Starting phenix.real_space_refine on Tue Nov 18 12:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.map" model { file = "/net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ir3_60799/11_2025/9ir3_60799.cif" } resolution = 3.19 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= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1802 atoms to isotropic. 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 Zn 2 6.06 5 S 82 5.16 5 C 7996 2.51 5 N 2154 2.21 5 O 2357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12591 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10093 Classifications: {'peptide': 1253} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1205} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 445 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "D" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 498 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 524 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 553 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 476 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8743 SG CYS A1236 36.080 60.468 102.269 1.00 80.01 S ATOM 8766 SG CYS A1239 36.736 64.072 103.526 1.00 76.43 S ATOM 8393 SG CYS A1191 55.880 53.394 106.349 1.00 73.66 S ATOM 9919 SG CYS A1428 51.600 54.357 104.734 1.00 91.69 S ATOM 9925 SG CYS A1429 55.234 55.045 102.702 1.00 92.26 S Time building chain proxies: 3.07, per 1000 atoms: 0.24 Number of scatterers: 12591 At special positions: 0 Unit cell: (103.36, 191.76, 121.04, 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) Zn 2 29.99 S 82 16.00 O 2357 8.00 N 2154 7.00 C 7996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 682.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1421 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1239 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1236 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1429 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1191 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1428 " Number of angles added : 1 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 7 sheets defined 65.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 22 through 33 removed outlier: 4.163A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.956A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.744A pdb=" N ILE A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.831A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 167 through 189 removed outlier: 4.002A pdb=" N LYS A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.893A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.640A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.840A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.690A pdb=" N HIS A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.723A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.800A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.616A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 410 removed outlier: 3.787A pdb=" N ILE A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.724A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.603A pdb=" N ARG A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.794A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.754A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.672A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix removed outlier: 3.612A pdb=" N PHE A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 911 removed outlier: 3.560A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 966 removed outlier: 3.621A pdb=" N SER A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.654A pdb=" N THR A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Proline residue: A 978 - end of helix removed outlier: 3.558A pdb=" N ASN A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 removed outlier: 3.621A pdb=" N LEU A 986 " --> pdb=" O ASN A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.998A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 4.114A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1110 Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'A' and resid 1126 through 1138 removed outlier: 3.575A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.695A pdb=" N VAL A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1236 through 1242 Processing helix chain 'A' and resid 1293 through 1308 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1391 through 1407 removed outlier: 3.524A pdb=" N ALA A1395 " --> pdb=" O ILE A1391 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.590A pdb=" N ARG C 659 " --> pdb=" O ASP C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 686 Processing helix chain 'C' and resid 688 through 704 Processing helix chain 'D' and resid 513 through 541 removed outlier: 3.934A pdb=" N GLN D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 573 removed outlier: 3.841A pdb=" N SER D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 541 removed outlier: 3.943A pdb=" N GLU E 538 " --> pdb=" O ASN E 534 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 578 removed outlier: 3.866A pdb=" N HIS E 570 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 571 " --> pdb=" O ILE E 567 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE E 576 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N MET E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 541 removed outlier: 3.519A pdb=" N HIS F 535 " --> pdb=" O MET F 531 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 541 " --> pdb=" O GLU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 574 removed outlier: 4.017A pdb=" N LYS F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU F 568 " --> pdb=" O LEU F 564 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 569 " --> pdb=" O SER F 565 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER F 573 " --> pdb=" O GLY F 569 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 541 Processing helix chain 'G' and resid 542 through 572 removed outlier: 3.792A pdb=" N ASN G 561 " --> pdb=" O LEU G 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 563 " --> pdb=" O LYS G 559 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL G 572 " --> pdb=" O GLU G 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.245A pdb=" N MET A 84 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N TYR A 229 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 555 removed outlier: 4.793A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.000A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 834 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1231 763 hydrogen bonds defined for protein. 