Starting phenix.real_space_refine on Thu Sep 18 18:55:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_22414_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_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/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_22414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_22414.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_22414_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpk_22414/09_2025/7jpk_22414_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.28, per 1000 atoms: 0.28 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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: 0.68 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: 3.68 Time building geometry restraints manager: 2.28 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- 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 : 0.010 0.641 19020 Z= 0.723 Angle : 0.857 9.987 25713 Z= 0.447 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 489 TYR 0.023 0.002 TYR F 629 PHE 0.022 0.002 PHE F 157 TRP 0.017 0.002 TRP A1016 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00730 (19005) covalent geometry : angle 0.85583 (25687) SS BOND : bond 0.00243 ( 13) SS BOND : angle 1.47413 ( 26) hydrogen bonds : bond 0.17294 ( 846) hydrogen bonds : angle 6.99566 ( 2483) Misc. bond : bond 0.61981 ( 2) *********************** 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 to be fit. rotamer outliers: 176 poor density : 255 time to evaluate : 0.642 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: 0.4242 time to fit residues: 198.1601 Evaluate side-chains 322 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 214 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.160602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111609 restraints weight = 33447.761| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.24 r_work: 0.2997 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19020 Z= 0.140 Angle : 0.617 8.892 25713 Z= 0.318 Chirality : 0.043 0.266 2848 Planarity : 0.005 0.066 3203 Dihedral : 15.484 100.499 3058 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 6.17 % Allowed : 26.56 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.16), residues: 2222 helix: -0.86 (0.15), residues: 1112 sheet: -1.11 (0.31), residues: 241 loop : -2.73 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 159 TYR 0.023 0.001 TYR F 629 PHE 0.014 0.001 PHE A 801 TRP 0.014 0.001 TRP F 187 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00318 (19005) covalent geometry : angle 0.61554 (25687) SS BOND : bond 0.00374 ( 13) SS BOND : angle 1.47103 ( 26) hydrogen bonds : bond 0.04321 ( 846) hydrogen bonds : angle 4.65780 ( 2483) Misc. bond : bond 0.00042 ( 2) *********************** 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 357 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 234 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3142 (OUTLIER) cc_final: 0.2887 (m90) REVERT: A 187 ASN cc_start: 0.6749 (t0) cc_final: 0.6074 (p0) REVERT: A 190 PHE cc_start: 0.7488 (t80) cc_final: 0.6359 (m-80) REVERT: A 479 MET cc_start: 0.6231 (pp-130) cc_final: 0.3120 (tpt) REVERT: A 491 TYR cc_start: 0.5292 (OUTLIER) cc_final: 0.4934 (t80) REVERT: A 535 LEU cc_start: 0.8454 (mp) cc_final: 0.8156 (mt) REVERT: A 538 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5606 (tt) REVERT: A 664 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6710 (mm) REVERT: A 883 MET cc_start: 0.4378 (ttt) cc_final: 0.3923 (tmm) REVERT: A 926 ARG cc_start: 0.6355 (mtt90) cc_final: 0.5453 (mtp85) REVERT: A 1057 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: A 1125 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6933 (t80) REVERT: A 1165 MET cc_start: 0.7599 (tmm) cc_final: 0.6937 (tmm) REVERT: A 1199 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7506 (mt) REVERT: A 1381 MET cc_start: 0.6626 (pp-130) cc_final: 0.5782 (mmm) REVERT: A 1384 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 1385 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7767 (p0) REVERT: F 205 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8683 (tt) REVERT: F 404 MET cc_start: 0.9352 (mtt) cc_final: 0.8996 (mtt) REVERT: F 501 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8341 (mtm110) REVERT: F 649 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6970 (mp0) outliers start: 123 outliers final: 52 residues processed: 330 average time/residue: 0.4248 time to fit residues: 163.0198 Evaluate side-chains 269 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 664 LEU 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 1057 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 193 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 199 optimal weight: 0.0970 chunk 155 optimal weight: 0.3980 chunk 174 optimal weight: 0.0020 chunk 126 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 464 GLN A 599 ASN A 829 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.162066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113838 restraints weight = 34343.729| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.34 