Starting phenix.real_space_refine on Thu Sep 18 20:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_11151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_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 { model { file = "/net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_11151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_11151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_11151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbd_11151/09_2025/6zbd_11151.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.62, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 606.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 3.89 Time building geometry restraints manager: 1.95 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: 0.00 - 1.59: 30397 1.59 - 3.18: 4945 3.18 - 4.77: 397 4.77 - 6.36: 81 6.36 - 7.95: 7 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 2.450 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.707 2.450 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.722 2.450 nonbonded pdb=" O ASN A 260 " pdb=" HG1 THR A 263 " model vdw 1.735 2.450 nonbonded pdb=" O GLN D1361 " pdb="HD22 ASN D1365 " model vdw 1.737 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.650 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.970 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- 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 0.069 9773 Z= 0.731 Angle : 1.227 29.724 13110 Z= 0.877 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (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 ARG 0.005 0.001 ARG A 225 TYR 0.026 0.003 TYR A 683 PHE 0.016 0.003 PHE C1055 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.01010 ( 9771) covalent geometry : angle 1.19096 (13106) SS BOND : bond 0.04982 ( 2) SS BOND : angle 16.82828 ( 4) hydrogen bonds : bond 0.17013 ( 716) hydrogen bonds : angle 5.72964 ( 2103) *********************** 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 to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.569 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: symmetry clash REVERT: A 253 MET cc_start: 0.7857 (mtp) cc_final: 0.7525 (mtt) 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: 0.3032 time to fit residues: 79.8971 Evaluate side-chains 101 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.077619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.061489 restraints weight = 98110.701| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.54 r_work: 0.3212 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9773 Z= 0.142 Angle : 0.562 5.920 13110 Z= 0.310 Chirality : 0.034 0.134 1476 Planarity : 0.004 0.044 1646 Dihedral : 4.187 21.909 1231 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.73 % Allowed : 7.25 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.24), residues: 1139 helix: 1.52 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.015 0.001 TYR D1347 PHE 0.019 0.002 PHE D1496 HIS 0.006 0.001 HIS B 896 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9771) covalent geometry : angle 0.55981 (13106) SS BOND : bond 0.00240 ( 2) SS BOND : angle 3.12056 ( 4) hydrogen bonds : bond 0.05909 ( 716) hydrogen bonds : angle 4.08462 ( 2103) *********************** 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 101 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.589 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 outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 0.2926 time to fit residues: 37.2364 Evaluate side-chains 86 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain C residue 1052 GLN Chi-restraints excluded: chain D residue 1496 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN D1502 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.076838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.060665 restraints weight = 98575.953| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.52 r_work: 0.3189 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9773 Z= 0.133 Angle : 0.510 7.261 13110 Z= 0.280 Chirality : 0.033 0.180 1476 Planarity : 0.003 0.041 1646 Dihedral : 4.051 33.840 1231 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.45 % Allowed : 8.34 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.25), residues: 1139 helix: 1.88 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 0.17 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 470 TYR 0.012 0.001 TYR D1347 PHE 0.022 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9771) covalent geometry : angle 0.50708 (13106) SS BOND : bond 0.00626 ( 2) SS BOND : angle 2.94913 ( 4) hydrogen bonds : bond 0.05233 ( 716) hydrogen bonds : angle 3.87812 ( 2103) *********************** 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 88 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.422 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: A 253 MET cc_start: 0.7975 (mtp) cc_final: 0.7645 (mtt) REVERT: C 1014 PHE cc_start: 0.8415 (m-80) cc_final: 0.8212 (m-80) REVERT: C 1161 GLN cc_start: 0.8198 (tp40) cc_final: 0.7856 (tm-30) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.2778 time to fit residues: 31.7623 Evaluate side-chains 78 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 1103 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 853 ASN B 856 ASN D1419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.075518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.059307 restraints weight = 100009.292| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.49 r_work: 0.3155 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9773 Z= 0.155 Angle : 0.496 5.719 13110 Z= 0.275 Chirality : 0.033 0.164 1476 Planarity : 0.003 0.040 1646 Dihedral : 3.914 36.678 1231 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.63 % Allowed : 8.25 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.25), residues: 