2196 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: 2.60 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4140 1.34 - 1.46: 2231 1.46 - 1.58: 6303 1.58 - 1.70: 0 1.70 - 1.81: 134 Bond restraints: 12808 Sorted by residual: bond pdb=" CA MET E 531 " pdb=" C MET E 531 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.35e-02 5.49e+03 3.62e+00 bond pdb=" C MET D 518 " pdb=" O MET D 518 " ideal model delta sigma weight residual 1.237 1.222 0.014 1.17e-02 7.31e+03 1.53e+00 bond pdb=" CG GLU D 538 " pdb=" CD GLU D 538 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CB PRO A 497 " pdb=" CG PRO A 497 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.93e-01 bond pdb=" C ILE E 578 " pdb=" N PRO E 579 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.80e-01 ... (remaining 12803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 16846 1.71 - 3.42: 393 3.42 - 5.13: 52 5.13 - 6.84: 16 6.84 - 8.56: 3 Bond angle restraints: 17310 Sorted by residual: angle pdb=" C PRO A 190 " pdb=" N LYS A 191 " pdb=" CA LYS A 191 " ideal model delta sigma weight residual 122.73 117.67 5.06 1.61e+00 3.86e-01 9.88e+00 angle pdb=" N GLU D 538 " pdb=" CA GLU D 538 " pdb=" CB GLU D 538 " ideal model delta sigma weight residual 110.01 114.47 -4.46 1.45e+00 4.76e-01 9.45e+00 angle pdb=" C ARG A1253 " pdb=" N ASP A1254 " pdb=" CA ASP A1254 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.38e+00 angle pdb=" C ASP F 554 " pdb=" N ARG F 555 " pdb=" CA ARG F 555 " ideal model delta sigma weight residual 121.94 116.03 5.91 2.00e+00 2.50e-01 8.72e+00 angle pdb=" C ILE A 209 " pdb=" N LEU A 210 " pdb=" CA LEU A 210 " ideal model delta sigma weight residual 122.37 117.69 4.68 1.72e+00 3.38e-01 7.41e+00 ... (remaining 17305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 7143 18.42 - 36.85: 595 36.85 - 55.27: 94 55.27 - 73.69: 17 73.69 - 92.12: 6 Dihedral angle restraints: 7855 sinusoidal: 3188 harmonic: 4667 Sorted by residual: dihedral pdb=" CA LYS A 189 " pdb=" C LYS A 189 " pdb=" N PRO A 190 " pdb=" CA PRO A 190 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA LYS A 191 " pdb=" C LYS A 191 " pdb=" N PHE A 192 " pdb=" CA PHE A 192 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA HIS A 887 " pdb=" C HIS A 887 " pdb=" N LEU A 888 " pdb=" CA LEU A 888 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1221 0.032 - 0.064: 529 0.064 - 0.096: 172 0.096 - 0.127: 66 0.127 - 0.159: 9 Chirality restraints: 1997 Sorted by residual: chirality pdb=" CA PRO A 190 " pdb=" N PRO A 190 " pdb=" C PRO A 190 " pdb=" CB PRO A 190 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA ASP A1254 " pdb=" N ASP A1254 " pdb=" C ASP A1254 " pdb=" CB ASP A1254 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A1445 " pdb=" N ILE A1445 " pdb=" C ILE A1445 " pdb=" CB ILE A1445 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1994 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 843 " 0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO A 844 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 844 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 844 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 754 " -0.011 2.00e-02 2.50e+03 1.11e-02 3.10e+00 pdb=" CG TRP A 754 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 754 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 754 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 754 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 754 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 754 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 754 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 754 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 754 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 211 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 212 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.023 5.00e-02 4.00e+02 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 208 2.69 - 3.24: 12794 3.24 - 3.80: 19405 3.80 - 4.35: 24109 4.35 - 4.90: 40890 Nonbonded interactions: 97406 Sorted by model distance: nonbonded pdb=" O CYS A1428 " pdb="ZN ZN A2302 " model vdw 2.141 2.230 nonbonded pdb=" NZ LYS A1073 " pdb=" O THR A1140 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A1214 " pdb=" O ALA A1434 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR A 439 " pdb=" OD1 ASP A 441 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP A1095 " pdb=" N LYS A1096 " model vdw 2.238 3.120 ... (remaining 97401 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 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 512 through 514 and (name N or name CA or name C or name \ O or name CB )) or resid 515 or (resid 516 and (name N or name CA or name C or n \ ame O or name CB )) or resid 517 through 521 or (resid 522 and (name N or name C \ A or name C or name O or name CB )) or resid 523 through 526 or (resid 527 and ( \ name N or name CA or name C or name O or name CB )) or resid 528 