Starting phenix.real_space_refine on Mon Oct 26 04:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbg_11154/10_2026/6zbg_11154.map" } resolution = 3.2 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 6194 2.51 5 N 1577 2.21 5 O 1842 1.98 5 H 9902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19534 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9553 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 14, 'TRANS': 547} 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: 3.29, per 1000 atoms: 0.17 Number of scatterers: 19534 At special positions: 0 Unit cell: (105.154, 138.417, 140.563, 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 1842 8.00 N 1577 7.00 C 6194 6.00 H 9902 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=2.07 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=2.01 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: 1.66 Conformation dependent library (CDL) restraints added in 682.0 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.594A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.212A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.278A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.919A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.507A pdb=" N TYR A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.628A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.352A 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: 4.126A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.629A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.513A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (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: 3.731A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.983A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.741A 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: 3.982A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.639A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.613A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.268A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.687A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.636A 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 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' 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: 3.690A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.947A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.000A 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: 3.770A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.239A 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 1100 removed outlier: 3.539A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (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: 3.702A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN C1130 " --> pdb=" O ASN C1126 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.048A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.638A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.532A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.538A 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: 3.623A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.648A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.612A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.675A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.547A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2109 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: 3.83 Time building geometry restraints manager: 2.29 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: 9900 1.04 - 1.23: 304 1.23 - 1.43: 3630 1.43 - 1.62: 5816 1.62 - 1.82: 32 Bond restraints: 19682 Sorted by residual: bond pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 1.454 1.481 -0.026 7.70e-03 1.69e+04 1.15e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.40e-03 1.83e+04 1.15e+01 bond pdb=" N VAL A 210 " pdb=" CA VAL A 210 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 bond pdb=" N ILE D1346 " pdb=" CA ILE D1346 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.04e+01 ... (remaining 19677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 30663 1.62 - 3.24: 4771 3.24 - 4.86: 355 4.86 - 6.48: 61 6.48 - 8.10: 4 Bond angle restraints: 35854 Sorted by residual: angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 114.51 6.41 1.12e+00 7.97e-01 3.28e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.26 6.02 1.09e+00 8.42e-01 3.06e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.86 7.14 1.30e+00 5.92e-01 3.01e+01 angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N PHE C1014 " pdb=" CA PHE C1014 " pdb=" C PHE C1014 " ideal model delta sigma weight residual 111.28 105.65 5.63 1.09e+00 8.42e-01 2.67e+01 ... (remaining 35849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8405 17.84 - 35.68: 530 35.68 - 53.51: 118 53.51 - 71.35: 33 71.35 - 89.19: 13 Dihedral angle restraints: 9099 sinusoidal: 5060 harmonic: 4039 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 93.00 148.23 -55.23 1 1.00e+01 1.00e-02 4.12e+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 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.12 -89.12 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 785 0.054 - 0.109: 486 0.109 - 0.163: 170 0.163 - 0.217: 30 0.217 - 0.272: 6 Chirality restraints: 1477 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 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA VAL C 988 " pdb=" N VAL C 988 " pdb=" C VAL C 988 " pdb=" CB VAL C 988 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL D1345 " pdb=" CA VAL D1345 " pdb=" CG1 VAL D1345 " pdb=" CG2 VAL D1345 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1474 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN A 217 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1109 " -0.017 2.00e-02 2.50e+03 1.67e-02 8.36e+00 pdb=" CG PHE C1109 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE C1109 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C1109 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C1109 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C1109 