r_work: 0.3080 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19020 Z= 0.120 Angle : 0.580 9.857 25713 Z= 0.297 Chirality : 0.042 0.318 2848 Planarity : 0.004 0.059 3203 Dihedral : 14.092 85.768 2948 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.72 % Allowed : 27.41 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2222 helix: -0.16 (0.15), residues: 1109 sheet: -0.88 (0.32), residues: 237 loop : -2.43 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 707 TYR 0.021 0.001 TYR F 629 PHE 0.019 0.001 PHE A 92 TRP 0.015 0.001 TRP A1112 HIS 0.025 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00272 (19005) covalent geometry : angle 0.57931 (25687) SS BOND : bond 0.00193 ( 13) SS BOND : angle 1.28335 ( 26) hydrogen bonds : bond 0.03687 ( 846) hydrogen bonds : angle 4.31705 ( 2483) Misc. bond : bond 0.00285 ( 2) *********************** 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 338 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 224 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6618 (t0) cc_final: 0.6109 (p0) REVERT: A 190 PHE cc_start: 0.7507 (t80) cc_final: 0.6268 (m-80) REVERT: A 449 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 491 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4829 (t80) REVERT: A 538 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5875 (tt) REVERT: A 547 ASN cc_start: 0.5505 (OUTLIER) cc_final: 0.4963 (p0) REVERT: A 664 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6786 (mm) REVERT: A 835 PHE cc_start: 0.7467 (m-10) cc_final: 0.7251 (m-10) REVERT: A 883 MET cc_start: 0.4186 (ttt) cc_final: 0.3960 (tmm) REVERT: A 926 ARG cc_start: 0.6402 (mtt90) cc_final: 0.5447 (mtp85) REVERT: A 1057 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: A 1091 TYR cc_start: 0.7612 (t80) cc_final: 0.7394 (t80) REVERT: A 1124 MET cc_start: 0.7594 (tpt) cc_final: 0.7249 (mmm) REVERT: A 1125 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6887 (t80) REVERT: A 1173 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5650 (tttt) REVERT: A 1199 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 1201 GLU cc_start: 0.6902 (pt0) cc_final: 0.6591 (mp0) REVERT: A 1381 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.5854 (mmm) REVERT: A 1384 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: A 1385 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 1401 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6536 (mm-30) REVERT: E 142 MET cc_start: 0.7035 (mtm) cc_final: 0.6674 (ptp) REVERT: F 205 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8615 (tt) REVERT: F 404 MET cc_start: 0.9280 (mtt) cc_final: 0.8833 (mtt) REVERT: F 501 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8211 (mtm110) REVERT: F 673 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8251 (pt) outliers start: 114 outliers final: 52 residues processed: 312 average time/residue: 0.4352 time to fit residues: 157.2675 Evaluate side-chains 274 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 548 LEU Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 664 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 1057 MET Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1125 PHE 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain A residue 1401 GLU Chi-restraints excluded: chain E residue 24 MET 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 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 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 673 LEU 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 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 110 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 103 optimal weight: 0.0670 chunk 115 optimal weight: 0.0670 chunk 201 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 930 ASN A1108 GLN E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 551 GLN F 726 GLN F 806 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115136 restraints weight = 33893.565| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.36 r_work: 0.3093 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19020 Z= 0.106 Angle : 0.564 10.787 25713 Z= 0.285 Chirality : 0.042 0.352 2848 Planarity : 0.004 0.059 3203 Dihedral : 13.068 85.744 2933 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.92 % Allowed : 28.41 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2222 helix: 0.24 (0.16), residues: 1114 sheet: -0.70 (0.32), residues: 239 loop : -2.19 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.020 0.001 TYR F 629 PHE 0.024 0.001 PHE F 689 TRP 0.018 0.001 TRP A1112 HIS 0.001 0.000 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00235 (19005) covalent geometry : angle 0.56273 (25687) SS BOND : bond 0.00123 ( 13) SS BOND : angle 1.25771 ( 26) hydrogen bonds : bond 0.03287 ( 846) hydrogen bonds : angle 4.10010 ( 2483) Misc. bond : bond 0.00114 ( 2) *********************** 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 335 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 237 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2970 (OUTLIER) cc_final: 0.2707 (m90) REVERT: A 187 ASN cc_start: 0.6714 (t0) cc_final: 0.6189 (p0) REVERT: A 190 PHE cc_start: 0.7473 (t80) cc_final: 0.6246 (m-80) REVERT: A 479 MET cc_start: 0.6263 (pp-130) cc_final: 0.5634 (pp-130) REVERT: A 491 TYR cc_start: 0.5221 (OUTLIER) cc_final: 0.4796 (t80) REVERT: A 535 LEU cc_start: 0.8284 (mp) cc_final: 0.8045 (mt) REVERT: A 538 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.5854 (tt) REVERT: A 540 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5441 (tptp) REVERT: A 547 ASN cc_start: 0.5655 (OUTLIER) cc_final: 0.5112 (p0) REVERT: A 647 CYS cc_start: 0.8680 (t) cc_final: 0.8462 (m) REVERT: A 664 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6765 (mm) REVERT: A 835 PHE cc_start: 0.7463 (m-10) cc_final: 0.7224 (m-10) REVERT: A 849 LEU cc_start: 0.3039 (OUTLIER) cc_final: 0.2509 (mt) REVERT: A 897 ARG cc_start: 0.7201 (mpt-90) cc_final: 0.6873 (mpt-90) REVERT: A 984 GLU cc_start: 0.8839 (pt0) cc_final: 0.8385 (pm20) REVERT: A 1057 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: A 1091 TYR cc_start: 0.7701 (t80) cc_final: 0.7468 (t80) REVERT: A 1124 MET cc_start: 0.7515 (tpt) cc_final: 0.7296 (mmm) REVERT: A 1125 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 1381 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5855 (mmm) REVERT: A 1384 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: E 142 MET cc_start: 0.6961 (mtm) cc_final: 0.6626 (ptp) REVERT: E 158 MET cc_start: 0.7079 (tpt) cc_final: 0.6808 (tpp) REVERT: F 42 GLU cc_start: 0.8069 (tt0) cc_final: 0.7839 (tm-30) REVERT: F 88 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8184 (tttm) REVERT: F 299 ASN cc_start: 0.7863 (t0) cc_final: 0.7569 (m-40) REVERT: F 404 MET cc_start: 0.9216 (mtt) cc_final: 0.8773 (mtt) REVERT: F 501 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8200 (mtm110) REVERT: F 673 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8186 (pp) outliers start: 98 outliers final: 41 residues processed: 310 average time/residue: 0.4762 time to fit residues: 171.5810 Evaluate side-chains 270 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 486 LEU 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 547 ASN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 669 SER 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 1039 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1125 PHE 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE 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 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 673 LEU Chi-restraints excluded: chain F residue 694 THR 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 1009 GLU 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 175 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 806 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124152 restraints weight = 29805.059| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.14 r_work: 0.2955 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19020 Z= 0.135 Angle : 0.587 12.447 25713 Z= 0.296 Chirality : 0.043 0.315 2848 Planarity : 0.004 0.057 3203 Dihedral : 12.581 82.444 2921 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.77 % Allowed : 28.87 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 2222 helix: 0.39 (0.16), residues: 1114 sheet: -0.59 (0.33), residues: 239 loop : -2.09 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 646 TYR 0.018 0.001 TYR A1109 PHE 0.021 0.001 PHE F 689 TRP 0.022 0.001 TRP A1112 HIS 0.015 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00317 (19005) covalent geometry : angle 0.58558 (25687) SS BOND : bond 0.00167 ( 13) SS BOND : angle 1.20425 ( 26) hydrogen bonds : bond 0.03506 ( 846) hydrogen bonds : angle 4.08849 ( 2483) Misc. bond : bond 0.00255 ( 2) *********************** 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 313 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 218 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6808 (t0) cc_final: 0.6181 (p0) REVERT: A 190 PHE cc_start: 0.7512 (t80) cc_final: 0.6281 (m-80) REVERT: A 449 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (tt) REVERT: A 479 MET cc_start: 0.6324 (pp-130) cc_final: 0.5866 (pp-130) REVERT: A 491 TYR cc_start: 0.5020 (OUTLIER) cc_final: 0.4604 (t80) REVERT: A 493 MET cc_start: 0.5138 (OUTLIER) cc_final: 0.4786 (mpt) REVERT: A 540 LYS cc_start: 0.5847 (OUTLIER) cc_final: 0.5489 (tptp) REVERT: A 547 ASN cc_start: 0.5356 (OUTLIER) cc_final: 0.4860 (p0) REVERT: A 647 CYS cc_start: 0.8706 (t) cc_final: 0.8504 (m) REVERT: A 664 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6932 (mm) REVERT: A 849 LEU cc_start: 0.3073 (OUTLIER) cc_final: 0.2482 (mt) REVERT: A 897 ARG cc_start: 0.7218 (mpt-90) cc_final: 0.6870 (mpt-90) REVERT: A 984 GLU cc_start: 0.8894 (pt0) cc_final: 0.8477 (pm20) REVERT: A 1031 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8780 (mtp) REVERT: A 1057 MET cc_start: 0.8438 (tpp) cc_final: 0.8108 (tpp) REVERT: A 1091 TYR cc_start: 0.7724 (t80) cc_final: 0.7487 (t80) REVERT: A 1124 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7211 (mmm) REVERT: A 1164 GLU cc_start: 0.8206 (tp30) cc_final: 0.8000 (tp30) REVERT: A 1173 