through 531 or \ (resid 532 through 533 and (name N or name CA or name C or name O or name CB )) \ or resid 534 or (resid 535 and (name N or name CA or name C or name O or name CB \ )) or resid 536 through 540 or (resid 541 and (name N or name CA or name C or n \ ame O or name CB )) or resid 542 through 549 or (resid 550 and (name N or name C \ A or name C or name O or name CB )) or resid 551 through 560 or (resid 561 and ( \ name N or name CA or name C or name O or name CB )) or resid 562 through 576)) selection = (chain 'E' and ((resid 512 through 514 and (name N or name CA or name C or name \ O or name CB )) or resid 515 or (resid 516 and (name N or name CA or name C or n \ ame O or name CB )) or resid 517 through 519 or (resid 520 through 522 and (name \ N or name CA or name C or name O or name CB )) or resid 523 through 525 or (res \ id 526 through 527 and (name N or name CA or name C or name O or name CB )) or r \ esid 528 or (resid 529 and (name N or name CA or name C or name O or name CB )) \ or resid 530 or (resid 531 through 533 and (name N or name CA or name C or name \ O or name CB )) or resid 534 through 540 or (resid 541 and (name N or name CA or \ name C or name O or name CB )) or resid 542 through 548 or (resid 549 through 5 \ 50 and (name N or name CA or name C or name O or name CB )) or resid 551 through \ 576)) selection = (chain 'F' and ((resid 512 through 514 and (name N or name CA or name C or name \ O or name CB )) or resid 515 through 520 or (resid 521 through 522 and (name N o \ r name CA or name C or name O or name CB )) or resid 523 through 528 or (resid 5 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 530 through \ 531 or (resid 532 through 533 and (name N or name CA or name C or name O or nam \ e CB )) or resid 534 or (resid 535 and (name N or name CA or name C or name O or \ name CB )) or resid 536 through 548 or (resid 549 through 550 and (name N or na \ me CA or name C or name O or name CB )) or resid 551 through 560 or (resid 561 a \ nd (name N or name CA or name C or name O or name CB )) or resid 562 through 576 \ )) selection = (chain 'G' and ((resid 512 through 514 and (name N or name CA or name C or name \ O or name CB )) or resid 515 or (resid 516 and (name N or name CA or name C or n \ ame O or name CB )) or resid 517 through 521 or (resid 522 and (name N or name C \ A or name C or name O or name CB )) or resid 523 through 524 or (resid 525 throu \ gh 527 and (name N or name CA or name C or name O or name CB )) or resid 528 or \ (resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ or (resid 531 through 533 and (name N or name CA or name C or name O or name CB \ )) or resid 534 or (resid 535 and (name N or name CA or name C or name O or nam \ e CB )) or resid 536 through 540 or (resid 541 and (name N or name CA or name C \ or name O or name CB )) or resid 542 through 560 or (resid 561 and (name N or na \ me CA or name C or name O or name CB )) or resid 562 through 576)) } 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.540 Find NCS groups from input model: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.006 0.552 12815 Z= 0.237 Angle : 0.636 8.556 17311 Z= 0.350 Chirality : 0.042 0.159 1997 Planarity : 0.004 0.094 2201 Dihedral : 13.705 92.116 4815 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.73 (0.22), residues: 1565 helix: 2.20 (0.18), residues: 945 sheet: 0.39 (0.53), residues: 101 loop : -0.70 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1082 TYR 0.015 0.002 TYR A 529 PHE 0.014 0.001 PHE A 914 TRP 0.029 0.002 TRP A 754 HIS 0.006 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00369 (12808) covalent geometry : angle 0.63560 (17310) hydrogen bonds : bond 0.13549 ( 763) hydrogen bonds : angle 4.78038 ( 2196) metal coordination : bond 0.21059 ( 7) metal coordination : angle 1.65100 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 15 CYS cc_start: 0.7517 (t) cc_final: 0.7278 (t) REVERT: A 57 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7998 (tppt) REVERT: A 112 LYS cc_start: 0.7980 (mttt) cc_final: 0.7710 (mttm) REVERT: A 179 GLU cc_start: 0.7577 (tp30) cc_final: 0.7280 (tp30) REVERT: A 186 ASN cc_start: 0.8658 (t0) cc_final: 0.8351 (t0) REVERT: A 189 LYS cc_start: 0.8402 (pptt) cc_final: 0.7761 (pptt) REVERT: A 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6854 (m-30) REVERT: A 262 ILE cc_start: 0.8335 (mt) cc_final: 0.8026 (mt) REVERT: A 282 ARG cc_start: 0.8133 (mtt90) cc_final: 0.7848 (mmm-85) REVERT: A 376 LYS cc_start: 0.7892 (tppt) cc_final: 0.7470 (tppp) REVERT: A 469 MET cc_start: 0.7068 (pmm) cc_final: 0.6601 (pmm) REVERT: A 512 ASP cc_start: 0.7399 (t0) cc_final: 0.7024 (t0) REVERT: A 530 LEU cc_start: 0.7961 (mt) cc_final: 0.7709 (mp) REVERT: A 732 TYR cc_start: 0.7907 (t80) cc_final: 0.7351 (t80) REVERT: A 740 GLU cc_start: 0.7371 (tp30) cc_final: 0.6858 (tp30) REVERT: A 857 LYS cc_start: 0.8207 (ttpp) cc_final: 0.8004 (mtpp) REVERT: A 864 GLU cc_start: 0.6892 (tp30) cc_final: 0.6557 (tp30) REVERT: A 876 ASN cc_start: 0.8099 (t0) cc_final: 0.7684 (t0) REVERT: A 885 SER cc_start: 0.8448 (t) cc_final: 0.8176 (t) REVERT: A 891 TYR cc_start: 0.7575 (t80) cc_final: 0.7293 (t80) REVERT: A 908 SER cc_start: 0.8349 (t) cc_final: 0.8115 (t) REVERT: A 964 GLU cc_start: 0.6384 (mp0) cc_final: 0.5831 (mp0) REVERT: A 981 ASN cc_start: 0.8034 (m110) cc_final: 0.7819 (m-40) REVERT: A 984 ASP cc_start: 0.6976 (p0) cc_final: 0.6637 (p0) REVERT: A 1047 ASP cc_start: 0.7104 (p0) cc_final: 0.6654 (p0) REVERT: A 1206 GLU cc_start: 0.7182 (tp30) cc_final: 0.6822 (tp30) REVERT: A 1300 ILE cc_start: 0.8337 (mm) cc_final: 0.8031 (mm) REVERT: A 1327 ASN cc_start: 0.7291 (p0) cc_final: 0.6999 (p0) REVERT: A 1336 ILE cc_start: 0.8945 (tp) cc_final: 0.8650 (tp) REVERT: A 1431 LYS cc_start: 0.8230 (pttm) cc_final: 0.8007 (pttm) REVERT: A 1438 GLN cc_start: 0.7896 (pt0) cc_final: 0.7668 (pp30) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1416 time to fit residues: 70.3775 Evaluate side-chains 336 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121759 restraints weight = 19788.790| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.43 r_work: 0.3502 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12815 Z= 0.171 Angle : 0.598 8.254 17311 Z= 0.312 Chirality : 0.043 0.190 1997 Planarity : 0.004 0.069 2201 Dihedral : 4.032 27.142 1707 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 1.15 % Allowed : 10.82 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.85 (0.22), residues: 1565 helix: 2.26 (0.17), residues: 960 sheet: 0.32 (0.54), residues: 99 loop : -0.64 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 761 TYR 0.011 0.001 TYR A 529 PHE 0.017 0.002 PHE A1107 TRP 0.014 0.001 TRP A 754 HIS 0.005 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00375 (12808) covalent geometry : angle 0.59760 (17310) hydrogen bonds : bond 0.05332 ( 763) hydrogen bonds : angle 3.96174 ( 2196) metal coordination : bond 0.02740 ( 7) metal coordination : angle 1.49703 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 354 time to evaluate : 0.413 Fit side-chains REVERT: A 15 CYS cc_start: 0.7999 (t) cc_final: 0.7785 (t) REVERT: A 31 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7244 (mp0) REVERT: A 57 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8120 (tppt) REVERT: A 112 LYS cc_start: 0.8366 (mttt) cc_final: 0.8160 (mtmm) REVERT: A 189 LYS cc_start: 0.8493 (pptt) cc_final: 0.8209 (pptt) REVERT: A 197 CYS cc_start: 0.8531 (t) cc_final: 0.7990 (p) REVERT: A 207 GLU cc_start: 0.7358 (mp0) cc_final: 0.7097 (mp0) REVERT: A 240 ASP cc_start: 0.7700 (m-30) cc_final: 0.7348 (m-30) REVERT: A 246 MET cc_start: 0.8079 (ttp) cc_final: 0.7741 (ttp) REVERT: A 259 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 262 ILE cc_start: 0.8201 (mt) cc_final: 0.7939 (mt) REVERT: A 282 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8258 (mmm-85) REVERT: A 315 CYS cc_start: 0.7843 (m) cc_final: 0.7566 (m) REVERT: A 355 GLU cc_start: 0.8071 (tp30) cc_final: 0.7685 (tp30) REVERT: A 376 LYS cc_start: 0.8136 (tppt) cc_final: 0.7838 (tppp) REVERT: A 423 HIS cc_start: 0.8130 (p-80) cc_final: 0.7617 (p-80) REVERT: A 469 MET cc_start: 0.7539 (pmm) cc_final: 0.7251 (pmm) REVERT: A 512 ASP cc_start: 0.7619 (t0) cc_final: 0.7191 (t0) REVERT: A 726 PHE cc_start: 0.8329 (m-80) cc_final: 0.7630 (t80) REVERT: A 732 TYR cc_start: 0.8178 (t80) cc_final: 0.7520 (t80) REVERT: A 740 GLU cc_start: 0.8010 (tp30) cc_final: 0.7388 (tp30) REVERT: A 777 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7647 (tptp) REVERT: A 822 ASN cc_start: 0.8122 (t0) cc_final: 0.7813 (t0) REVERT: A 864 GLU cc_start: 0.7522 (tp30) cc_final: 0.7078 (tp30) REVERT: A 876 ASN cc_start: 0.8515 (t0) cc_final: 0.8104 (t0) REVERT: A 885 SER cc_start: 0.8453 (t) cc_final: 0.8095 (p) REVERT: A 891 TYR cc_start: 0.8174 (t80) cc_final: 0.7767 (t80) REVERT: A 939 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 984 ASP cc_start: 0.7493 (p0) cc_final: 0.7106 (p0) REVERT: A 1041 MET cc_start: 0.8456 (mtp) cc_final: 0.8171 (mtt) REVERT: A 1047 ASP cc_start: 0.7511 (p0) cc_final: 0.7047 (p0) REVERT: A 1206 GLU cc_start: 0.7753 (tp30) cc_final: 0.7416 (tp30) REVERT: A 1241 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 1300 ILE cc_start: 0.8474 (mm) cc_final: 0.8131 (mm) REVERT: A 1327 ASN cc_start: 0.7355 (p0) cc_final: 0.7062 (p0) REVERT: A 1336 ILE cc_start: 0.9142 (tp) cc_final: 0.8858 (tp) REVERT: A 1396 MET cc_start: 0.7520 (mmp) cc_final: 0.7215 (mmt) REVERT: A 1431 LYS cc_start: 0.8331 (pttm) cc_final: 0.8043 (pttm) REVERT: A 1438 GLN cc_start: 0.8383 (pt0) cc_final: 0.7885 (pp30) REVERT: F 542 GLU cc_start: 0.5698 (mp0) cc_final: 0.5334 (mp0) REVERT: G 575 MET cc_start: 0.6880 (mmt) cc_final: 0.6674 (mmt) outliers start: 16 outliers final: 13 residues processed: 362 average time/residue: 0.1380 time to fit residues: 67.0135 Evaluate side-chains 349 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 336 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 567 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 GLN A1364 ASN A1376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121561 restraints weight = 20013.001| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.43 r_work: 0.3494 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12815 Z= 0.162 Angle : 0.569 7.311 17311 Z= 0.298 Chirality : 0.042 0.170 1997 Planarity : 0.004 0.057 2201 Dihedral : 3.952 24.690 1707 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.22 % Allowed : 12.97 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.91 (0.22), residues: 1565 helix: 2.37 (0.17), residues: 957 sheet: 0.24 (0.53), residues: 99 loop : -0.70 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1082 TYR 0.011 0.001 TYR A 801 PHE 0.013 0.001 PHE A 889 TRP 0.010 0.001 TRP A1248 HIS 0.006 0.001 HIS A 843 Details of bonding type rmsd covalent geometry : bond 0.00355 (12808) covalent geometry : angle 0.56877 (17310) hydrogen bonds : bond 0.05051 ( 763) hydrogen bonds : angle 3.83559 ( 2196) metal coordination : bond 0.01121 ( 7) metal coordination : angle 1.68069 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 0.368 Fit side-chains REVERT: A 15 CYS cc_start: 0.8006 (t) cc_final: 0.7786 (t) REVERT: A 43 ASP cc_start: 0.6990 (t0) cc_final: 0.6708 (t0) REVERT: A 57 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8117 (tppt) REVERT: A 112 LYS cc_start: 0.8371 (mttt) cc_final: 0.8157 (mtmm) REVERT: A 150 GLU cc_start: 0.7884 (tp30) cc_final: 0.7267 (tp30) REVERT: A 197 CYS cc_start: 0.8593 (t) cc_final: 0.8385 (t) REVERT: A 240 ASP cc_start: 0.7702 (m-30) cc_final: 0.7388 (m-30) REVERT: A 315 