Starting phenix.real_space_refine on Sat Jul 20 05:12:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_2024/8jwf_36681_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_2024/8jwf_36681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_2024/8jwf_36681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_2024/8jwf_36681_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jwf_36681/07_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 Residue "A ARG 1116": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.72, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.7 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: 1.13 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: 3.35 Time building geometry restraints manager: 4.38 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: 98.36 - 105.47: 114 105.47 - 112.58: 5080 112.58 - 119.69: 3399 119.69 - 126.81: 4684 126.81 - 133.92: 60 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 2.520 nonbonded pdb=" N PHE A 385 " pdb=" OE2 GLU A 394 " model vdw 2.222 2.520 nonbonded pdb=" O LEU A 518 " pdb=" NZ LYS A 522 " model vdw 2.229 2.520 nonbonded pdb=" O ASP A1014 " pdb=" NZ LYS A1018 " model vdw 2.231 2.520 nonbonded pdb=" O GLU A 824 " pdb=" OG SER A 827 " model vdw 2.233 2.440 ... (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: 1.070 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.100 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.146 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: 0.2577 time to fit residues: 67.6687 Evaluate side-chains 103 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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: 0.6980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 0.1980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 108 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 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9896 Z= 0.200 Angle : 0.628 10.381 13337 Z= 0.327 Chirality : 0.043 0.139 1529 Planarity : 0.004 0.040 1654 Dihedral : 6.644 68.196 1318 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.20 % Allowed : 7.37 % Favored : 91.44 % 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: -1.20 (0.24), residues: 1190 helix: 0.24 (0.19), residues: 716 sheet: -1.65 (0.78), residues: 40 loop : -2.48 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 453 HIS 0.006 0.001 HIS A 892 PHE 0.017 0.002 PHE A 257 TYR 0.021 0.002 TYR A 477 ARG 0.007 0.000 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 139 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.107 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 161 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8072 (tm-30) REVERT: A 202 PHE cc_start: 0.8487 (m-10) cc_final: 0.8179 (t80) REVERT: A 404 LYS cc_start: 0.7987 (mttt) cc_final: 0.7526 (tptp) REVERT: A 575 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7351 (ttp80) REVERT: A 922 MET cc_start: 0.8150 (mmp) cc_final: 0.7907 (mmp) REVERT: A 1091 LYS cc_start: 0.8308 (mttt) cc_final: 0.7926 (mttm) REVERT: A 1414 TYR cc_start: 0.8227 (m-10) cc_final: 0.7902 (m-10) outliers start: 13 outliers final: 7 residues processed: 133 average time/residue: 0.2313 time to fit residues: 42.8610 Evaluate side-chains 105 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 542 HIS Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1120 ASN 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: 6.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 0.0980 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9896 Z= 0.202 Angle : 0.579 11.813 13337 Z= 0.305 Chirality : 0.042 0.149 1529 Planarity : 0.004 0.042 1654 Dihedral : 5.865 72.118 1318 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.12 % Allowed : 9.02 % Favored : 88.86 % 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: -0.52 (0.24), residues: 1190 helix: 0.83 (0.19), residues: 704 sheet: -0.96 (0.84), residues: 41 loop : -2.27 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 453 HIS 0.019 0.002 HIS A 542 PHE 0.015 0.001 PHE A 257 TYR 0.018 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 127 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.081 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 202 PHE cc_start: 0.8529 (m-10) cc_final: 0.8223 (t80) REVERT: A 404 LYS cc_start: 0.7969 (mttt) cc_final: 0.7508 (tptp) REVERT: A 430 TYR cc_start: 0.6040 (m-80) cc_final: 0.5521 (m-80) REVERT: A 453 TRP cc_start: 0.7354 (t-100) cc_final: 0.7124 (t-100) REVERT: A 575 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7605 (ttp80) REVERT: A 578 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6808 (mmt) REVERT: A 841 MET cc_start: 0.7825 (tpp) cc_final: 0.7338 (tpt) REVERT: A 922 MET cc_start: 0.8158 (mmp) cc_final: 0.7900 (mmp) REVERT: A 1091 LYS cc_start: 0.8247 (mttt) cc_final: 0.7899 (mttm) outliers start: 23 outliers final: 14 residues processed: 117 average time/residue: 0.2413 time to fit residues: 38.8206 Evaluate side-chains 111 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 146 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 LEU 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 578 MET Chi-restraints excluded: chain A residue 1120 ASN 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: 0.0870 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9896 Z= 0.234 Angle : 0.585 8.417 13337 Z= 0.314 Chirality : 0.043 0.142 1529 Planarity : 0.004 0.042 1654 Dihedral : 5.728 68.660 1318 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.85 % Allowed : 10.77 % Favored : 86.37 % 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: -0.33 (0.25), residues: 1190 helix: 0.98 (0.20), residues: 705 sheet: -0.90 (0.85), residues: 41 loop : -2.17 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.014 0.002 PHE A 257 TYR 0.021 0.002 TYR A 813 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 138 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8568 (m-10) cc_final: 0.8268 (t80) REVERT: A 404 LYS cc_start: 0.8019 (mttt) cc_final: 0.7580 (tptp) REVERT: A 575 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7826 (ttp80) REVERT: A 841 MET cc_start: 0.7865 (tpp) cc_final: 0.7580 (tmm) REVERT: A 922 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7737 (mmp) REVERT: A 1259 MET cc_start: 0.7980 (tpp) cc_final: 0.7699 (ttm) outliers start: 31 outliers final: 21 residues processed: 123 average time/residue: 0.2506 time to fit residues: 42.6593 Evaluate side-chains 119 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain A residue 118 VAL 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 324 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1121 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 Chi-restraints excluded: chain A residue 1336 ASP 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN A 853 ASN A1243 ASN A1370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9896 Z= 0.398 Angle : 0.734 10.148 13337 Z= 0.390 Chirality : 0.047 0.178 1529 Planarity : 0.005 0.050 1654 Dihedral : 6.189 72.068 1318 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.78 % Allowed : 12.43 % Favored : 83.79 % 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: -0.82 (0.24), residues: 1190 helix: 0.52 (0.19), residues: 715 sheet: -1.29 (0.83), residues: 40 loop : -2.29 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 453 HIS 0.029 0.003 HIS A 542 PHE 0.022 0.002 PHE A 78 TYR 0.028 0.002 TYR A 813 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 142 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8701 (m-10) cc_final: 0.8354 (t80) REVERT: A 231 MET cc_start: 0.9055 (mmm) cc_final: 0.8701 (mmm) REVERT: A 404 LYS cc_start: 0.8112 (mttt) cc_final: 0.7650 (tptp) REVERT: A 575 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7990 (ttp80) REVERT: A 788 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8348 (t70) REVERT: A 834 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 922 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7827 (mmp) outliers start: 41 outliers final: 27 residues processed: 127 average time/residue: 0.2223 time to fit residues: 40.2540 Evaluate side-chains 123 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 118 VAL 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 324 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 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1336 ASP 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: 0.9980 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 HIS A 580 ASN A 826 ASN A 998 ASN A1243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9896 Z= 0.177 Angle : 0.563 9.136 13337 Z= 0.297 Chirality : 0.041 0.138 1529 Planarity : 0.004 0.046 1654 Dihedral : 5.745 68.792 1318 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.67 % Allowed : 14.18 % Favored : 83.15 % 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: -0.19 (0.25), residues: 1190 helix: 1.07 (0.19), residues: 728 sheet: -0.93 (0.84), residues: 41 loop : -2.24 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 453 HIS 0.007 0.001 HIS A 542 PHE 0.014 0.001 PHE A 202 TYR 0.014 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 135 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 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 202 PHE cc_start: 0.8709 (m-10) cc_final: 0.8408 (t80) REVERT: A 231 MET cc_start: 0.9138 (mmm) cc_final: 0.8805 (mmm) REVERT: A 354 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6984 (t80) REVERT: A 404 LYS cc_start: 0.8026 (mttt) cc_final: 0.7572 (tptp) REVERT: A 542 HIS cc_start: 0.4160 (OUTLIER) cc_final: 0.3375 (p-80) REVERT: A 575 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7892 (ttp80) REVERT: A 690 MET cc_start: 0.9240 (mmp) cc_final: 0.8998 (mmm) REVERT: A 788 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8018 (t70) REVERT: A 841 MET cc_start: 0.7794 (tpp) cc_final: 0.7516 (tmm) REVERT: A 922 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7712 (mmp) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.2305 time to fit residues: 40.0348 Evaluate side-chains 118 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 81 ILE 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 350 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0170 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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: 0.7382 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9896 Z= 0.161 Angle : 0.547 8.704 13337 Z= 0.288 Chirality : 0.040 0.134 1529 Planarity : 0.004 0.047 1654 Dihedral : 5.494 64.852 1318 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.04 % Allowed : 14.55 % Favored : 82.41 % 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: 0.15 (0.25), residues: 1190 helix: 1.39 (0.20), residues: 716 sheet: -0.80 (0.86), residues: 41 loop : -2.10 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 453 HIS 0.017 0.002 HIS A 542 PHE 0.033 0.001 PHE A1033 TYR 0.022 0.001 TYR A1414 ARG 0.002 0.000 ARG A 133 *********************** 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 130 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8670 (m-10) cc_final: 0.8386 (t80) REVERT: A 231 MET cc_start: 0.9152 (mmm) cc_final: 0.8844 (mmm) REVERT: A 354 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6983 (t80) REVERT: A 404 LYS cc_start: 0.8040 (mttt) cc_final: 0.7593 (tptp) REVERT: A 575 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7813 (ttp80) REVERT: A 680 MET cc_start: 0.7616 (mmm) cc_final: 0.7396 (mmm) REVERT: A 690 MET cc_start: 0.9269 (mmp) cc_final: 0.9019 (mmm) REVERT: A 788 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7768 (t70) REVERT: A 802 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6635 (tt) REVERT: A 841 MET cc_start: 0.7771 (tpp) cc_final: 0.7534 (tmm) REVERT: A 922 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7642 (mmp) outliers start: 33 outliers final: 19 residues processed: 117 average time/residue: 0.2231 time to fit residues: 36.8583 Evaluate side-chains 115 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS 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 350 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 452 TRP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1336 ASP 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: 6.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7370 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9896 Z= 0.161 Angle : 0.553 8.944 13337 Z= 0.290 Chirality : 0.040 0.133 1529 Planarity : 0.003 0.046 1654 Dihedral : 5.185 59.071 1318 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.04 % Allowed : 14.36 % Favored : 82.60 % 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: 0.36 (0.25), residues: 1190 helix: 1.50 (0.20), residues: 722 sheet: -0.65 (0.87), residues: 41 loop : -1.96 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 453 HIS 0.004 0.001 HIS A 278 PHE 0.028 0.001 PHE A1033 TYR 0.016 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 136 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8635 (m-10) cc_final: 0.8327 (t80) REVERT: A 231 MET cc_start: 0.9150 (mmm) cc_final: 0.8830 (mmm) REVERT: A 354 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 404 LYS cc_start: 0.7977 (mttt) cc_final: 0.7520 (tptp) REVERT: A 575 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7781 (ttp80) REVERT: A 802 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6578 (tt) REVERT: A 922 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7633 (mmp) REVERT: A 1027 ASN cc_start: 0.8240 (m-40) cc_final: 0.8001 (m110) outliers start: 33 outliers final: 26 residues processed: 125 average time/residue: 0.2375 time to fit residues: 41.4883 Evaluate side-chains 123 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR 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 298 THR 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 526 THR Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1120 