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5815 (tttt) REVERT: A 1295 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8578 (t) REVERT: A 1381 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5879 (mmm) REVERT: A 1384 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: E 59 LYS cc_start: 0.3636 (OUTLIER) cc_final: 0.2530 (pttt) REVERT: E 142 MET cc_start: 0.6977 (mtm) cc_final: 0.6563 (ptp) REVERT: E 158 MET cc_start: 0.7163 (tpt) cc_final: 0.6873 (tpp) REVERT: E 216 MET cc_start: 0.7019 (ttp) cc_final: 0.6796 (ttp) REVERT: F 42 GLU cc_start: 0.8154 (tt0) cc_final: 0.7903 (tm-30) REVERT: F 205 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8691 (tt) REVERT: F 311 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: F 404 MET cc_start: 0.9261 (mtt) cc_final: 0.8836 (mtt) REVERT: F 501 ARG cc_start: 0.8529 (mtt90) cc_final: 0.8247 (mtm110) REVERT: F 673 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8112 (pp) REVERT: F 681 GLU cc_start: 0.4859 (mp0) cc_final: 0.4601 (mp0) REVERT: F 1045 ASP cc_start: 0.8583 (t0) cc_final: 0.8277 (t70) outliers start: 95 outliers final: 51 residues processed: 294 average time/residue: 0.4500 time to fit residues: 153.3111 Evaluate side-chains 280 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 486 LEU 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 558 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER 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 1039 VAL Chi-restraints excluded: chain A residue 1124 MET 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 1332 CYS Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1384 PHE 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 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 311 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 673 LEU 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 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 218 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 197 optimal weight: 0.0570 chunk 96 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 overall best weight: 0.7708 ------------------------------------------------------------------------------- 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 930 ASN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 644 GLN F 806 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116304 restraints weight = 36836.363| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.39 r_work: 0.3117 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19020 Z= 0.110 Angle : 0.562 13.022 25713 Z= 0.283 Chirality : 0.041 0.277 2848 Planarity : 0.004 0.058 3203 Dihedral : 12.058 80.906 2912 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.27 % Allowed : 29.52 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.18), residues: 2222 helix: 0.60 (0.16), residues: 1114 sheet: -0.52 (0.32), residues: 246 loop : -2.00 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.016 0.001 TYR F 629 PHE 0.021 0.001 PHE F 689 TRP 0.025 0.001 TRP A1112 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00249 (19005) covalent geometry : angle 0.56159 (25687) SS BOND : bond 0.00146 ( 13) SS BOND : angle 0.88717 ( 26) hydrogen bonds : bond 0.03228 ( 846) hydrogen bonds : angle 4.00202 ( 2483) Misc. bond : bond 0.00354 ( 2) *********************** 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 312 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 227 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.6793 (t0) cc_final: 0.6194 (p0) REVERT: A 190 PHE cc_start: 0.7456 (t80) cc_final: 0.6241 (m-80) REVERT: A 449 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (tt) REVERT: A 479 MET cc_start: 0.6109 (pp-130) cc_final: 0.5796 (pp-130) REVERT: A 491 TYR cc_start: 0.5009 (OUTLIER) cc_final: 0.4598 (t80) REVERT: A 493 MET cc_start: 0.5041 (OUTLIER) cc_final: 0.4770 (mpt) REVERT: A 519 MET cc_start: 0.6464 (mtt) cc_final: 0.5472 (ppp) REVERT: A 540 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5546 (tptp) REVERT: A 547 ASN cc_start: 0.5506 (OUTLIER) cc_final: 0.5033 (p0) REVERT: A 664 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6965 (mm) REVERT: A 849 LEU cc_start: 0.2890 (OUTLIER) cc_final: 0.2330 (mt) REVERT: A 897 ARG cc_start: 0.7223 (mpt-90) cc_final: 0.6897 (mpt-90) REVERT: A 984 GLU cc_start: 0.8827 (pt0) cc_final: 0.8438 (pm20) REVERT: A 1057 MET cc_start: 0.8390 (tpp) cc_final: 0.8060 (tpp) REVERT: A 1091 TYR cc_start: 0.7794 (t80) cc_final: 0.7542 (t80) REVERT: A 1124 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7196 (mmm) REVERT: A 1173 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5833 (tttt) REVERT: A 1234 PHE cc_start: 0.8710 (p90) cc_final: 0.8473 (p90) REVERT: A 1295 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8591 (t) REVERT: A 1381 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.5890 (mmm) REVERT: A 1384 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: E 59 LYS cc_start: 0.3642 (OUTLIER) cc_final: 0.2506 (pttt) REVERT: E 142 MET cc_start: 0.6912 (mtm) cc_final: 0.6582 (ptp) REVERT: E 158 MET cc_start: 0.7139 (tpt) cc_final: 0.6911 (tpp) REVERT: E 216 MET cc_start: 0.6867 (ttp) cc_final: 