CYS cc_start: 0.7860 (m) cc_final: 0.7581 (m) REVERT: A 339 ASP cc_start: 0.7723 (t0) cc_final: 0.7387 (t0) REVERT: A 355 GLU cc_start: 0.8104 (tp30) cc_final: 0.7741 (tp30) REVERT: A 376 LYS cc_start: 0.8289 (tppt) cc_final: 0.8006 (tppt) REVERT: A 423 HIS cc_start: 0.8137 (p-80) cc_final: 0.7686 (p-80) REVERT: A 512 ASP cc_start: 0.7635 (t0) cc_final: 0.7182 (t0) REVERT: A 530 LEU cc_start: 0.8061 (mt) cc_final: 0.7643 (mp) REVERT: A 726 PHE cc_start: 0.8372 (m-80) cc_final: 0.7622 (t80) REVERT: A 732 TYR cc_start: 0.8203 (t80) cc_final: 0.7598 (t80) REVERT: A 740 GLU cc_start: 0.8005 (tp30) cc_final: 0.7422 (tp30) REVERT: A 799 GLU cc_start: 0.7616 (tt0) cc_final: 0.7286 (tm-30) REVERT: A 822 ASN cc_start: 0.8189 (t0) cc_final: 0.7876 (t0) REVERT: A 845 ASN cc_start: 0.8313 (p0) cc_final: 0.7907 (p0) REVERT: A 864 GLU cc_start: 0.7541 (tp30) cc_final: 0.7114 (tp30) REVERT: A 876 ASN cc_start: 0.8552 (t0) cc_final: 0.8113 (t0) REVERT: A 885 SER cc_start: 0.8482 (t) cc_final: 0.8135 (p) REVERT: A 891 TYR cc_start: 0.8202 (t80) cc_final: 0.7782 (t80) REVERT: A 893 LYS cc_start: 0.8516 (mppt) cc_final: 0.8125 (mppt) REVERT: A 907 LYS cc_start: 0.8411 (tttp) cc_final: 0.8199 (ttmm) REVERT: A 909 MET cc_start: 0.8108 (mpp) cc_final: 0.7888 (mmp) REVERT: A 939 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 984 ASP cc_start: 0.7514 (p0) cc_final: 0.7155 (p0) REVERT: A 1041 MET cc_start: 0.8440 (mtp) cc_final: 0.7786 (mtt) REVERT: A 1047 ASP cc_start: 0.7556 (p0) cc_final: 0.7068 (p0) REVERT: A 1064 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7555 (t0) REVERT: A 1090 LYS cc_start: 0.8085 (mttt) cc_final: 0.7858 (mttt) REVERT: A 1206 GLU cc_start: 0.7774 (tp30) cc_final: 0.7326 (tp30) REVERT: A 1220 ASP cc_start: 0.6791 (t70) cc_final: 0.6585 (t70) REVERT: A 1241 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 1300 ILE cc_start: 0.8493 (mm) cc_final: 0.8123 (mm) REVERT: A 1302 THR cc_start: 0.8854 (t) cc_final: 0.8582 (p) REVERT: A 1327 ASN cc_start: 0.7255 (p0) cc_final: 0.6986 (p0) REVERT: A 1336 ILE cc_start: 0.9126 (tp) cc_final: 0.8847 (tp) REVERT: A 1412 GLU cc_start: 0.7279 (mp0) cc_final: 0.7059 (mp0) REVERT: A 1431 LYS cc_start: 0.8340 (pttm) cc_final: 0.8051 (pttm) REVERT: A 1438 GLN cc_start: 0.8405 (pt0) cc_final: 0.7884 (pp30) REVERT: F 542 GLU cc_start: 0.5438 (mp0) cc_final: 0.5143 (mp0) outliers start: 31 outliers final: 18 residues processed: 355 average time/residue: 0.1298 time to fit residues: 62.2824 Evaluate side-chains 351 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 332 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 567 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 0.9980 chunk 104 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 ASN A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.141571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.122078 restraints weight = 20010.958| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.45 r_work: 0.3496 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12815 Z= 0.150 Angle : 0.579 9.171 17311 Z= 0.299 Chirality : 0.042 0.173 1997 Planarity : 0.004 0.054 2201 Dihedral : 3.936 25.415 1707 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.37 % Allowed : 13.76 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.88 (0.22), residues: 1565 helix: 2.37 (0.17), residues: 951 sheet: 0.14 (0.52), residues: 99 loop : -0.71 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1082 TYR 0.011 0.001 TYR A 470 PHE 0.012 0.001 PHE A 889 TRP 0.009 0.001 TRP A1248 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00329 (12808) covalent geometry : angle 0.57923 (17310) hydrogen bonds : bond 0.04789 ( 763) hydrogen bonds : angle 3.74955 ( 2196) metal coordination : bond 0.01038 ( 7) metal coordination : angle 1.15375 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8479 (tt) cc_final: 0.8153 (mm) REVERT: A 15 CYS cc_start: 0.8000 (t) cc_final: 0.7785 (t) REVERT: A 57 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8182 (tppp) REVERT: A 128 MET cc_start: 0.8678 (ttp) cc_final: 0.8435 (ttm) REVERT: A 150 GLU cc_start: 0.7963 (tp30) cc_final: 0.7265 (tp30) REVERT: A 207 GLU cc_start: 0.7320 (mp0) cc_final: 0.7103 (mp0) REVERT: A 240 ASP cc_start: 0.7647 (m-30) cc_final: 0.7286 (m-30) REVERT: A 315 CYS cc_start: 0.7808 (m) cc_final: 0.7527 (m) REVERT: A 339 ASP cc_start: 0.7742 (t0) cc_final: 0.7375 (t0) REVERT: A 355 GLU cc_start: 0.8096 (tp30) cc_final: 0.7717 (tp30) REVERT: A 376 LYS cc_start: 0.8296 (tppt) cc_final: 0.8004 (tppt) REVERT: A 423 HIS cc_start: 0.8127 (p-80) cc_final: 0.7613 (p-80) REVERT: A 430 ARG cc_start: 0.6931 (mtm110) cc_final: 0.6431 (mtm110) REVERT: A 459 MET cc_start: 0.8302 (mmt) cc_final: 0.8096 (mmm) REVERT: A 470 TYR cc_start: 0.7859 (m-80) cc_final: 0.7575 (m-80) REVERT: A 512 ASP cc_start: 0.7805 (t0) cc_final: 0.7391 (t0) REVERT: A 530 LEU cc_start: 0.8048 (mt) cc_final: 0.7627 (mp) REVERT: A 726 PHE cc_start: 0.8356 (m-80) cc_final: 0.7780 (t80) REVERT: A 732 TYR cc_start: 0.8183 (t80) cc_final: 0.7527 (t80) REVERT: A 740 GLU cc_start: 0.8034 (tp30) cc_final: 0.7462 (tp30) REVERT: A 799 GLU cc_start: 0.7608 (tt0) cc_final: 0.7254 (tm-30) REVERT: A 822 ASN cc_start: 0.8197 (t0) cc_final: 0.7891 (t0) REVERT: A 841 LYS cc_start: 0.7907 (mppt) cc_final: 0.7673 (mppt) REVERT: A 843 HIS cc_start: 0.7928 (t-90) cc_final: 0.7638 (t-90) REVERT: A 845 ASN cc_start: 0.8294 (p0) cc_final: 0.7760 (p0) REVERT: A 864 GLU cc_start: 0.7524 (tp30) cc_final: 0.7105 (tp30) REVERT: A 876 ASN cc_start: 0.8589 (t0) cc_final: 0.8115 (t0) REVERT: A 885 SER cc_start: 0.8487 (t) cc_final: 0.8144 (p) REVERT: A 891 TYR cc_start: 0.8172 (t80) cc_final: 0.7754 (t80) REVERT: A 907 LYS cc_start: 0.8544 (tttp) cc_final: 0.8271 (ttmm) REVERT: A 939 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 