1139 helix: 2.16 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.15 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.015 0.001 TYR D1455 PHE 0.027 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9771) covalent geometry : angle 0.49506 (13106) SS BOND : bond 0.02127 ( 2) SS BOND : angle 1.65459 ( 4) hydrogen bonds : bond 0.04783 ( 716) hydrogen bonds : angle 3.76605 ( 2103) *********************** 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 91 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.622 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: A 253 MET cc_start: 0.8075 (mtp) cc_final: 0.7715 (mtt) REVERT: A 532 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8803 (mmtp) REVERT: C 1095 LYS cc_start: 0.8708 (tttp) cc_final: 0.8465 (ttpt) REVERT: C 1161 GLN cc_start: 0.8270 (tp40) cc_final: 0.7920 (tm-30) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.2836 time to fit residues: 34.4282 Evaluate side-chains 77 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 1005 ASN Chi-restraints excluded: chain C residue 1103 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN D1400 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.074418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057944 restraints weight = 101715.641| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.59 r_work: 0.3114 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9773 Z= 0.174 Angle : 0.500 5.697 13110 Z= 0.279 Chirality : 0.033 0.141 1476 Planarity : 0.003 0.042 1646 Dihedral : 3.876 39.277 1231 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.91 % Allowed : 8.88 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.24), residues: 1139 helix: 2.29 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.08 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.012 0.001 TYR D1347 PHE 0.031 0.002 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9771) covalent geometry : angle 0.50002 (13106) SS BOND : bond 0.01706 ( 2) SS BOND : angle 0.79586 ( 4) hydrogen bonds : bond 0.04674 ( 716) hydrogen bonds : angle 3.76476 ( 2103) *********************** 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 85 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.509 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: C 1095 LYS cc_start: 0.8748 (tttp) cc_final: 0.8534 (ttpt) REVERT: C 1161 GLN cc_start: 0.8301 (tp40) cc_final: 0.7901 (tm-30) REVERT: D 1356 ARG cc_start: 0.8499 (mmt180) cc_final: 0.8147 (mmp80) outliers start: 10 outliers final: 8 residues processed: 81 average time/residue: 0.2685 time to fit residues: 29.0452 Evaluate side-chains 81 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1103 HIS Chi-restraints excluded: chain D residue 1376 ILE Chi-restraints excluded: chain D residue 1459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.074884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058414 restraints weight = 100698.528| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.59 r_work: 0.3122 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9773 Z= 0.125 Angle : 0.466 6.392 13110 Z= 0.257 Chirality : 0.032 0.157 1476 Planarity : 0.003 0.040 1646 Dihedral : 3.792 38.456 1231 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.91 % Allowed : 9.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.25), residues: 1139 helix: 2.49 (0.17), residues: 917 sheet: None (None), residues: 0 loop : 0.18 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.011 0.001 TYR B 865 PHE 0.022 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9771) covalent geometry : angle 0.46576 (13106) SS BOND : bond 0.00783 ( 2) SS BOND : angle 0.72072 ( 4) hydrogen bonds : bond 0.04517 ( 716) hydrogen bonds : angle 3.61378 ( 2103) *********************** 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 to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.537 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: A 253 MET cc_start: 0.8173 (mtp) cc_final: 0.7927 (mtm) REVERT: C 1095 LYS cc_start: 0.8708 (tttp) cc_final: 0.8507 (ttpt) REVERT: C 1161 GLN cc_start: 0.8287 (tp40) cc_final: 0.7883 (tm-30) REVERT: D 1356 ARG cc_start: 0.8506 (mmt180) cc_final: 0.8143 (mmp80) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.2949 time to fit residues: 33.9782 Evaluate side-chains 76 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 D residue 1376 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.074335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057852 restraints weight = 101337.966| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.61 r_work: 0.3109 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9773 Z= 0.153 Angle : 0.484 6.534 13110 Z= 0.267 Chirality : 0.032 0.143 1476 Planarity : 0.003 0.040 1646 Dihedral : 3.764 37.116 1231 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.73 % Allowed : 10.52 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.25), residues: 1139 helix: 2.57 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.27 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 240 TYR 0.012 0.001 TYR D1455 PHE 0.017 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9771) covalent geometry : angle 0.48353 (13106) SS BOND : bond 0.00623 ( 2) SS BOND : angle 0.65614 ( 4) hydrogen bonds : bond 0.04450 ( 716) hydrogen bonds : angle 3.62565 ( 2103) *********************** 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 77 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.637 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: 0.8201 (mtp) cc_final: 0.7853 (mtt) REVERT: C 1095 LYS cc_start: 0.8715 (tttp) cc_final: 0.8512 (ttpt) REVERT: C 1161 GLN cc_start: 0.8309 (tp40) cc_final: 0.7849 (tm-30) REVERT: D 1356 ARG cc_start: 0.8517 (mmt180) cc_final: 0.8152 (mmp80) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.3019 time to fit residues: 31.0001 Evaluate side-chains 73 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 511 GLU 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 D residue 1376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.074919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058526 restraints weight = 101053.983| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.60 r_work: 0.3131 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9773 Z= 0.113 Angle : 0.452 5.755 13110 Z= 0.247 Chirality : 0.032 0.134 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.650 36.112 1231 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.63 % Allowed : 11.