0.6619 (ttp) REVERT: F 42 GLU cc_start: 0.8118 (tt0) cc_final: 0.7892 (tm-30) REVERT: F 205 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (tt) REVERT: F 311 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: F 404 MET cc_start: 0.9186 (mtt) cc_final: 0.8757 (mtt) REVERT: F 501 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8258 (mtm110) REVERT: F 673 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8024 (pp) REVERT: F 681 GLU cc_start: 0.5151 (mp0) cc_final: 0.4846 (mp0) REVERT: F 1045 ASP cc_start: 0.8561 (t0) cc_final: 0.8255 (t70) outliers start: 85 outliers final: 50 residues processed: 295 average time/residue: 0.4378 time to fit residues: 150.6927 Evaluate side-chains 278 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 486 LEU 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 664 LEU Chi-restraints excluded: chain A residue 669 SER 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 983 MET Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1124 MET Chi-restraints excluded: chain A residue 1173 LYS 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE 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 205 LEU 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 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 673 LEU 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 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 35 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 687 ASN F 806 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116797 restraints weight = 38340.235| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.36 r_work: 0.3101 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19020 Z= 0.114 Angle : 0.562 14.666 25713 Z= 0.282 Chirality : 0.042 0.271 2848 Planarity : 0.004 0.057 3203 Dihedral : 11.744 79.849 2912 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.27 % Allowed : 29.87 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.18), residues: 2222 helix: 0.72 (0.16), residues: 1115 sheet: -0.46 (0.33), residues: 246 loop : -1.93 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.014 0.001 TYR F 629 PHE 0.022 0.001 PHE F 689 TRP 0.013 0.001 TRP A1112 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00262 (19005) covalent geometry : angle 0.56168 (25687) SS BOND : bond 0.00142 ( 13) SS BOND : angle 0.86502 ( 26) hydrogen bonds : bond 0.03216 ( 846) hydrogen bonds : angle 3.95367 ( 2483) Misc. bond : bond 0.00254 ( 2) *********************** 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 302 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 217 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3048 (OUTLIER) cc_final: 0.2789 (m170) REVERT: A 187 ASN cc_start: 0.6831 (t0) cc_final: 0.6243 (p0) REVERT: A 190 PHE cc_start: 0.7415 (t80) cc_final: 0.6162 (m-80) REVERT: A 449 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 479 MET cc_start: 0.6411 (pp-130) cc_final: 0.6055 (pp-130) REVERT: A 491 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.4681 (t80) REVERT: A 493 MET cc_start: 0.4971 (OUTLIER) cc_final: 0.4709 (mpt) REVERT: A 519 MET cc_start: 0.6403 (mtt) cc_final: 0.5548 (ppp) REVERT: A 540 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5526 (tptp) REVERT: A 547 ASN cc_start: 0.5531 (OUTLIER) cc_final: 0.5060 (p0) REVERT: A 664 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 849 LEU cc_start: 0.3028 (OUTLIER) cc_final: 0.2440 (mt) REVERT: A 897 ARG cc_start: 0.7299 (mpt-90) cc_final: 0.6948 (mpt-90) REVERT: A 984 GLU cc_start: 0.8850 (pt0) cc_final: 0.8482 (pm20) REVERT: A 1057 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8118 (tpp) REVERT: A 1091 TYR cc_start: 0.7802 (t80) cc_final: 0.7552 (t80) REVERT: A 1124 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7074 (mmm) REVERT: A 1234 PHE cc_start: 0.8707 (p90) cc_final: 0.8490 (p90) REVERT: A 1295 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8603 (t) REVERT: A 1381 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.5964 (mmm) REVERT: A 1384 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: E 59 LYS cc_start: 0.3736 (OUTLIER) cc_final: 0.2535 (pttt) REVERT: E 118 LEU cc_start: 0.7595 (mm) cc_final: 0.7309 (mm) REVERT: E 142 MET cc_start: 0.6979 (mtm) cc_final: 0.6569 (ptp) REVERT: E 158 MET cc_start: 0.7252 (tpt) cc_final: 0.7026 (tpp) REVERT: F 205 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8662 (tt) REVERT: F 311 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: F 404 MET cc_start: 0.9207 (mtt) cc_final: 0.8768 (mtt) REVERT: F 501 ARG cc_start: 0.8560 (mtt90) cc_final: 0.8324 (mtm110) REVERT: F 557 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7601 (mm-30) REVERT: F 673 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8043 (pp) REVERT: F 681 GLU cc_start: 0.5182 (mp0) cc_final: 0.4777 (mm-30) REVERT: F 1045 ASP cc_start: 0.8509 (t0) cc_final: 0.8164 (t70) outliers start: 85 outliers final: 52 residues processed: 284 average time/residue: 0.4683 time to fit residues: 153.5876 Evaluate side-chains 279 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 210 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 161 VAL