.50 (0.32), residues: 243 loop : -1.92 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1112 HIS 0.002 0.001 HIS A 113 PHE 0.023 0.001 PHE F 689 TYR 0.016 0.001 TYR F 629 ARG 0.012 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 217 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6811 (t0) cc_final: 0.6429 (p0) REVERT: A 190 PHE cc_start: 0.7490 (t80) cc_final: 0.6403 (m-80) REVERT: A 449 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8242 (tt) REVERT: A 479 MET cc_start: 0.6431 (pp-130) cc_final: 0.5549 (ppp) REVERT: A 491 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.4837 (t80) REVERT: A 493 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5064 (mpt) REVERT: A 519 MET cc_start: 0.6349 (mtp) cc_final: 0.5537 (ppp) REVERT: A 540 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5490 (tptp) REVERT: A 547 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5250 (p0) REVERT: A 659 ILE cc_start: 0.8205 (mm) cc_final: 0.7948 (mt) REVERT: A 849 LEU cc_start: 0.3316 (OUTLIER) cc_final: 0.2750 (mt) REVERT: A 883 MET cc_start: 0.4756 (tmm) cc_final: 0.4508 (tmm) REVERT: A 897 ARG cc_start: 0.7160 (mpt-90) cc_final: 0.6809 (mpt-90) REVERT: A 1165 MET cc_start: 0.6873 (tmm) cc_final: 0.6040 (tmm) REVERT: A 1234 PHE cc_start: 0.8667 (p90) cc_final: 0.8450 (p90) REVERT: A 1295 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 1334 TYR cc_start: 0.6513 (t80) cc_final: 0.6260 (t80) REVERT: E 59 LYS cc_start: 0.3745 (OUTLIER) cc_final: 0.2627 (ptmm) REVERT: E 118 LEU cc_start: 0.7485 (mm) cc_final: 0.7258 (mm) REVERT: E 158 MET cc_start: 0.7121 (tpp) cc_final: 0.6874 (tpp) REVERT: E 209 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7349 (mm-40) REVERT: F 141 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5654 (tt0) REVERT: F 404 MET cc_start: 0.8806 (mtt) cc_final: 0.8311 (mtt) REVERT: F 557 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7161 (mm-30) REVERT: F 681 GLU cc_start: 0.4693 (mp0) cc_final: 0.4265 (mm-30) REVERT: F 717 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: F 1045 ASP cc_start: 0.8022 (t0) cc_final: 0.7674 (t70) REVERT: F 1068 LEU cc_start: 0.8054 (pp) cc_final: 0.7772 (tp) outliers start: 78 outliers final: 50 residues processed: 281 average time/residue: 1.0146 time to fit residues: 331.4261 Evaluate side-chains 270 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 210 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19005 Z= 0.299 Angle : 0.649 18.521 25687 Z= 0.327 Chirality : 0.045 0.268 2848 Planarity : 0.005 0.058 3203 Dihedral : 11.883 81.099 2910 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.07 % Allowed : 31.02 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.76 (0.18), residues: 2222 helix: 0.58 (0.16), residues: 1114 sheet: -0.42 (0.32), residues: 247 loop : -1.99 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1112 HIS 0.003 0.001 HIS F 867 PHE 0.019 0.002 PHE F 689 TYR 0.015 0.002 TYR F 767 ARG 0.013 0.000 ARG F 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 208 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6881 (t0) cc_final: 0.6362 (p0) REVERT: A 190 PHE cc_start: 0.7550 (t80) cc_final: 0.6445 (m-80) REVERT: A 449 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8338 (tt) REVERT: A 479 MET cc_start: 0.6440 (pp-130) cc_final: 0.5616 (ppp) REVERT: A 491 TYR cc_start: 0.5135 (OUTLIER) cc_final: 0.4844 (t80) REVERT: A 493 MET cc_start: 0.4932 (OUTLIER) cc_final: 0.4696 (mpt) REVERT: A 519 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5565 (ppp) REVERT: A 547 ASN cc_start: 0.5604 (OUTLIER) cc_final: 0.5212 (p0) REVERT: A 849 LEU cc_start: 0.3318 (OUTLIER) cc_final: 0.2738 (mt) REVERT: A 897 ARG cc_start: 0.7130 (mpt-90) cc_final: 0.6774 (mpt-90) REVERT: A 1031 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: A 1124 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6755 (mmm) REVERT: A 1125 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 1165 MET cc_start: 0.6955 (tmm) cc_final: 0.6338 (tmm) REVERT: A 1173 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5796 (tttt) REVERT: E 8 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5623 (ttmm) REVERT: E 118 LEU cc_start: 0.7398 (mm) cc_final: 0.7168 (mm) REVERT: E 158 MET cc_start: 0.7192 (tpp) cc_final: 0.6983 (tpp) REVERT: E 209 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7346 (mm-40) REVERT: F 141 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5768 (tt0) REVERT: F 404 MET cc_start: 0.8952 (mtt) cc_final: 0.8444 (mtt) REVERT: F 681 GLU cc_start: 0.4242 (mp0) cc_final: 0.3761 (mm-30) REVERT: F 717 GLU cc_start: 0.7912 (tt0) cc_final: 0.7633 (tt0) REVERT: F 1045 ASP cc_start: 0.8106 (t0) cc_final: 0.7715 (t70) outliers start: 81 outliers final: 52 residues processed: 272 average time/residue: 1.0102 time to fit residues: 317.7482 Evaluate side-chains 263 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 147 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19005 Z= 0.170 Angle : 0.604 18.129 25687 Z= 0.302 Chirality : 0.042 0.286 2848 Planarity : 0.004 0.057 3203 Dihedral : 11.459 79.355 2910 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.36 % Allowed : 31.93 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2222 helix: 0.78 (0.16), residues: 1116 sheet: -0.49 (0.32), residues: 243 loop : -1.91 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1112 HIS 0.002 0.000 HIS F 888 PHE 0.023 0.001 PHE F 689 TYR 0.016 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4444 Ramachandran restraints generated. 2222 Oldfield, 0 Emsley, 2222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 205 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3010 (OUTLIER) cc_final: 0.2635 (m170) REVERT: A 187 ASN cc_start: 0.6752 (t0) cc_final: 0.6357 (p0) REVERT: A 190 PHE cc_start: 0.7473 (t80) cc_final: 0.6403 (m-80) REVERT: A 447 LEU cc_start: 0.8304 (tt) cc_final: 0.8033 (tp) REVERT: A 449 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 479 MET cc_start: 0.6436 (pp-130) cc_final: 0.5626 (ppp) REVERT: A 491 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4732 (t80) REVERT: A 493 MET cc_start: 0.5334 (OUTLIER) cc_final: 0.5054 (mpt) REVERT: A 519 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5426 (ppp) REVERT: A 547 ASN cc_start: 0.5639 (OUTLIER) cc_final: 0.5172 (p0) REVERT: A 849 LEU cc_start: 0.3271 (OUTLIER) cc_final: 0.2700 (mt) REVERT: A 897 ARG cc_start: 0.7172 (mpt-90) cc_final: 0.6820 (mpt-90) REVERT: A 1124 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6792 (mmm) REVERT: A 1125 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6862 (t80) REVERT: A 1295 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8626 (t) REVERT: E 59 LYS cc_start: 0.3741 (OUTLIER) cc_final: 0.2593 (ptmm) REVERT: E 118 LEU cc_start: 0.7441 (mm) cc_final: 0.7232 (mm) REVERT: E 142 MET cc_start: 0.7508 (ptp) cc_final: 0.7177 (mtm) REVERT: E 158 MET cc_start: 0.7160 (tpp) cc_final: 0.6902 (tpp) REVERT: E 209 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7306 (mm-40) REVERT: F 141 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5758 (tt0) REVERT: F 404 MET cc_start: 0.8831 (mtt) cc_final: 0.8316 (mtt) REVERT: F 681 GLU cc_start: 0.4521 (mp0) cc_final: 0.4089 (mm-30) REVERT: F 717 GLU cc_start: 0.7866 (tt0) cc_final: 0.7649 (tp30) REVERT: F 1045 ASP cc_start: 0.7994 (t0) cc_final: 0.7650 (t70) REVERT: F 1068 LEU cc_start: 0.8216 (pp) cc_final: 0.7861 (tp) outliers start: 67 outliers final: 46 residues processed: 259 average time/residue: 0.9828 time to fit residues: 296.8478 Evaluate side-chains 261 residues out of total 1991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 491 TYR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 871 THR Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 930 ASN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 726 GLN F 806 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114527 restraints weight = 36631.257| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.36 r_work: 0.3061 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19005 Z= 0.219 Angle : 0.608 12.485 25687 Z= 0.305 Chirality : 0.043 0.237 2848 Planarity : 0.004 0.058 3203 Dihedral : 11.452 79.535 2909 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.21 % Allowed : 32.28 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.56 (0.18), residues: 2222 helix: 0.78 (0.16), residues: 1116 sheet: -0.42 (0.33), residues: 238 loop : -1.91 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1112 HIS 0.002 0.001 HIS F 888 PHE 0.022 0.001 PHE F 689 TYR 0.013 0.001 TYR F 629 ARG 0.013 0.000 ARG F 501 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6485.96 seconds wall clock time: 114 minutes 26.79 seconds (6866.79 seconds total)