ASN Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7375 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9896 Z= 0.173 Angle : 0.588 11.136 13337 Z= 0.307 Chirality : 0.041 0.132 1529 Planarity : 0.003 0.046 1654 Dihedral : 5.072 55.548 1318 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.85 % Allowed : 14.36 % Favored : 82.78 % 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: 0.35 (0.25), residues: 1190 helix: 1.50 (0.20), residues: 726 sheet: -0.68 (0.87), residues: 41 loop : -2.00 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.022 0.001 PHE A1033 TYR 0.016 0.001 TYR A1097 ARG 0.002 0.000 ARG A 133 *********************** 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 130 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7600 (mmmt) cc_final: 0.6971 (mptt) REVERT: A 202 PHE cc_start: 0.8591 (m-10) cc_final: 0.8339 (t80) REVERT: A 231 MET cc_start: 0.9157 (mmm) cc_final: 0.8809 (mmm) REVERT: A 281 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 354 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7089 (t80) REVERT: A 404 LYS cc_start: 0.7969 (mttt) cc_final: 0.7516 (tptp) REVERT: A 575 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7880 (ttp80) REVERT: A 922 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7626 (mmp) REVERT: A 1017 ASN cc_start: 0.8288 (m-40) cc_final: 0.7848 (p0) outliers start: 31 outliers final: 25 residues processed: 120 average time/residue: 0.2421 time to fit residues: 40.9320 Evaluate side-chains 123 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 THR 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 526 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 863 MET Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1336 ASP 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: 2.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9896 Z= 0.215 Angle : 0.614 10.498 13337 Z= 0.322 Chirality : 0.042 0.140 1529 Planarity : 0.004 0.045 1654 Dihedral : 5.068 52.973 1318 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.85 % Allowed : 14.64 % Favored : 82.50 % 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: 0.32 (0.25), residues: 1190 helix: 1.40 (0.19), residues: 726 sheet: -0.77 (0.86), residues: 41 loop : -1.86 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.023 0.001 PHE A 170 TYR 0.018 0.001 TYR A1097 ARG 0.002 0.000 ARG A 133 ********************** 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 130 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.8627 (m-10) cc_final: 0.8396 (t80) REVERT: A 231 MET cc_start: 0.9123 (mmm) cc_final: 0.8801 (mmm) REVERT: A 281 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 354 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.7042 (t80) REVERT: A 404 LYS cc_start: 0.7960 (mttt) cc_final: 0.7543 (tptp) REVERT: A 575 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8067 (ttp80) REVERT: A 922 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7745 (mmp) REVERT: A 1017 ASN cc_start: 0.8288 (m-40) cc_final: 0.7860 (p0) outliers start: 31 outliers final: 25 residues processed: 121 average time/residue: 0.2401 time to fit residues: 40.9964 Evaluate side-chains 125 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 THR 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 201 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 336 ILE 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 526 THR Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 937 THR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1320 ILE Chi-restraints excluded: chain A residue 1336 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.138689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.101480 restraints weight = 22672.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.104518 restraints weight = 8862.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.107481 restraints weight = 4955.194| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9896 Z= 0.171 Angle : 0.575 10.550 13337 Z= 0.299 Chirality : 0.041 0.133 1529 Planarity : 0.003 0.046 1654 Dihedral : 4.810 47.342 1318 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.67 % Allowed : 14.83 % Favored : 82.50 % 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: 0.56 (0.25), residues: 1190 helix: 1.61 (0.20), residues: 718 sheet: -0.74 (0.86), residues: 41 loop : -1.72 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 453 HIS 0.005 0.001 HIS A 278 PHE 0.022 0.001 PHE A 170 TYR 0.016 0.001 TYR A1097 ARG 0.002 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.10 seconds wall clock time: 35 minutes 22.50 seconds (2122.50 seconds total)