Starting phenix.real_space_refine on Mon Mar 18 00:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbd_11151/03_2024/6zbd_11151.pdb" } resolution = 3.21 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= -0.002 sd= 0.042 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 19 5.16 5 C 6189 2.51 5 N 1576 2.21 5 O 1839 1.98 5 H 9896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 9538 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 14, 'TRANS': 546} Chain breaks: 4 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1901 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "C" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4679 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3401 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 8.94, per 1000 atoms: 0.46 Number of scatterers: 19519 At special positions: 0 Unit cell: (104.081, 134.125, 139.49, 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 19 16.00 O 1839 8.00 N 1576 7.00 C 6189 6.00 H 9896 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.10 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=2.02 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: 13.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.600A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.218A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.256A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.903A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.638A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.128A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.960A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.705A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.736A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.980A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 removed outlier: 3.742A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.612A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.609A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 666 removed outlier: 4.279A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.645A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'B' and resid 795 through 822 Processing helix chain 'B' and resid 825 through 831 removed outlier: 4.167A pdb=" N VAL B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.696A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.953A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 3.995A pdb=" N VAL C 966 " --> pdb=" O PRO C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.764A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1025 removed outlier: 3.606A pdb=" N LYS C1019 " --> pdb=" O ASN C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1033 through 1101 removed outlier: 3.535A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1108 No H-bonds generated for 'chain 'C' and resid 1106 through 1108' Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.696A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.063A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.628A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.524A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.530A pdb=" N LEU C1239 " --> pdb=" O GLU C1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1236 through 1239' Processing helix chain 'D' and resid 1342 through 1346 Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.620A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.643A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.606A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.681A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.553A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 14.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9894 1.04 - 1.23: 273 1.23 - 1.43: 3661 1.43 - 1.62: 5807 1.62 - 1.82: 32 Bond restraints: 19667 Sorted by residual: bond pdb=" N VAL A 419 " pdb=" CA VAL A 419 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.45e+01 bond pdb=" N VAL B 819 " pdb=" CA VAL B 819 " ideal model delta sigma weight residual 1.460 1.505 -0.045 1.19e-02 7.06e+03 1.42e+01 bond pdb=" N ILE C1211 " pdb=" CA ILE C1211 " ideal model delta sigma weight residual 1.462 1.504 -0.042 1.14e-02 7.69e+03 1.36e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.485 -0.027 7.40e-03 1.83e+04 1.35e+01 bond pdb=" N LEU B 834 " pdb=" CA LEU B 834 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.27e-02 6.20e+03 1.29e+01 ... (remaining 19662 not shown) Histogram of bond angle deviations from ideal: 99.34 - 105.85: 292 105.85 - 112.36: 23187 112.36 - 118.88: 4877 118.88 - 125.39: 7273 125.39 - 131.91: 198 Bond angle restraints: 35827 Sorted by residual: angle pdb=" CA GLY A 424 " pdb=" C GLY A 424 " pdb=" O GLY A 424 " ideal model delta sigma weight residual 121.55 114.32 7.23 1.22e+00 6.72e-01 3.51e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.03 6.25 1.09e+00 8.42e-01 3.28e+01 angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 114.84 6.08 1.12e+00 7.97e-01 2.94e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.95 7.05 1.30e+00 5.92e-01 2.94e+01 angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.16 -5.80 1.09e+00 8.42e-01 2.84e+01 ... (remaining 35822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8388 17.90 - 35.79: 537 35.79 - 53.69: 122 53.69 - 71.58: 33 71.58 - 89.48: 12 Dihedral angle restraints: 9092 sinusoidal: 5056 harmonic: 4036 Sorted by residual: dihedral pdb=" CB CYS B 813 " pdb=" SG CYS B 813 " pdb=" SG CYS B 845 " pdb=" CB CYS B 845 " ideal model delta sinusoidal sigma weight residual 93.00 148.35 -55.35 1 1.00e+01 1.00e-02 4.14e+01 dihedral pdb=" C VAL C1210 " pdb=" N VAL C1210 " pdb=" CA VAL C1210 " pdb=" CB VAL C1210 " ideal model delta harmonic sigma weight residual -122.00 -131.92 9.92 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA ASP A 466 " pdb=" C ASP A 466 " pdb=" N ASN A 467 " pdb=" CA ASN A 467 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 9089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 802 0.059 - 0.117: 498 0.117 - 0.176: 141 0.176 - 0.234: 31 0.234 - 0.293: 4 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA VAL C1105 " pdb=" N VAL C1105 " pdb=" C VAL C1105 " pdb=" CB VAL C1105 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB VAL B 819 " pdb=" CA VAL B 819 " pdb=" CG1 VAL B 819 " pdb=" CG2 VAL B 819 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE D1401 " pdb=" N ILE D1401 " pdb=" C ILE D1401 " pdb=" CB ILE D1401 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1473 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 424 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C GLY A 424 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 424 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 425 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C1099 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LEU C1099 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C1099 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C1100 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C GLN A 217 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.019 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2154 2.28 - 2.86: 46217 2.86 - 3.44: 48462 3.44 - 4.02: 62538 4.02 - 4.60: 99541 Nonbonded interactions: 258912 Sorted by model distance: nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.701 1.850 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.707 1.850 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.722 1.850 nonbonded pdb=" O ASN A 260 " pdb=" HG1 THR A 263 " model vdw 1.735 1.850 nonbonded pdb=" O GLN D1361 " pdb="HD22 ASN D1365 " model vdw 1.737 1.850 ... (remaining 258907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.260 Extract box with map and model: 5.970 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 56.560 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.048 9771 Z= 0.634 Angle : 1.191 7.516 13106 Z= 0.866 Chirality : 0.077 0.293 1476 Planarity : 0.006 0.044 1646 Dihedral : 13.677 89.475 3840 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.87 (0.23), residues: 1139 helix: 0.89 (0.16), residues: 898 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 814 PHE 0.016 0.003 PHE C1055 TYR 0.026 0.003 TYR A 683 ARG 0.005 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.546 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: symmetry clash 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: symmetry clash 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: 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 253 MET cc_start: 0.7857 (mtp) cc_final: 0.7525 (mtt) REVERT: C 1013 TYR cc_start: 0.7888 (t80) cc_final: 0.7597 (t80) REVERT: D 1459 LEU cc_start: 0.8547 (tp) cc_final: 0.8232 (tp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.6290 time to fit residues: 166.7838 Evaluate side-chains 102 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 640 GLN B 821 ASN B 853 ASN C1081 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9771 Z= 0.186 Angle : 0.556 5.617 13106 Z= 0.310 Chirality : 0.034 0.133 1476 Planarity : 0.004 0.044 1646 Dihedral : 4.197 22.037 1231 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.91 % Allowed : 6.89 % Favored : 92.20 % 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: 1.67 (0.24), residues: 1139 helix: 1.44 (0.17), residues: 910 sheet: None (None), residues: 0 loop : 0.01 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 896 PHE 0.013 0.001 PHE D1387 TYR 0.015 0.001 TYR D1347 ARG 0.002 0.000 ARG C1173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.750 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 0.6548 time to fit residues: 85.9996 Evaluate side-chains 88 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain C residue 1052 GLN Chi-restraints excluded: chain C residue 1056 ASP Chi-restraints excluded: chain D residue 1460 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 853 ASN B 856 ASN D1400 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9771 Z= 0.228 Angle : 0.530 5.839 13106 Z= 0.294 Chirality : 0.033 0.147 1476 Planarity : 0.003 0.042 1646 Dihedral : 4.101 34.962 1231 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.63 % Allowed : 8.07 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1139 helix: 1.77 (0.17), residues: 910 sheet: None (None), residues: 0 loop : 0.06 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 896 PHE 0.016 0.002 PHE B 806 TYR 0.013 0.001 TYR D1347 ARG 0.002 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.592 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: symmetry clash 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: symmetry clash 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 253 MET cc_start: 0.7991 (mtp) cc_final: 0.7563 (mtt) outliers start: 7 outliers final: 6 residues processed: 89 average time/residue: 0.6010 time to fit residues: 71.8324 Evaluate side-chains 81 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1052 GLN Chi-restraints excluded: chain C residue 1056 ASP Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain D residue 1460 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1161 GLN C1183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9771 Z= 0.158 Angle : 0.477 5.582 13106 Z= 0.262 Chirality : 0.032 0.161 1476 Planarity : 0.003 0.040 1646 Dihedral : 3.864 35.713 1231 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.91 % Allowed : 8.34 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.25), residues: 1139 helix: 2.18 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.18 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 814 PHE 0.017 0.001 PHE B 806 TYR 0.012 0.001 TYR D1347 ARG 0.001 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.709 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8064 (mtp) cc_final: 0.7684 (mtt) REVERT: C 1009 ASN cc_start: 0.7295 (m-40) cc_final: 0.7019 (m110) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.5790 time to fit residues: 71.6781 Evaluate side-chains 79 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1459 LEU Chi-restraints excluded: chain D residue 1460 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9771 Z= 0.279 Angle : 0.515 6.094 