Chi-restraints excluded: chain A residue 164 LEU 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 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 664 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER 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 983 MET Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1124 MET 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE 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 132 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 205 LEU 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 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 673 LEU 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 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 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 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 = 0.3883 r_free = 0.3883 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115995 restraints weight = 41192.438| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.70 r_work: 0.3087 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19020 Z= 0.117 Angle : 0.570 16.801 25713 Z= 0.285 Chirality : 0.042 0.247 2848 Planarity : 0.004 0.056 3203 Dihedral : 11.514 79.120 2912 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 30.22 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.18), residues: 2222 helix: 0.79 (0.16), residues: 1116 sheet: -0.42 (0.33), residues: 246 loop : -1.89 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.013 0.001 TYR A1109 PHE 0.023 0.001 PHE F 689 TRP 0.026 0.001 TRP A1112 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00272 (19005) covalent geometry : angle 0.56932 (25687) SS BOND : bond 0.00139 ( 13) SS BOND : angle 0.86485 ( 26) hydrogen bonds : bond 0.03206 ( 846) hydrogen bonds : angle 3.93833 ( 2483) Misc. bond : bond 0.00283 ( 2) *********************** 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 297 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 216 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6966 (mp) REVERT: A 113 HIS cc_start: 0.3169 (OUTLIER) cc_final: 0.2916 (m170) REVERT: A 187 ASN cc_start: 0.6857 (t0) cc_final: 0.6224 (p0) REVERT: A 190 PHE cc_start: 0.7454 (t80) cc_final: 0.6165 (m-80) REVERT: A 449 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 479 MET cc_start: 0.6175 (pp-130) cc_final: 0.5953 (pp-130) REVERT: A 491 TYR cc_start: 0.4915 (OUTLIER) cc_final: 0.4581 (t80) REVERT: A 493 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4511 (mpt) REVERT: A 519 MET cc_start: 0.6578 (mtt) cc_final: 0.5728 (ppp) REVERT: A 540 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5529 (tptp) REVERT: A 547 ASN cc_start: 0.5577 (OUTLIER) cc_final: 0.5129 (p0) REVERT: A 664 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7026 (mm) REVERT: A 849 LEU cc_start: 0.3001 (OUTLIER) cc_final: 0.2416 (mt) REVERT: A 897 ARG cc_start: 0.7304 (mpt-90) cc_final: 0.6966 (mpt-90) REVERT: A 984 GLU cc_start: 0.8909 (pt0) cc_final: 0.8535 (pm20) REVERT: A 1057 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8143 (tpp) REVERT: A 1091 TYR cc_start: 0.7806 (t80) cc_final: 0.7548 (t80) REVERT: A 1234 PHE cc_start: 0.8704 (p90) cc_final: 0.8485 (p90) REVERT: A 1295 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8623 (t) REVERT: A 1381 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5959 (mmm) REVERT: A 1384 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: E 59 LYS cc_start: 0.3730 (OUTLIER) cc_final: 0.2540 (pttt) REVERT: E 118 LEU cc_start: 0.7520 (mm) cc_final: 0.7213 (mm) REVERT: E 142 MET cc_start: 0.6890 (mtm) cc_final: 0.6452 (ptp) REVERT: E 158 MET cc_start: 0.7519 (tpt) cc_final: 0.7316 (tpp) REVERT: E 213 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6908 (pt0) REVERT: F 141 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5414 (tt0) REVERT: F 311 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: F 404 MET cc_start: 0.9209 (mtt) cc_final: 0.8775 (mtt) REVERT: F 501 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8342 (mtm110) REVERT: F 547 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.7363 (mtt180) REVERT: F 557 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7741 (mm-30) REVERT: F 673 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8075 (pt) REVERT: F 681 GLU cc_start: 0.5203 (mp0) cc_final: 0.4838 (mm-30) REVERT: F 1045 ASP cc_start: 0.8422 (t0) cc_final: 0.8133 (t70) outliers start: 81 outliers final: 46 residues processed: 279 average time/residue: 0.4722 time to fit residues: 152.0490 Evaluate side-chains 274 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 143 ASN 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 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 636 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 669 SER 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 983 MET Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1104 LYS 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 213 GLU 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 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 673 LEU 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 