Starting phenix.real_space_refine on Sun Dec 29 06:17:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwf_36681/12_2024/8jwf_36681_neut.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.050 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 6300 2.51 5 N 1600 2.21 5 O 1771 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1204, 9691 Classifications: {'peptide': 1204} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1177} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'YMZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.93, per 1000 atoms: 0.61 Number of scatterers: 9717 At special positions: 0 Unit cell: (70.4, 116.6, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 F 6 9.00 O 1771 8.00 N 1600 7.00 C 6300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2286 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.800A pdb=" N GLU A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.776A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 4.503A pdb=" N PHE A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 87 removed outlier: 3.518A pdb=" N PHE A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 136 removed outlier: 4.576A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.584A pdb=" N ASP A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.827A pdb=" N ARG A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.572A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 184 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.565A pdb=" N LEU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 removed outlier: 3.509A pdb=" N ILE A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.635A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 249 through 305 removed outlier: 3.680A pdb=" N ILE A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 358 removed outlier: 3.787A pdb=" N ILE A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.545A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.592A pdb=" N TRP A 453 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 489 removed outlier: 4.555A pdb=" N SER A 478 " --> pdb=" O ASN A 474 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.652A pdb=" N TYR A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 529 through 537 Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.744A pdb=" N VAL A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'A' and resid 588 through 593 removed outlier: 4.279A pdb=" N SER A 592 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 593 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 4.036A pdb=" N ASN A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 676 through 681 removed outlier: 4.138A pdb=" N LYS A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 694 Processing helix chain 'A' and resid 772 through 784 removed outlier: 4.046A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 801 removed outlier: 3.795A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 817 removed outlier: 4.064A pdb=" N PHE A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 872 removed outlier: 4.073A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 4.256A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 removed outlier: 3.725A pdb=" N LEU A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS A 898 " --> pdb=" O ASN A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 929 removed outlier: 3.836A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 928 " --> pdb=" O MET A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 Processing helix chain 'A' and resid 948 through 962 removed outlier: 3.543A pdb=" N ARG A 952 " --> pdb=" O ALA A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 990 removed outlier: 3.783A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 999 Processing helix chain 'A' and resid 1001 through 1036 removed outlier: 3.894A pdb=" N PHE A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR A1015 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS A1018 " --> pdb=" O ASP A1014 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A1019 " --> pdb=" O TYR A1015 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1036 " --> pdb=" O GLY A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 3.955A pdb=" N ARG A1055 " --> pdb=" O PHE A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 4.035A pdb=" N PHE A1063 " --> pdb=" O LEU A1059 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A1082 " --> pdb=" O GLY A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1098 