984 ASP cc_start: 0.7525 (p0) cc_final: 0.7216 (p0) REVERT: A 1041 MET cc_start: 0.8499 (mtp) cc_final: 0.8091 (mtp) REVERT: A 1047 ASP cc_start: 0.7570 (p0) cc_final: 0.7091 (p0) REVERT: A 1064 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7562 (t0) REVERT: A 1090 LYS cc_start: 0.8085 (mttt) cc_final: 0.7852 (mttt) REVERT: A 1133 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7773 (mt-10) REVERT: A 1206 GLU cc_start: 0.7826 (tp30) cc_final: 0.7539 (tp30) REVERT: A 1220 ASP cc_start: 0.6865 (t70) cc_final: 0.6660 (t70) REVERT: A 1241 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 1300 ILE cc_start: 0.8533 (mm) cc_final: 0.8127 (mm) REVERT: A 1327 ASN cc_start: 0.6970 (p0) cc_final: 0.6714 (p0) REVERT: A 1336 ILE cc_start: 0.9144 (tp) cc_final: 0.8862 (tp) REVERT: A 1396 MET cc_start: 0.7486 (mmp) cc_final: 0.7183 (mmt) REVERT: A 1412 GLU cc_start: 0.7291 (mp0) cc_final: 0.7091 (mp0) REVERT: A 1431 LYS cc_start: 0.8339 (pttm) cc_final: 0.8043 (pttm) REVERT: A 1438 GLN cc_start: 0.8416 (pt0) cc_final: 0.7863 (pp30) REVERT: F 542 GLU cc_start: 0.5555 (mp0) cc_final: 0.5219 (mp0) REVERT: G 575 MET cc_start: 0.6624 (mmm) cc_final: 0.6240 (mmt) outliers start: 33 outliers final: 21 residues processed: 355 average time/residue: 0.1402 time to fit residues: 66.6000 Evaluate side-chains 362 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 340 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 562 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 981 ASN A1165 HIS A1364 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.120278 restraints weight = 20021.463| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.43 r_work: 0.3473 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12815 Z= 0.203 Angle : 0.612 7.701 17311 Z= 0.318 Chirality : 0.043 0.184 1997 Planarity : 0.004 0.054 2201 Dihedral : 4.044 25.722 1707 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 2.65 % Allowed : 15.48 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.76 (0.22), residues: 1565 helix: 2.24 (0.17), residues: 952 sheet: 0.15 (0.52), residues: 99 loop : -0.72 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1082 TYR 0.012 0.002 TYR A 529 PHE 0.016 0.002 PHE A 889 TRP 0.008 0.001 TRP A1204 HIS 0.005 0.001 HIS A1423 Details of bonding type rmsd covalent geometry : bond 0.00450 (12808) covalent geometry : angle 0.61177 (17310) hydrogen bonds : bond 0.05317 ( 763) hydrogen bonds : angle 3.87658 ( 2196) metal coordination : bond 0.01226 ( 7) metal coordination : angle 0.84727 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8511 (tt) cc_final: 0.8164 (mm) REVERT: A 12 TYR cc_start: 0.8229 (m-10) cc_final: 0.8027 (m-10) REVERT: A 57 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8181 (tppp) REVERT: A 150 GLU cc_start: 0.7989 (tp30) cc_final: 0.7268 (tp30) REVERT: A 197 CYS cc_start: 0.8628 (t) cc_final: 0.8399 (t) REVERT: A 240 ASP cc_start: 0.7723 (m-30) cc_final: 0.7407 (m-30) REVERT: A 315 CYS cc_start: 0.7904 (m) cc_final: 0.7608 (m) REVERT: A 319 MET cc_start: 0.8007 (mmm) cc_final: 0.7620 (ttp) REVERT: A 339 ASP cc_start: 0.7745 (t0) cc_final: 0.7399 (t0) REVERT: A 355 GLU cc_start: 0.8067 (tp30) cc_final: 0.7685 (tp30) REVERT: A 376 LYS cc_start: 0.8253 (tppt) cc_final: 0.7958 (tppt) REVERT: A 423 HIS cc_start: 0.8114 (p-80) cc_final: 0.7828 (p-80) REVERT: A 430 ARG cc_start: 0.6905 (mtm110) cc_final: 0.6404 (mtm110) REVERT: A 512 ASP cc_start: 0.7850 (t0) cc_final: 0.7475 (t0) REVERT: A 556 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: A 726 PHE cc_start: 0.8382 (m-80) cc_final: 0.7724 (t80) REVERT: A 732 TYR cc_start: 0.8251 (t80) cc_final: 0.7699 (t80) REVERT: A 740 GLU cc_start: 0.8037 (tp30) cc_final: 0.7470 (tp30) REVERT: A 799 GLU cc_start: 0.7657 (tt0) cc_final: 0.7305 (tm-30) REVERT: A 822 ASN cc_start: 0.8231 (t0) cc_final: 0.7949 (t0) REVERT: A 843 HIS cc_start: 0.7951 (t-90) cc_final: 0.7749 (t-90) REVERT: A 845 ASN cc_start: 0.8274 (p0) cc_final: 0.7831 (p0) REVERT: A 853 GLU cc_start: 0.7140 (pt0) cc_final: 0.6802 (pp20) REVERT: A 864 GLU cc_start: 0.7523 (tp30) cc_final: 0.7099 (tp30) REVERT: A 876 ASN cc_start: 0.8553 (t0) cc_final: 0.8134 (t0) REVERT: A 885 SER cc_start: 0.8621 (t) cc_final: 0.8188 (p) REVERT: A 891 TYR cc_start: 0.8191 (t80) cc_final: 0.7710 (t80) REVERT: A 907 LYS cc_start: 0.8536 (tttp) cc_final: 0.8288 (ttmm) REVERT: A 923 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8145 (m) REVERT: A 939 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 954 LYS cc_start: 0.8915 (tppt) cc_final: 0.8677 (mmtt) REVERT: A 984 ASP cc_start: 0.7545 (p0) cc_final: 0.7248 (p0) REVERT: A 1047 ASP cc_start: 0.7602 (p0) cc_final: 0.7135 (p0) REVERT: A 1090 LYS cc_start: 0.8089 (mttt) cc_final: 0.7858 (mttt) REVERT: A 1092 LEU cc_start: 0.8207 (mt) cc_final: 0.7768 (tp) REVERT: A 1133 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7821 (mt-10) REVERT: A 1206 GLU cc_start: 0.7790 (tp30) cc_final: 0.7524 (tp30) REVERT: A 1241 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 1300 ILE cc_start: 0.8506 (mm) cc_final: 0.8117 (mm) REVERT: A 1327 ASN cc_start: 0.6960 (p0) cc_final: 0.6701 (p0) REVERT: A 1336 ILE cc_start: 0.9134 (tp) cc_final: 0.8849 (tp) REVERT: A 1376 ASN cc_start: 0.8178 (t0) cc_final: 0.7961 (t0) REVERT: A 1396 MET cc_start: 0.7561 (mmp) cc_final: 0.7251 (mmt) REVERT: A 1431 LYS cc_start: 0.8360 (pttm) cc_final: 0.8085 (pttm) REVERT: A 1438 GLN cc_start: 0.8400 (pt0) cc_final: 0.7860 (pp30) REVERT: F 542 GLU cc_start: 0.5576 (mp0) cc_final: 0.5183 (mp0) outliers start: 37 outliers final: 26 residues processed: 374 average time/residue: 0.1360 time to fit residues: 68.5638 Evaluate side-chains 378 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 350 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 562 