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C1109 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE C1109 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C1109 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE C1109 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 PHE C1109 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE C1109 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 327 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ASN A 327 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 327 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 328 " -0.015 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 2420 2.29 - 2.87: 46247 2.87 - 3.44: 48537 3.44 - 4.02: 62345 4.02 - 4.60: 99515 Nonbonded interactions: 259064 Sorted by model distance: nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.709 2.450 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.716 2.450 nonbonded pdb=" O THR C1050 " pdb=" HG SER C1054 " model vdw 1.716 2.450 nonbonded pdb=" OE1 GLU A 680 " pdb=" H SER B 823 " model vdw 1.717 2.450 nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.717 2.450 ... (remaining 259059 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: 2.360 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: 0.040 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.020 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 0.053 9782 Z= 0.720 Angle : 1.198 35.089 13122 Z= 0.846 Chirality : 0.074 0.272 1477 Planarity : 0.006 0.043 1648 Dihedral : 13.623 89.189 3844 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 are not related in a simple way. whole: 0.72 (0.24), residues: 1140 helix: 0.81 (0.16), residues: 893 sheet: None (None), residues: 0 loop : -0.42 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 225 TYR 0.022 0.003 TYR B 865 PHE 0.016 0.003 PHE C1109 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd/Z covalent geometry : bond 0.01009 / 0.72 ( 9780) covalent geometry : angle 1.15258 / 0.83 (13118) SS BOND : bond 0.02946 / 1.53 ( 2) SS BOND : angle 18.83552 / 10.90 ( 4) hydrogen bonds : bond 0.16783 / 11.11 ( 717) hydrogen bonds : angle 5.80909 / 4.22 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.524 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 165 LEU cc_start: 0.8599 (tp) cc_final: 0.7369 (tp) REVERT: A 253 MET cc_start: 0.8573 (mtp) cc_final: 0.8061 (mtt) REVERT: A 395 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7453 (ttp80) REVERT: A 447 TYR cc_start: 0.8302 (m-80) cc_final: 0.8069 (m-10) REVERT: B 802 LYS cc_start: 0.8055 (mttt) cc_final: 0.7840 (tmtt) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2720 time to fit residues: 74.2990 Evaluate side-chains 101 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 100] chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN C 981 ASN C1081 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.077794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060855 restraints weight = 100737.479| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.66 r_work: 0.3196 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9782 Z= 0.138 Angle : 0.571 6.565 13122 Z= 0.313 Chirality : 0.034 0.140 1477 Planarity : 0.003 0.043 1648 Dihedral : 4.186 21.304 1232 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.91 % Allowed : 6.70 % Favored : 92.39 % 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 are not related in a simple way. whole: 1.66 (0.24), residues: 1140 helix: 1.51 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1384 TYR 0.016 0.001 TYR D1347 PHE 0.017 0.001 PHE A 163 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9780) covalent geometry : angle 0.57043 / 0.31 (13118) SS BOND : bond 0.00155 / 0.08 ( 2) SS BOND : angle 1.27750 / 0.71 ( 4) hydrogen bonds : bond 0.05793 / 3.70 ( 717) hydrogen bonds : angle 4.15189 / 3.02 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.490 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 447 TYR cc_start: 0.8482 (m-80) cc_final: 0.8188 (m-10) REVERT: A 519 MET cc_start: 0.8730 (mtm) cc_final: 0.8465 (ttm) REVERT: C 1170 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7903 (tt0) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.2152 time to fit residues: 29.7595 Evaluate side-chains 75 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain D residue 1348 LEU Chi-restraints excluded: chain D residue 1466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [64, 82, 37, 66, 92, 26, 55, 9, 76, 79, 27] chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 638 GLN A 640 GLN D1419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.076580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.059627 restraints weight = 101816.328| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.62 r_work: 0.3168 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9782 Z= 0.143 Angle : 0.523 6.615 13122 Z= 0.287 Chirality : 0.033 0.140 1477 Planarity : 0.003 0.038 1648 Dihedral : 4.026 20.210 1232 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.82 % Allowed : 6.70 % Favored : 92.48 % 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 are not related in a simple way. whole: 2.15 (0.24), residues: 1140 helix: 1.84 (0.17), residues: 909 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.012 0.001 TYR C1013 PHE 0.009 0.001 PHE A 163 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9780) covalent geometry : angle 0.51848 / 0.29 (13118) SS BOND : bond 0.00995 / 0.52 ( 2) SS BOND : angle 4.12553 / 2.34 ( 4) hydrogen bonds : bond 0.05193 / 3.29 ( 717) hydrogen bonds : angle 3.96031 / 2.87 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.529 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: A 253 MET cc_start: 0.8843 (mtp) cc_final: 0.8235 (mtt) REVERT: A 519 MET cc_start: 0.8732 (mtm) cc_final: 0.8443 (ttm) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.2091 time to fit residues: 24.5718 Evaluate side-chains 71 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain D residue 1348 LEU Chi-restraints excluded: chain