13106 Z= 0.289 Chirality : 0.034 0.155 1476 Planarity : 0.003 0.042 1646 Dihedral : 3.906 38.913 1231 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.36 % Allowed : 8.98 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.24), residues: 1139 helix: 2.17 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.08 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C1103 PHE 0.016 0.002 PHE D1496 TYR 0.014 0.001 TYR D1355 ARG 0.002 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.594 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1009 ASN cc_start: 0.7439 (m-40) cc_final: 0.7140 (m110) REVERT: D 1396 MET cc_start: 0.7381 (ptm) cc_final: 0.7050 (ptt) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.5532 time to fit residues: 65.9071 Evaluate side-chains 80 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1056 ASP Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Chi-restraints excluded: chain D residue 1460 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS C1108 ASN C1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9771 Z= 0.143 Angle : 0.462 5.704 13106 Z= 0.252 Chirality : 0.032 0.163 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.749 38.057 1231 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 10.06 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.22 (0.25), residues: 1139 helix: 2.56 (0.17), residues: 914 sheet: None (None), residues: 0 loop : 0.34 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS A 490 PHE 0.012 0.001 PHE B 806 TYR 0.010 0.001 TYR B 865 ARG 0.001 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.643 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: symmetry clash 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: symmetry clash REVERT: A 253 MET cc_start: 0.8119 (mtp) cc_final: 0.7777 (mtt) outliers start: 12 outliers final: 12 residues processed: 82 average time/residue: 0.5539 time to fit residues: 62.3484 Evaluate side-chains 82 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain C residue 1207 LEU Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9771 Z= 0.177 Angle : 0.464 5.425 13106 Z= 0.255 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.696 37.055 1231 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.91 % Allowed : 10.43 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.33 (0.25), residues: 1139 helix: 2.64 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.37 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1103 PHE 0.011 0.001 PHE B 852 TYR 0.012 0.001 TYR B 865 ARG 0.006 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.634 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8224 (mtp) cc_final: 0.7862 (mtt) outliers start: 10 outliers final: 10 residues processed: 74 average time/residue: 0.5704 time to fit residues: 58.2715 Evaluate side-chains 79 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9771 Z= 0.167 Angle : 0.458 5.231 13106 Z= 0.253 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.657 36.411 1231 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.18 % Allowed : 10.24 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.49 (0.25), residues: 1139 helix: 2.75 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.39 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1103 PHE 0.018 0.001 PHE B 806 TYR 0.011 0.001 TYR B 865 ARG 0.007 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.630 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8184 (mtp) cc_final: 0.7876 (mtt) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.5412 time to fit residues: 57.9490 Evaluate side-chains 79 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9771 Z= 0.200 Angle : 0.467 5.435 13106 Z= 0.258 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.659 35.709 1231 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.18 % Allowed : 10.15 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.48 (0.25), residues: 1139 helix: 2.76 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.33 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1103 PHE 0.018 0.001 PHE B 806 TYR 0.013 0.001 TYR B 865 ARG 0.006 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.579 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8257 (mtp) cc_final: 0.8039 (mtm) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 0.5689 time to fit residues: 60.0542 Evaluate side-chains 80 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9771 Z= 0.160 Angle : 0.458 5.645 13106 Z= 0.252 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.038 1646 Dihedral : 3.610 34.928 1231 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 10.43 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.65 (0.25), residues: 1139 helix: 2.87 (0.17), residues: 918 sheet: None (None), residues: 0 loop : 0.37 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1103 PHE 0.018 0.001 PHE B 806 TYR 0.011 0.001 TYR B 865 ARG 0.006 0.000 ARG A 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 1.705 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.5714 time to fit residues: 59.5391 Evaluate side-chains 80 residues out of total 1103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain C residue 1161 GLN Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.075193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058855 restraints weight = 100836.314| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.57 r_work: 0.3149 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9771 Z= 0.143 Angle : 0.446 5.644 13106 Z= 0.243 Chirality : 0.031 0.133 1476 Planarity : 0.003 0.038 1646 Dihedral : 3.556 33.549 1231 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.09 % Allowed : 10.61 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3.81 (0.25), residues: 1139 helix: 2.98 (0.17), residues: 918 sheet: None (None), residues: 0 loop : 0.46 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C1103 PHE 0.017 0.001 PHE B 806 TYR 0.010 0.001 TYR B 865 ARG 0.006 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.17 seconds wall clock time: 74 minutes 8.72 seconds (4448.72 seconds total)