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 84 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 176 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- 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** E 209 GLN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 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 = 0.3855 r_free = 0.3855 target = 0.161352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112426 restraints weight = 43690.726| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.55 r_work: 0.3015 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19020 Z= 0.170 Angle : 0.615 17.879 25713 Z= 0.309 Chirality : 0.044 0.267 2848 Planarity : 0.004 0.057 3203 Dihedral : 11.696 80.323 2911 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.82 % Allowed : 30.67 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.18), residues: 2222 helix: 0.71 (0.16), residues: 1115 sheet: -0.37 (0.33), residues: 241 loop : -1.94 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.014 0.001 TYR F 514 PHE 0.020 0.001 PHE F 689 TRP 0.019 0.001 TRP A1112 HIS 0.003 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00410 (19005) covalent geometry : angle 0.61463 (25687) SS BOND : bond 0.00214 ( 13) SS BOND : angle 1.11161 ( 26) hydrogen bonds : bond 0.03700 ( 846) hydrogen bonds : angle 4.06116 ( 2483) Misc. bond : bond 0.00241 ( 2) *********************** 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 284 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3009 (OUTLIER) cc_final: 0.2775 (m170) REVERT: A 187 ASN cc_start: 0.6923 (t0) cc_final: 0.6259 (p0) REVERT: A 190 PHE cc_start: 0.7462 (t80) cc_final: 0.6147 (m-80) REVERT: A 449 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 479 MET cc_start: 0.6244 (pp-130) cc_final: 0.5324 (ppp) REVERT: A 491 TYR cc_start: 0.4972 (OUTLIER) cc_final: 0.4650 (t80) REVERT: A 493 MET cc_start: 0.4811 (OUTLIER) cc_final: 0.4578 (mpt) REVERT: A 519 MET cc_start: 0.6682 (mtt) cc_final: 0.5828 (ppp) REVERT: A 540 LYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5524 (tptp) REVERT: A 547 ASN cc_start: 0.5540 (OUTLIER) cc_final: 0.5103 (p0) REVERT: A 664 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7063 (mm) REVERT: A 849 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2423 (mt) REVERT: A 984 GLU cc_start: 0.8877 (pt0) cc_final: 0.8504 (pm20) REVERT: A 1031 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8446 (mtm) REVERT: A 1057 MET cc_start: 0.8512 (tpp) cc_final: 0.8118 (tpp) REVERT: A 1091 TYR cc_start: 0.7896 (t80) cc_final: 0.7602 (t80) REVERT: A 1164 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: A 1173 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5978 (tttt) REVERT: A 1295 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8593 (t) REVERT: A 1381 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.5928 (mmm) REVERT: A 1384 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: E 8 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5578 (ttmm) REVERT: E 59 LYS cc_start: 0.3768 (OUTLIER) cc_final: 0.2542 (ptmm) REVERT: E 118 LEU cc_start: 0.7515 (mm) cc_final: 0.7162 (mm) REVERT: E 158 MET cc_start: 0.7224 (tpt) cc_final: 0.6989 (tpp) REVERT: F 141 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5623 (tt0) REVERT: F 311 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: F 404 MET cc_start: 0.9301 (mtt) cc_final: 0.8845 (mtt) REVERT: F 501 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8266 (mtm110) REVERT: F 681 GLU cc_start: 0.5187 (mp0) cc_final: 0.4804 (mm-30) REVERT: F 990 SER cc_start: 0.8265 (m) cc_final: 0.7922 (t) REVERT: F 1045 ASP cc_start: 0.8510 (t0) cc_final: 0.8181 (t70) outliers start: 76 outliers final: 48 residues processed: 268 average time/residue: 0.5025 time to fit residues: 154.8193 Evaluate side-chains 272 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 636 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER 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 1031 MET Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1164 GLU 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 8 LYS 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 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 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 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 26 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** E 209 GLN F 186 ASN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN F 806 GLN F1065 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113083 restraints weight = 40657.237| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.44 r_work: 0.3020 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19020 Z= 0.181 Angle : 0.626 14.884 25713 Z= 0.316 Chirality : 0.044 0.265 2848 Planarity : 0.004 0.057 3203 Dihedral : 11.752 80.539 2911 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.66 % Allowed : 30.92 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.18), residues: 2222 helix: 0.63 (0.16), residues: 1116 sheet: -0.35 (0.33), residues: 243 loop : -1.96 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.013 