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121349 restraints weight = 19838.396| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.41 r_work: 0.3486 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12815 Z= 0.164 Angle : 0.611 10.405 17311 Z= 0.312 Chirality : 0.042 0.179 1997 Planarity : 0.004 0.053 2201 Dihedral : 3.979 25.622 1707 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.58 % Allowed : 16.63 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.83 (0.22), residues: 1565 helix: 2.32 (0.17), residues: 952 sheet: 0.19 (0.53), residues: 99 loop : -0.74 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1082 TYR 0.011 0.001 TYR A 529 PHE 0.013 0.001 PHE A 889 TRP 0.009 0.001 TRP A 754 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00366 (12808) covalent geometry : angle 0.61051 (17310) hydrogen bonds : bond 0.04919 ( 763) hydrogen bonds : angle 3.78950 ( 2196) metal coordination : bond 0.01051 ( 7) metal coordination : angle 0.78328 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8517 (tt) cc_final: 0.8273 (mm) REVERT: A 14 GLU cc_start: 0.7174 (pm20) cc_final: 0.6946 (pm20) REVERT: A 57 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8047 (tppp) REVERT: A 150 GLU cc_start: 0.7957 (tp30) cc_final: 0.7593 (tm-30) REVERT: A 179 GLU cc_start: 0.8239 (tp30) cc_final: 0.7860 (tp30) REVERT: A 193 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7633 (mtt90) REVERT: A 197 CYS cc_start: 0.8611 (t) cc_final: 0.8246 (p) REVERT: A 198 ILE cc_start: 0.8748 (tt) cc_final: 0.8548 (pt) REVERT: A 240 ASP cc_start: 0.7708 (m-30) cc_final: 0.7396 (m-30) REVERT: A 315 CYS cc_start: 0.7794 (m) cc_final: 0.7550 (m) REVERT: A 339 ASP cc_start: 0.7754 (t0) cc_final: 0.7421 (t0) REVERT: A 355 GLU cc_start: 0.8053 (tp30) cc_final: 0.7687 (tp30) REVERT: A 376 LYS cc_start: 0.8261 (tppt) cc_final: 0.7969 (tppt) REVERT: A 423 HIS cc_start: 0.8098 (p-80) cc_final: 0.7817 (p-80) REVERT: A 430 ARG cc_start: 0.6889 (mtm110) cc_final: 0.6527 (mtm110) REVERT: A 459 MET cc_start: 0.8209 (mmm) cc_final: 0.7963 (mmt) REVERT: A 460 GLU cc_start: 0.7518 (tp30) cc_final: 0.7229 (tp30) REVERT: A 512 ASP cc_start: 0.7829 (t0) cc_final: 0.7486 (t0) REVERT: A 520 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7902 (mtt) REVERT: A 530 LEU cc_start: 0.8091 (mt) cc_final: 0.7777 (mp) REVERT: A 531 GLU cc_start: 0.7518 (pm20) cc_final: 0.7310 (pm20) REVERT: A 732 TYR cc_start: 0.8215 (t80) cc_final: 0.7616 (t80) REVERT: A 740 GLU cc_start: 0.7979 (tp30) cc_final: 0.7464 (tp30) REVERT: A 743 ASP cc_start: 0.7289 (t0) cc_final: 0.7004 (t0) REVERT: A 799 GLU cc_start: 0.7605 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 803 GLN cc_start: 0.7593 (tp40) cc_final: 0.7249 (tp-100) REVERT: A 822 ASN cc_start: 0.8202 (t0) cc_final: 0.7937 (t0) REVERT: A 845 ASN cc_start: 0.8338 (p0) cc_final: 0.7983 (p0) REVERT: A 853 GLU cc_start: 0.7128 (pt0) cc_final: 0.6781 (pp20) REVERT: A 864 GLU cc_start: 0.7527 (tp30) cc_final: 0.7115 (tp30) REVERT: A 876 ASN cc_start: 0.8555 (t0) cc_final: 0.8086 (t0) REVERT: A 885 SER cc_start: 0.8615 (t) cc_final: 0.8203 (p) REVERT: A 891 TYR cc_start: 0.8203 (t80) cc_final: 0.7749 (t80) REVERT: A 893 LYS cc_start: 0.8496 (mppt) cc_final: 0.8091 (mppt) REVERT: A 939 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 954 LYS cc_start: 0.8916 (tppt) cc_final: 0.8712 (mmtt) REVERT: A 957 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: A 984 ASP cc_start: 0.7520 (p0) cc_final: 0.7233 (p0) REVERT: A 1047 ASP cc_start: 0.7584 (p0) cc_final: 0.7121 (p0) REVERT: A 1090 LYS cc_start: 0.8087 (mttt) cc_final: 0.7856 (mttt) REVERT: A 1092 LEU cc_start: 0.8182 (mt) cc_final: 0.7747 (tp) REVERT: A 1206 GLU cc_start: 0.7799 (tp30) cc_final: 0.7409 (tp30) REVERT: A 1241 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 1300 ILE cc_start: 0.8514 (mm) cc_final: 0.8088 (mm) REVERT: A 1327 ASN cc_start: 0.6940 (p0) cc_final: 0.6686 (p0) REVERT: A 1336 ILE cc_start: 0.9078 (tp) cc_final: 0.8798 (tp) REVERT: A 1431 LYS cc_start: 0.8329 (pttm) cc_final: 0.8046 (pttm) REVERT: A 1438 GLN cc_start: 0.8389 (pt0) cc_final: 0.7861 (pp30) REVERT: F 542 GLU cc_start: 0.5650 (mp0) cc_final: 0.5237 (mp0) outliers start: 36 outliers final: 24 residues processed: 372 average time/residue: 0.1354 time to fit residues: 67.9679 Evaluate side-chains 375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 562 THR Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119990 restraints weight = 19910.484| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.40 r_work: 0.3468 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12815 Z= 0.191 Angle : 0.635 10.064 17311 Z= 0.325 Chirality : 0.043 0.184 1997 Planarity : 0.004 0.052 2201 Dihedral : 4.037 25.790 1707 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.94 % Allowed : 16.92 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.73 (0.22), residues: 1565 helix: 2.25 (0.17), residues: 952 sheet: 0.21 (0.52), residues: 99 loop : -0.80 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1082 TYR 0.012 0.002 TYR A 529 PHE 0.015 0.002 PHE A 889 TRP 0.008 0.001 TRP A 754 HIS 0.004 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00428 (12808) covalent geometry : angle 0.63526 (17310) hydrogen bonds : bond 0.05189 ( 763) hydrogen bonds : angle 3.85689 ( 2196) metal coordination : bond 0.01116 ( 7) metal coordination : angle 1.52354 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 0.461 Fit side-chains REVERT: A 10 ILE cc_start: 0.8527 (tt) cc_final: 0.8287 (mm) REVERT: A 14 GLU cc_start: 0.7197 (pm20) cc_final: 0.6961 (pm20) REVERT: A 57 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8085 (tppp) REVERT: A 150 GLU cc_start: 0.7982 (tp30) cc_final: 0.7230 (tp30) REVERT: A 179 GLU cc_start: 0.8256 (tp30) cc_final: 0.7868 (tp30) REVERT: A 193 