removed outlier: 3.825A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1102 Processing helix chain 'A' and resid 1118 through 1122 removed outlier: 3.904A pdb=" N ILE A1122 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.536A pdb=" N THR A1169 " --> pdb=" O GLY A1166 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET A1171 " --> pdb=" O SER A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 removed outlier: 4.012A pdb=" N ASP A1241 " --> pdb=" O ASN A1238 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A1242 " --> pdb=" O ILE A1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1238 through 1242' Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 4.014A pdb=" N LEU A1247 " --> pdb=" O ASN A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1269 Processing helix chain 'A' and resid 1277 through 1289 Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 3.512A pdb=" N LYS A1310 " --> pdb=" O PRO A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1327 removed outlier: 3.561A pdb=" N ALA A1325 " --> pdb=" O ALA A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1360 removed outlier: 4.004A pdb=" N LYS A1360 " --> pdb=" O ASP A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1376 Processing helix chain 'A' and resid 1410 through 1417 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.544A pdb=" N ILE A 378 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.521A pdb=" N HIS A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.858A pdb=" N LEU A 584 " --> pdb=" O ILE A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 633 through 636 removed outlier: 6.989A pdb=" N VAL A 634 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1150 through 1151 removed outlier: 3.812A pdb=" N CYS A1151 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1126 " --> pdb=" O CYS A1151 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A1129 " --> pdb=" O GLU A1231 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1366 through 1368 removed outlier: 3.604A pdb=" N THR A1367 " --> pdb=" O THR A1157 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA A1158 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE A1384 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A1160 " --> pdb=" O PHE A1384 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A1381 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N HIS A1397 " --> pdb=" O ILE A1381 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL A1383 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A1395 " --> pdb=" O VAL A1383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 5.923A pdb=" N SER A1252 " --> pdb=" O LEU A1334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 515 hydrogen bonds defined for protein. 1506 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: 3.96 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2717 1.33 - 1.45: 1744 1.45 - 1.58: 5368 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9896 Sorted by residual: bond pdb=" CAR YMZ A1500 " pdb=" NAP YMZ A1500 " ideal model delta sigma weight residual 1.298 1.373 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CA LYS A1104 " pdb=" CB LYS A1104 " ideal model delta sigma weight residual 1.528 1.569 -0.041 1.35e-02 5.49e+03 9.11e+00 bond pdb=" C GLU A1267 " pdb=" N ASN A1268 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.31e-02 5.83e+03 7.46e+00 bond pdb=" N ILE A1107 " pdb=" CA ILE A1107 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.60e+00 bond pdb=" CAJ YMZ A1500 " pdb=" CAU YMZ A1500 " ideal model delta sigma weight residual 1.414 1.369 0.045 2.00e-02 2.50e+03 5.16e+00 ... (remaining 9891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 12298 1.36 - 2.73: 892 2.73 - 4.09: 108 4.09 - 5.46: 31 5.46 - 6.82: 8 Bond angle restraints: 13337 Sorted by residual: angle pdb=" N SER A1105 " pdb=" CA SER A1105 " pdb=" C SER A1105 " ideal model delta sigma weight residual 111.28 117.83 -6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" C ILE A 336 " pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 120.58 125.66 -5.08 1.32e+00 5.74e-01 1.48e+01 angle pdb=" N ILE A1107 " pdb=" CA ILE A1107 " pdb=" CB ILE A1107 " ideal model delta sigma weight residual 111.23 104.98 6.25 1.65e+00 3.67e-01 1.43e+01 angle pdb=" O SER A1105 " pdb=" C SER A1105 " pdb=" N ASN A1106 " ideal model delta sigma weight residual 122.12 126.06 -3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" CA LYS A1104 " pdb=" C LYS A1104 " pdb=" O LYS A1104 " ideal model delta sigma weight residual 120.43 124.43 -4.00 1.12e+00 7.97e-01 1.28e+01 ... (remaining 13332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 5864 23.51 - 47.02: 108 47.02 - 70.53: 6 70.53 - 94.04: 7 94.04 - 117.55: 2 Dihedral angle restraints: 5987 sinusoidal: 2447 harmonic: 3540 Sorted by residual: dihedral pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N LEU A 183 " pdb=" CA LEU A 183 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA SER A1168 " pdb=" C SER A1168 " pdb=" N THR A1169 " pdb=" CA THR A1169 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU A 593 " pdb=" C LEU A 593 " pdb=" N ASP A 594 " pdb=" CA ASP A 594 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1388 0.081 - 0.162: 137 0.162 - 0.243: 1 0.243 - 0.324: 1 0.324 - 0.405: 2 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CA LYS A1104 " pdb=" N LYS A1104 " pdb=" C LYS A1104 " pdb=" CB LYS A1104 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA ILE A1107 " pdb=" N ILE A1107 " pdb=" C ILE A1107 " pdb=" CB ILE A1107 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA ASN A1106 " pdb=" N ASN A1106 " pdb=" C ASN A1106 " pdb=" CB ASN A1106 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1526 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1104 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C LYS A1104 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS A1104 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A1105 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 885 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 886 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 886 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 886 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 108 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C LEU A 108 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A 108 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 109 " 0.013 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1114 2.75 - 3.28: 10704 3.28 - 3.82: 14601 3.82 - 4.36: 17538 4.36 - 4.90: 29415 Nonbonded interactions: 73372 Sorted by model distance: nonbonded pdb=" O LEU A 540 " pdb=" NH1 ARG A 570 " model vdw 2.208 3.120 nonbonded pdb=" N PHE A 385 " pdb=" OE2 GLU A 394 " model vdw 2.222 3.120 nonbonded pdb=" O LEU A 518 " pdb=" NZ LYS A 522 " model vdw 2.229 3.120 nonbonded pdb=" O ASP A1014 " pdb=" NZ LYS A1018 " model vdw 2.231 3.120 nonbonded pdb=" O GLU A 824 " pdb=" OG SER A 827 " model vdw 2.233 3.040 ... (remaining 73367 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.320 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 9896 Z= 0.424 Angle : 0.797 6.822 13337 Z= 0.463 Chirality : 0.048 0.405 1529 Planarity : 0.005 0.056 1654 Dihedral : 10.453 117.551 3701 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.09 % Allowed : 1.47 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.21), residues: 1190 helix: -1.69 (0.16), residues: 707 sheet: -2.94 (0.78), residues: 34 loop : -3.03 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.010 0.002 HIS A 892 PHE 0.027 0.003 PHE A 868 TYR 0.026 0.003 TYR A 851 ARG 0.010 0.001 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8392 (m-10) cc_final: 0.8108 (t80) REVERT: A 344 MET cc_start: 0.6850 (mtp) cc_final: 0.6413 (mtt) REVERT: A 348 GLU cc_start: 0.7574 (pp20) cc_final: 0.7366 (pm20) REVERT: A 575 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7500 (ttp80) REVERT: A 580 ASN cc_start: 0.7986 (m110) cc_final: 0.7691 (m-40) REVERT: A 785 TYR cc_start: 0.8580 (m-80) cc_final: 0.8004 (m-80) REVERT: A 959 ILE cc_start: 0.9243 (tt) cc_final: 0.9011 (mm) REVERT: A 1027 ASN cc_start: 0.7975 (m-40) cc_final: 0.7746 (m110) REVERT: A 1091 LYS cc_start: 0.8466 (mttt) cc_final: 0.7999 (mttm) REVERT: A 1414 TYR cc_start: 0.8348 (m-10) cc_final: 0.8125 (m-10) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2724 time to fit residues: 71.7071 Evaluate side-chains 103 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9896 Z= 0.195 Angle : 0.632 9.610 13337 Z= 0.330 Chirality : 0.042 0.137 1529 Planarity : 0.004 0.043 1654 Dihedral : 6.735 68.364 1318 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.01 % Allowed : 7.18 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1190 helix: 0.26 (0.19), residues: 715 sheet: -1.59 (0.78), residues: 40 loop : -2.44 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 453 HIS 0.007 0.001 HIS A 892 PHE 0.016 0.001 PHE A 157 TYR 0.020 0.001 