0.001 TYR F 514 PHE 0.020 0.001 PHE F 689 TRP 0.035 0.001 TRP A1112 HIS 0.003 0.001 HIS A1139 Details of bonding type rmsd covalent geometry : bond 0.00438 (19005) covalent geometry : angle 0.62558 (25687) SS BOND : bond 0.00216 ( 13) SS BOND : angle 1.15941 ( 26) hydrogen bonds : bond 0.03811 ( 846) hydrogen bonds : angle 4.12665 ( 2483) Misc. bond : bond 0.00246 ( 2) ********************** 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 281 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.3152 (OUTLIER) cc_final: 0.2895 (m170) REVERT: A 187 ASN cc_start: 0.6847 (t0) cc_final: 0.6201 (p0) REVERT: A 190 PHE cc_start: 0.7624 (t80) cc_final: 0.6277 (m-80) REVERT: A 449 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (tt) REVERT: A 491 TYR cc_start: 0.4991 (OUTLIER) cc_final: 0.4632 (t80) REVERT: A 493 MET cc_start: 0.4816 (OUTLIER) cc_final: 0.4588 (mpt) REVERT: A 519 MET cc_start: 0.6618 (mtt) cc_final: 0.5767 (ppp) REVERT: A 547 ASN cc_start: 0.5609 (OUTLIER) cc_final: 0.5088 (p0) REVERT: A 668 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: A 849 LEU cc_start: 0.3056 (OUTLIER) cc_final: 0.2455 (mt) REVERT: A 984 GLU cc_start: 0.8885 (pt0) cc_final: 0.8520 (pm20) REVERT: A 1031 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: A 1057 MET cc_start: 0.8572 (tpp) cc_final: 0.8206 (tpp) REVERT: A 1091 TYR cc_start: 0.7855 (t80) cc_final: 0.7550 (t80) REVERT: A 1125 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7302 (t80) REVERT: A 1164 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: A 1165 MET cc_start: 0.7229 (tmm) cc_final: 0.6796 (tmm) REVERT: A 1173 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5870 (tttt) REVERT: A 1295 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8577 (t) REVERT: A 1381 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.5996 (mmm) REVERT: A 1384 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: E 118 LEU cc_start: 0.7561 (mm) cc_final: 0.7210 (mm) REVERT: E 158 MET cc_start: 0.7235 (tpt) cc_final: 0.6984 (tpp) REVERT: E 213 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6937 (pt0) REVERT: F 141 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5696 (tt0) REVERT: F 311 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: F 404 MET cc_start: 0.9313 (mtt) cc_final: 0.8936 (mtt) REVERT: F 501 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8295 (mtm110) REVERT: F 990 SER cc_start: 0.8278 (m) cc_final: 0.7949 (t) REVERT: F 1045 ASP cc_start: 0.8510 (t0) cc_final: 0.8171 (t70) outliers start: 73 outliers final: 50 residues processed: 265 average time/residue: 0.4725 time to fit residues: 143.4307 Evaluate side-chains 271 residues out of total 1991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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 558 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 669 SER 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 1031 MET Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1125 PHE Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1164 GLU 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 1381 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1385 ASP Chi-restraints excluded: chain E residue 17 LEU 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 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 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 1008 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1065 ASN 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 97 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 138 optimal weight: 0.0470 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 118 optimal weight: 8.9990 chunk 93 optimal weight: 0.0040 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.4490 ------------------------------------------------------------------------------- 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** E 209 GLN F 186 ASN ** F 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 GLN ** F1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124298 restraints weight = 29766.032| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.89 r_work: 0.2927 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 19020 Z= 0.215 Angle : 0.795 59.184 25713 Z= 0.454 Chirality : 0.043 0.359 2848 Planarity : 0.005 0.102 3203 Dihedral : 11.782 80.555 2911 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.69 % Rotamer: Outliers : 3.77 % Allowed : 30.87 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.18), residues: 2222 helix: 0.65 (0.16), residues: 1116 sheet: -0.39 (0.33), residues: 241 loop : -1.96 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 646 TYR 0.014 0.001 TYR F 514 PHE 0.020 0.001 PHE F 689 TRP 0.032 0.001 TRP A1112 HIS 0.002 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00435 (19005) covalent geometry : angle 0.79412 (25687) SS BOND : bond 0.00153 ( 13) SS BOND : angle 1.13259 ( 26) hydrogen bonds : bond 0.03711 ( 846) hydrogen bonds : angle 4.12599 ( 2483) Misc. bond : bond 0.00256 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7313.20 seconds wall clock time: 124 minutes 50.60 seconds (7490.60 seconds total)