D residue 1466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [112, 98, 29, 51, 2, 31, 28, 15, 111, 57, 20] chunk 112 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 0.0570 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN A 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.077146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060140 restraints weight = 100985.681| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.62 r_work: 0.3183 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9782 Z= 0.112 Angle : 0.474 6.077 13122 Z= 0.257 Chirality : 0.032 0.132 1477 Planarity : 0.003 0.036 1648 Dihedral : 3.815 30.798 1232 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.91 % Allowed : 7.07 % Favored : 92.03 % 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 are not related in a simple way. whole: 2.85 (0.24), residues: 1140 helix: 2.33 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.24 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 240 TYR 0.011 0.001 TYR D1347 PHE 0.010 0.001 PHE B 852 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9780) covalent geometry : angle 0.47342 / 0.26 (13118) SS BOND : bond 0.00085 / 0.04 ( 2) SS BOND : angle 0.98471 / 0.55 ( 4) hydrogen bonds : bond 0.04643 / 2.95 ( 717) hydrogen bonds : angle 3.68717 / 2.68 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.518 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 outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.2018 time to fit residues: 26.0521 Evaluate side-chains 75 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain D residue 1348 LEU Chi-restraints excluded: chain D residue 1466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [109, 73, 95, 64, 10, 78, 87, 84, 100, 63, 7] chunk 109 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.075667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.058522 restraints weight = 102024.839| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.61 r_work: 0.3146 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9782 Z= 0.148 Angle : 0.486 6.271 13122 Z= 0.267 Chirality : 0.033 0.140 1477 Planarity : 0.003 0.037 1648 Dihedral : 3.709 22.929 1232 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.82 % Allowed : 7.79 % Favored : 91.39 % 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 are not related in a simple way. whole: 3.09 (0.24), residues: 1140 helix: 2.48 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 0.32 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 240 TYR 0.015 0.001 TYR C1013 PHE 0.011 0.001 PHE A 163 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 9780) covalent geometry : angle 0.48444 / 0.27 (13118) SS BOND : bond 0.02558 / 1.35 ( 2) SS BOND : angle 2.20868 / 1.29 ( 4) hydrogen bonds : bond 0.04473 / 2.81 ( 717) hydrogen bonds : angle 3.69341 / 2.67 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.560 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 1209 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8086 (mm-30) outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.2157 time to fit residues: 25.0861 Evaluate side-chains 68 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [44, 41, 8, 103, 29, 69, 70, 78, 45, 6, 76] chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 29 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.225 > 50:) chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.075069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057896 restraints weight = 102938.095| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.57 r_work: 0.3130 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9782 Z= 0.172 Angle : 0.498 6.646 13122 Z= 0.273 Chirality : 0.033 0.131 1477 Planarity : 0.003 0.031 1648 Dihedral : 3.732 33.321 1232 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.63 % Allowed : 8.97 % Favored : 90.40 % 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 are not related in a simple way. whole: 3.19 (0.24), residues: 1140 helix: 2.57 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 0.26 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 537 TYR 0.022 0.001 TYR D1455 PHE 0.022 0.001 PHE A 163 HIS 0.003 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 9780) covalent geometry : angle 0.49804 / 0.27 (13118) SS BOND : bond 0.00480 / 0.24 ( 2) SS BOND : angle 0.92462 / 0.53 ( 4) hydrogen bonds : bond 0.04446 / 2.79 ( 717) hydrogen bonds : angle 3.72843 / 2.69 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.505 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: C 1209 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8108 (mm-30) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.2096 time to fit residues: 20.9313 Evaluate side-chains 63 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [26, 74, 18, 28, 23, 33, 53, 71, 72, 80, 51] chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.075113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057795 restraints weight = 102934.344| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.63 r_work: 0.3131 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9782 Z= 0.140 Angle : 0.480 6.882 13122 Z= 0.260 Chirality : 0.032 0.129 1477 Planarity : 0.003 0.029 1648 Dihedral : 3.596 18.334 1232 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.82 % Allowed : 9.33 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.24), residues: 1140 helix: 2.73 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.23 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.016 0.001 TYR D1455 PHE 0.015 0.001 PHE A 163 HIS 0.003 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9780) covalent geometry : angle 0.47885 / 0.26 (13118) SS BOND : bond 0.00473 / 0.24 ( 2) SS BOND : angle 1.75261 / 1.02 ( 4) hydrogen bonds : bond 0.04269 / 2.70 ( 717) hydrogen bonds : angle 3.60853 / 2.61 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.538 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: C 1209 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8200 (mm-30) outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.2108 