TYR A 477 ARG 0.006 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8064 (tm-30) REVERT: A 202 PHE cc_start: 0.8418 (m-10) cc_final: 0.8166 (t80) REVERT: A 231 MET cc_start: 0.9207 (mmm) cc_final: 0.8910 (mmm) REVERT: A 404 LYS cc_start: 0.7977 (mttt) cc_final: 0.7524 (tptp) REVERT: A 575 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7311 (ttp80) REVERT: A 580 ASN cc_start: 0.7729 (m110) cc_final: 0.7415 (m-40) REVERT: A 1027 ASN cc_start: 0.8089 (m-40) cc_final: 0.7882 (m-40) REVERT: A 1091 LYS cc_start: 0.8325 (mttt) cc_final: 0.7945 (mttm) outliers start: 11 outliers final: 7 residues processed: 130 average time/residue: 0.2476 time to fit residues: 44.4849 Evaluate side-chains 106 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.0020 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 0.0670 chunk 108 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 0.9930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS A 569 GLN A 676 HIS A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9896 Z= 0.175 Angle : 0.563 7.713 13337 Z= 0.299 Chirality : 0.041 0.151 1529 Planarity : 0.004 0.038 1654 Dihedral : 5.779 70.801 1318 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.84 % Allowed : 8.38 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1190 helix: 0.83 (0.19), residues: 716 sheet: -0.85 (0.83), residues: 41 loop : -2.30 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 453 HIS 0.018 0.002 HIS A 542 PHE 0.014 0.001 PHE A 257 TYR 0.017 0.001 TYR A1097 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9273 (mm-30) REVERT: A 202 PHE cc_start: 0.8494 (m-10) cc_final: 0.8192 (t80) REVERT: A 231 MET cc_start: 0.9206 (mmm) cc_final: 0.8928 (mmm) REVERT: A 404 LYS cc_start: 0.7964 (mttt) cc_final: 0.7508 (tptp) REVERT: A 520 MET cc_start: 0.5302 (mmt) cc_final: 0.4898 (pmm) REVERT: A 575 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7442 (ttp80) REVERT: A 578 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6745 (mmt) REVERT: A 580 ASN cc_start: 0.7435 (m110) cc_final: 0.7172 (m-40) REVERT: A 993 MET cc_start: 0.7941 (tpp) cc_final: 0.7663 (mmm) REVERT: A 1091 LYS cc_start: 0.8224 (mttt) cc_final: 0.7891 (mttm) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.2537 time to fit residues: 44.0824 Evaluate side-chains 109 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9896 Z= 0.172 Angle : 0.546 8.741 13337 Z= 0.290 Chirality : 0.041 0.134 1529 Planarity : 0.004 0.039 1654 Dihedral : 5.501 66.058 1318 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.75 % Allowed : 10.22 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1190 helix: 1.20 (0.20), residues: 718 sheet: -0.56 (0.87), residues: 41 loop : -2.17 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.012 0.001 HIS A 542 PHE 0.012 0.001 PHE A 257 TYR 0.017 0.001 TYR A1097 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.5893 (mmtt) cc_final: 0.5557 (mptt) REVERT: A 20 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9303 (mm-30) REVERT: A 202 PHE cc_start: 0.8505 (m-10) cc_final: 0.8197 (t80) REVERT: A 231 MET cc_start: 0.9201 (mmm) cc_final: 0.8887 (mmm) REVERT: A 354 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7030 (t80) REVERT: A 384 ARG cc_start: 0.8090 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: A 404 LYS cc_start: 0.7980 (mttt) cc_final: 0.7557 (tptp) REVERT: A 430 TYR cc_start: 0.5877 (m-10) cc_final: 0.5327 (m-80) REVERT: A 520 MET cc_start: 0.5342 (mmt) cc_final: 0.5048 (pmm) REVERT: A 575 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7628 (ttp80) REVERT: A 580 ASN cc_start: 0.7410 (m110) cc_final: 0.7144 (m-40) REVERT: A 680 MET cc_start: 0.7236 (mmm) cc_final: 0.6858 (mmm) REVERT: A 841 MET cc_start: 0.7782 (tpp) cc_final: 0.7563 (tmm) REVERT: A 1091 LYS cc_start: 0.8175 (mttt) cc_final: 0.7866 (mttm) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2525 time to fit residues: 40.1625 Evaluate side-chains 109 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9896 Z= 0.202 Angle : 0.572 12.335 13337 Z= 0.300 Chirality : 0.041 0.135 1529 Planarity : 0.004 0.038 1654 Dihedral : 5.370 62.962 1318 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.49 % Allowed : 10.87 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1190 helix: 1.29 (0.20), residues: 717 sheet: -0.54 (0.86), residues: 41 loop : -2.03 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.013 0.001 PHE A 257 TYR 0.036 0.001 TYR A 477 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.6432 (mmtt) cc_final: 0.6164 (mmtt) REVERT: A 202 PHE cc_start: 0.8514 (m-10) cc_final: 0.8236 (t80) REVERT: A 354 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7040 (t80) REVERT: A 372 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4295 (tt) REVERT: A 404 LYS cc_start: 0.8045 (mttt) cc_final: 0.7632 (tptp) REVERT: A 430 TYR cc_start: 0.5869 (m-10) cc_final: 0.5267 (m-80) REVERT: A 520 MET cc_start: 0.5290 (mmt) cc_final: 0.5037 (pmm) REVERT: A 575 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7721 (ttp80) REVERT: A 580 ASN cc_start: 0.7483 (m110) cc_final: 0.7219 (m-40) REVERT: A 993 MET cc_start: 0.7920 (tpp) cc_final: 0.7600 (mmm) REVERT: A 1414 TYR cc_start: 0.8079 (m-10) cc_final: 0.7857 (m-80) outliers start: 27 outliers final: 18 residues processed: 126 average time/residue: 0.2656 time to fit residues: 45.8597 Evaluate side-chains 120 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9896 Z= 0.159 Angle : 0.548 9.408 13337 Z= 0.286 Chirality : 0.040 0.136 1529 Planarity : 0.003 0.039 1654 Dihedral : 5.124 57.959 1318 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.93 % Allowed : 12.15 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1190 helix: 1.38 (0.19), residues: 726 sheet: -0.47 (0.87), residues: 41 loop : -2.05 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 453 HIS 0.005 0.001 HIS A 676 PHE 0.010 0.001 PHE A 257 TYR 0.015 0.001 TYR A1097 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8578 (m-10) cc_final: 0.8282 (t80) REVERT: A 354 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.6984 (t80) REVERT: A 372 LEU cc_start: 0.4696 (OUTLIER) cc_final: 0.4276 (tt) REVERT: A 404 LYS cc_start: 0.8024 (mttt) cc_final: 0.7621 (tptp) REVERT: A 520 MET cc_start: 0.5284 (mmt) cc_final: 0.5052 (pmm) REVERT: A 575 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7697 (ttp80) REVERT: A 580 ASN cc_start: 0.7534 (m110) cc_final: 0.7277 (m110) REVERT: A 680 MET cc_start: 0.7265 (mmm) cc_final: 0.6747 (mmm) REVERT: A 690 MET cc_start: 0.9298 (mmp) cc_final: 0.9070 (mmm) REVERT: A 1027 ASN cc_start: 0.8247 (m110) cc_final: 0.8028 (m110) outliers start: 21 outliers final: 14 residues processed: 120 average time/residue: 0.2508 time to fit residues: 42.9179 Evaluate side-chains 113 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 998 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9896 Z= 0.189 Angle : 0.565 9.757 13337 Z= 0.295 Chirality : 0.041 0.131 1529 Planarity : 0.003 0.039 1654 Dihedral : 5.022 54.214 1318 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.75 % Allowed : 12.80 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1190 helix: 1.44 (0.19), residues: 722 sheet: -0.50 (0.87), residues: 41 loop : -1.99 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.011 0.001 PHE A 257 TYR 0.017 0.001 TYR A1097 ARG 0.004 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8580 (m-10) cc_final: 0.8294 (t80) REVERT: A 354 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7083 (t80) REVERT: A 372 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4309 (tt) REVERT: A 404 LYS cc_start: 0.8060 (mttt) cc_final: 0.7647 (tptp) REVERT: A 575 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7822 (ttp80) REVERT: A 580 ASN cc_start: 0.7476 (m110) cc_final: 0.7227 (m110) REVERT: A 680 MET cc_start: 0.7233 (mmm) cc_final: 0.7028 (mmm) REVERT: A 1027 ASN cc_start: 0.8257 (m110) cc_final: 0.8026 (m110) REVERT: A 1169 THR cc_start: 0.7803 (p) cc_final: 0.7564 (t) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.2371 time to fit residues: 39.1722 Evaluate side-chains 114 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1237 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.0980 chunk 34 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9896 Z= 0.142 Angle : 0.553 9.724 13337 Z= 0.286 Chirality : 0.040 0.163 1529 Planarity : 0.003 0.040 1654 Dihedral : 4.763 48.054 1318 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.75 % Allowed : 14.00 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1190 helix: 1.65 (0.20), residues: 721 sheet: -0.36 (0.88), residues: 41 loop : -1.96 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 453 HIS 0.004 0.001 HIS A 278 PHE 0.008 0.001 PHE A 257 TYR 0.015 0.001 TYR A1097 ARG 0.003 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8515 (m-10) cc_final: 0.8273 (t80) REVERT: A 354 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7065 (t80) REVERT: A 372 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4254 (tt) REVERT: A 404 LYS cc_start: 0.8146 (mttt) cc_final: 0.7721 (tptp) REVERT: A 542 HIS cc_start: 0.3971 (OUTLIER) cc_final: 0.3627 (p-80) REVERT: A 575 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7824 (ttp80) REVERT: A 580 ASN cc_start: 0.7492 (m110) cc_final: 0.7232 (m110) REVERT: A 690 MET cc_start: 0.9284 (mmp) cc_final: 0.9058 (mmm) REVERT: A 1027 ASN cc_start: 0.8280 (m110) cc_final: 0.8045 (m110) REVERT: A 1169 THR cc_start: 0.7799 (p) cc_final: 0.7556 (t) REVERT: A 1388 ASP cc_start: 0.8730 (t0) cc_final: 0.8441 (p0) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.2618 time to fit residues: 43.4692 Evaluate side-chains 115 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1135 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9896 Z= 0.163 Angle : 0.554 9.621 13337 Z= 0.287 Chirality : 0.041 0.156 1529 Planarity : 0.004 0.054 1654 Dihedral : 4.653 44.397 1318 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.66 % Allowed : 14.00 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1190 helix: 1.69 (0.20), residues: 717 sheet: -0.41 (0.89), residues: 41 loop : -1.97 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 453 HIS 0.008 0.001 HIS A 676 PHE 0.028 0.001 PHE A 170 TYR 0.016 0.001 TYR A1097 ARG 0.012 0.000 ARG A 866 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8504 (m-10) cc_final: 0.8261 (t80) REVERT: A 354 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 372 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.4245 (tt) REVERT: A 404 LYS cc_start: 0.8138 (mttt) cc_final: 0.7717 (tptp) REVERT: A 575 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7914 (ttp80) REVERT: A 580 ASN cc_start: 0.7506 (m110) cc_final: 0.7246 (m110) REVERT: A 690 MET cc_start: 0.9286 (mmp) cc_final: 0.9056 (mmm) REVERT: A 1027 ASN cc_start: 0.8299 (m110) cc_final: 0.8054 (m110) REVERT: A 1169 THR cc_start: 0.7759 (p) cc_final: 0.7512 (t) REVERT: A 1388 ASP cc_start: 0.8750 (t0) cc_final: 0.8462 (p0) outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 0.2467 time to fit residues: 39.0455 Evaluate side-chains 112 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1135 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 40.0000 chunk 75 optimal weight: 0.0040 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9896 Z= 0.151 Angle : 0.569 10.890 13337 Z= 0.290 Chirality : 0.041 0.157 1529 Planarity : 0.004 0.056 1654 Dihedral : 4.458 38.002 1318 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.29 % Allowed : 14.55 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1190 helix: 1.76 (0.20), residues: 722 sheet: -0.36 (0.89), residues: 41 loop : -1.96 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 453 HIS 0.007 0.001 HIS A 676 PHE 0.009 0.001 PHE A 257 TYR 0.015 0.001 TYR A1097 ARG 0.012 0.000 ARG A 866 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8511 (m-10) cc_final: 0.8189 (t80) REVERT: A 372 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.4190 (tt) REVERT: A 404 LYS cc_start: 0.8177 (mttt) cc_final: 0.7741 (tptp) REVERT: A 575 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7924 (ttp80) REVERT: A 690 MET cc_start: 0.9291 (mmp) cc_final: 0.9062 (mmm) REVERT: A 1169 THR cc_start: 0.7792 (p) cc_final: 0.7552 (t) REVERT: A 1388 ASP cc_start: 0.8669 (t0) cc_final: 0.8429 (p0) outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 0.2457 time to fit residues: 38.7620 Evaluate side-chains 111 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1135 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.140033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100963 restraints weight = 21945.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.104697 restraints weight = 8499.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107061 restraints weight = 4723.786| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9896 Z= 0.183 Angle : 0.583 10.670 13337 Z= 0.299 Chirality : 0.041 0.154 1529 Planarity : 0.004 0.051 1654 Dihedral : 4.341 32.066 1318 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.38 % Allowed : 14.92 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1190 helix: 1.68 (0.20), residues: 721 sheet: -0.45 (0.89), residues: 41 loop : -1.85 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 453 HIS 0.006 0.001 HIS A 676 PHE 0.024 0.001 PHE A 170 TYR 0.017 0.001 TYR A1097 ARG 0.012 0.000 ARG A 866 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.07 seconds wall clock time: 37 minutes 35.18 seconds (2255.18 seconds total)