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.56 (0.25), residues: 1139 helix: 2.80 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.43 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.010 0.001 TYR B 865 PHE 0.013 0.001 PHE B 806 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9771) covalent geometry : angle 0.45233 (13106) SS BOND : bond 0.00727 ( 2) SS BOND : angle 0.63299 ( 4) hydrogen bonds : bond 0.04269 ( 716) hydrogen bonds : angle 3.44945 ( 2103) *********************** 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 77 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.611 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: C 1161 GLN cc_start: 0.8273 (tp40) cc_final: 0.7834 (tm-30) REVERT: D 1356 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8273 (mmp-170) outliers start: 7 outliers final: 7 residues processed: 76 average time/residue: 0.2923 time to fit residues: 30.0811 Evaluate side-chains 73 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 698 ILE Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN B 853 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.074375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057954 restraints weight = 101150.969| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.60 r_work: 0.3116 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9773 Z= 0.135 Angle : 0.463 5.607 13110 Z= 0.254 Chirality : 0.032 0.134 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.606 34.440 1231 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.91 % Allowed : 10.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.24), residues: 1139 helix: 2.87 (0.17), residues: 910 sheet: None (None), residues: 0 loop : 0.50 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.012 0.001 TYR B 865 PHE 0.013 0.001 PHE B 806 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9771) covalent geometry : angle 0.46285 (13106) SS BOND : bond 0.00755 ( 2) SS BOND : angle 0.80830 ( 4) hydrogen bonds : bond 0.04242 ( 716) hydrogen bonds : angle 3.50192 ( 2103) *********************** 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 80 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.605 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: 0.8125 (mtp) cc_final: 0.7834 (mtm) REVERT: C 1161 GLN cc_start: 0.8286 (tp40) cc_final: 0.7821 (tm-30) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.2622 time to fit residues: 28.9847 Evaluate side-chains 75 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 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 D residue 1376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.074456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058162 restraints weight = 101490.488| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.57 r_work: 0.3130 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9773 Z= 0.121 Angle : 0.458 5.555 13110 Z= 0.250 Chirality : 0.032 0.133 1476 Planarity : 0.003 0.039 1646 Dihedral : 3.583 33.926 1231 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.82 % Allowed : 10.79 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.24), residues: 1139 helix: 2.95 (0.16), residues: 909 sheet: None (None), residues: 0 loop : 0.55 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.015 0.001 TYR C1138 PHE 0.013 0.001 PHE B 806 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9771) covalent geometry : angle 0.45811 (13106) SS BOND : bond 0.00847 ( 2) SS BOND : angle 0.83782 ( 4) hydrogen bonds : bond 0.04198 ( 716) hydrogen bonds : angle 3.44175 ( 2103) ********************** 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 76 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.534 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: 0.8047 (mtp) cc_final: 0.7757 (mtm) REVERT: C 1161 GLN cc_start: 0.8280 (tp40) cc_final: 0.7821 (tm-30) outliers start: 9 outliers final: 9 residues processed: 75 average time/residue: 0.2392 time to fit residues: 24.9645 Evaluate side-chains 75 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 D residue 1376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 853 ASN C1213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056426 restraints weight = 102646.350| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.54 r_work: 0.3087 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9773 Z= 0.221 Angle : 0.519 6.096 13110 Z= 0.292 Chirality : 0.034 0.137 1476 Planarity : 0.003 0.041 1646 Dihedral : 3.742 34.285 1231 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 10.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.24), residues: 1139 helix: 2.59 (0.16), residues: 912 sheet: None (None), residues: 0 loop : 0.35 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 240 TYR 0.013 0.001 TYR B 865 PHE 0.014 0.002 PHE B 806 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 9771) covalent geometry : angle 0.51923 (13106) SS BOND : bond 0.00964 ( 2) SS BOND : angle 0.87651 ( 4) hydrogen bonds : bond 0.04559 ( 716) hydrogen bonds : angle 3.78181 ( 2103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4393.88 seconds wall clock time: 75 minutes 20.36 seconds (4520.36 seconds total)