time to fit residues: 19.2002 Evaluate side-chains 61 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1133 ILE Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [59, 69, 45, 113, 105, 40, 72, 47, 17, 64, 112] chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 ASN C1224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058221 restraints weight = 102955.622| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.62 r_work: 0.3142 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9782 Z= 0.111 Angle : 0.456 7.451 13122 Z= 0.246 Chirality : 0.031 0.129 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.492 19.385 1232 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.63 % Allowed : 9.78 % Favored : 89.58 % 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 are not related in a simple way. whole: 3.73 (0.25), residues: 1140 helix: 2.95 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 0.49 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.012 0.001 TYR D1455 PHE 0.014 0.001 PHE A 163 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9780) covalent geometry : angle 0.45596 / 0.25 (13118) SS BOND : bond 0.00226 / 0.11 ( 2) SS BOND : angle 1.22010 / 0.66 ( 4) hydrogen bonds : bond 0.04132 / 2.62 ( 717) hydrogen bonds : angle 3.47820 / 2.52 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.551 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: A 253 MET cc_start: 0.9055 (mtp) cc_final: 0.8565 (mtt) REVERT: C 1209 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8315 (mm-30) outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1979 time to fit residues: 18.4169 Evaluate side-chains 58 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [30, 27, 35, 25, 50, 63, 37, 24, 72, 109, 48] chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.075257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.057931 restraints weight = 101625.266| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.57 r_work: 0.3135 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9782 Z= 0.128 Angle : 0.465 7.825 13122 Z= 0.251 Chirality : 0.032 0.174 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.503 28.804 1232 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.45 % Allowed : 9.96 % Favored : 89.58 % 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 are not related in a simple way. whole: 3.73 (0.25), residues: 1140 helix: 2.94 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.40 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.015 0.001 TYR C1145 PHE 0.017 0.001 PHE A 163 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9780) covalent geometry : angle 0.46475 / 0.25 (13118) SS BOND : bond 0.00450 / 0.23 ( 2) SS BOND : angle 1.02274 / 0.59 ( 4) hydrogen bonds : bond 0.04110 / 2.59 ( 717) hydrogen bonds : angle 3.50071 / 2.53 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.538 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: A 253 MET cc_start: 0.9044 (mtp) cc_final: 0.8544 (mtt) REVERT: C 1209 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8287 (mm-30) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.2124 time to fit residues: 18.3458 Evaluate side-chains 58 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [8, 6, 28, 60, 67, 55, 102, 40, 108, 11, 77] chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 67 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.076068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058654 restraints weight = 102095.045| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.64 r_work: 0.3155 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9782 Z= 0.099 Angle : 0.448 9.054 13122 Z= 0.238 Chirality : 0.031 0.158 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.416 21.820 1232 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.45 % Allowed : 10.24 % Favored : 89.31 % 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 are not related in a simple way. whole: 4.04 (0.25), residues: 1140 helix: 3.15 (0.17), residues: 908 sheet: None (None), residues: 0 loop : 0.62 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.011 0.001 TYR D1355 PHE 0.014 0.001 PHE A 163 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 9780) covalent geometry : angle 0.44712 / 0.24 (13118) SS BOND : bond 0.00599 / 0.31 ( 2) SS BOND : angle 1.94530 / 1.06 ( 4) hydrogen bonds : bond 0.03939 / 2.49 ( 717) hydrogen bonds : angle 3.34243 / 2.42 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.781 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: A 253 MET cc_start: 0.9078 (mtp) cc_final: 0.8606 (mtt) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.2097 time to fit residues: 19.4150 Evaluate side-chains 59 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 634 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: [57, 69, 65, 36, 18, 56, 28, 89, 107, 58, 104] chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.075905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058660 restraints weight = 102630.908| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.62 r_work: 0.3149 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9782 Z= 0.109 Angle : 0.454 8.919 13122 Z= 0.242 Chirality : 0.032 0.134 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.424 30.328 1232 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.45 % Allowed : 10.33 % Favored : 89.22 % 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 are not related in a simple way. whole: 4.08 (0.25), residues: 1140 helix: 3.17 (0.16), residues: 909 sheet: None (None), residues: 0 loop : 0.67 (0.44), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.019 0.001 TYR D1455 PHE 0.014 0.001 PHE A 163 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 9780) covalent geometry : angle 0.45374 / 0.24 (13118) SS BOND : bond 0.00208 / 0.10 ( 2) SS BOND : angle 1.50603 / 0.86 ( 4) hydrogen bonds : bond 0.03913 / 2.47 ( 717) hydrogen bonds : angle 3.35745 / 2.43 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.11 seconds wall clock time: 68 minutes 14.06 seconds (4094.06 seconds total)