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7572 (mtt90) REVERT: A 197 CYS cc_start: 0.8611 (t) cc_final: 0.8251 (p) REVERT: A 240 ASP cc_start: 0.7693 (m-30) cc_final: 0.7377 (m-30) REVERT: A 315 CYS cc_start: 0.7828 (m) cc_final: 0.7578 (m) REVERT: A 339 ASP cc_start: 0.7754 (t0) cc_final: 0.7436 (t0) REVERT: A 355 GLU cc_start: 0.8031 (tp30) cc_final: 0.7664 (tp30) REVERT: A 376 LYS cc_start: 0.8282 (tppt) cc_final: 0.7985 (tppt) REVERT: A 423 HIS cc_start: 0.8103 (p-80) cc_final: 0.7804 (p-80) REVERT: A 430 ARG cc_start: 0.6890 (mtm110) cc_final: 0.6527 (mtm110) REVERT: A 459 MET cc_start: 0.8232 (mmm) cc_final: 0.7980 (mmt) REVERT: A 460 GLU cc_start: 0.7631 (tp30) cc_final: 0.7407 (tp30) REVERT: A 469 MET cc_start: 0.7651 (pmm) cc_final: 0.7248 (pmm) REVERT: A 470 TYR cc_start: 0.8061 (m-80) cc_final: 0.7528 (m-80) REVERT: A 507 ASP cc_start: 0.7980 (t70) cc_final: 0.7723 (t0) REVERT: A 512 ASP cc_start: 0.7846 (t0) cc_final: 0.7516 (t0) REVERT: A 520 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7884 (mtt) REVERT: A 537 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 726 PHE cc_start: 0.8387 (m-80) cc_final: 0.7750 (t80) REVERT: A 732 TYR cc_start: 0.8238 (t80) cc_final: 0.7697 (t80) REVERT: A 740 GLU cc_start: 0.8013 (tp30) cc_final: 0.7498 (tp30) REVERT: A 743 ASP cc_start: 0.7235 (t0) cc_final: 0.6884 (t0) REVERT: A 798 ILE cc_start: 0.7865 (mt) cc_final: 0.7538 (mm) REVERT: A 799 GLU cc_start: 0.7669 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 803 GLN cc_start: 0.7652 (tp40) cc_final: 0.7307 (tp-100) REVERT: A 822 ASN cc_start: 0.8320 (t0) cc_final: 0.8011 (t0) REVERT: A 845 ASN cc_start: 0.8239 (p0) cc_final: 0.7988 (p0) REVERT: A 853 GLU cc_start: 0.7149 (pt0) cc_final: 0.6826 (pp20) REVERT: A 864 GLU cc_start: 0.7551 (tp30) cc_final: 0.7128 (tp30) REVERT: A 876 ASN cc_start: 0.8565 (t0) cc_final: 0.8115 (t0) REVERT: A 885 SER cc_start: 0.8622 (t) cc_final: 0.8220 (p) REVERT: A 891 TYR cc_start: 0.8205 (t80) cc_final: 0.7748 (t80) REVERT: A 893 LYS cc_start: 0.8521 (mppt) cc_final: 0.8114 (mppt) REVERT: A 907 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8495 (tttp) REVERT: A 939 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 954 LYS cc_start: 0.8929 (tppt) cc_final: 0.8700 (mmtt) REVERT: A 957 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: A 984 ASP cc_start: 0.7549 (p0) cc_final: 0.7292 (p0) REVERT: A 1047 ASP cc_start: 0.7602 (p0) cc_final: 0.7152 (p0) REVERT: A 1064 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7595 (t0) REVERT: A 1080 ILE cc_start: 0.8806 (tp) cc_final: 0.8447 (tp) REVERT: A 1090 LYS cc_start: 0.8090 (mttt) cc_final: 0.7853 (mttt) REVERT: A 1092 LEU cc_start: 0.8198 (mt) cc_final: 0.7779 (tp) REVERT: A 1122 ILE cc_start: 0.8637 (tt) cc_final: 0.8334 (mt) REVERT: A 1206 GLU cc_start: 0.7808 (tp30) cc_final: 0.7431 (tp30) REVERT: A 1241 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 1327 ASN cc_start: 0.6925 (p0) cc_final: 0.6646 (p0) REVERT: A 1336 ILE cc_start: 0.9084 (tp) cc_final: 0.8806 (tp) REVERT: A 1431 LYS cc_start: 0.8346 (pttm) cc_final: 0.8065 (pttm) REVERT: A 1438 GLN cc_start: 0.8399 (pt0) cc_final: 0.7864 (pp30) REVERT: F 542 GLU cc_start: 0.5683 (mp0) cc_final: 0.5247 (mp0) outliers start: 41 outliers final: 32 residues processed: 372 average time/residue: 0.1413 time to fit residues: 70.6770 Evaluate side-chains 383 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 562 THR Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.120912 restraints weight = 19716.824| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.41 r_work: 0.3486 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12815 Z= 0.152 Angle : 0.622 9.631 17311 Z= 0.316 Chirality : 0.042 0.179 1997 Planarity : 0.004 0.051 2201 Dihedral : 3.972 26.123 1707 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 2.65 % Allowed : 17.78 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.81 (0.22), residues: 1565 helix: 2.32 (0.17), residues: 951 sheet: 0.27 (0.52), residues: 99 loop : -0.79 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1082 TYR 0.010 0.001 TYR A1320 PHE 0.013 0.001 PHE A 889 TRP 0.008 0.001 TRP A 754 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00342 (12808) covalent geometry : angle 0.62199 (17310) hydrogen bonds : bond 0.04752 ( 763) hydrogen bonds : angle 3.75741 ( 2196) metal coordination : bond 0.00931 ( 7) metal coordination : angle 1.47638 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 351 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8510 (tt) cc_final: 0.8293 (mm) REVERT: A 14 GLU cc_start: 0.7216 (pm20) cc_final: 0.6977 (pm20) REVERT: A 57 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8063 (tppp) REVERT: A 76 ASN cc_start: 0.8503 (m-40) cc_final: 0.7659 (m110) REVERT: A 150 GLU cc_start: 0.7996 (tp30) cc_final: 0.7231 (tp30) REVERT: A 179 GLU cc_start: 0.8244 (tp30) cc_final: 0.7877 (tp30) REVERT: A 193 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7533 (mtt90) REVERT: A 233 GLU cc_start: 0.7204 (pp20) cc_final: 0.6908 (pp20) REVERT: A 240 ASP cc_start: 0.7682 (m-30) cc_final: 0.7363 (m-30) REVERT: A 249 GLU cc_start: 0.7900 (tp30) cc_final: 0.7678 (tp30) REVERT: A 315 CYS cc_start: 0.7891 (m) cc_final: 0.7636 (m) REVERT: A 318 GLU cc_start: 0.8180 (tp30) cc_final: 0.7904 (tp30) REVERT: A 339 ASP cc_start: 0.7778 (t0) cc_final: 0.7460 (t0) REVERT: A 355 GLU cc_start: 0.7980 (tp30) cc_final: 0.7650 (tp30) REVERT: A 376 LYS cc_start: 0.8262 (tppt) cc_final: 0.7959 (tppt) REVERT: A 423 HIS cc_start: 0.8078 (p-80) cc_final: 0.7775 (p-80) REVERT: A 430 ARG cc_start: 0.6879 (mtm110) cc_final: 0.6507 (mtm110) REVERT: A 459 MET cc_start: 0.8234 (mmm) cc_final: 0.7966 (mmt) REVERT: A 469 MET cc_start: 0.7640 (pmm) cc_final: 0.7276 (pmm) REVERT: A 507 ASP cc_start: 0.7984 (t70) cc_final: 0.7725 (t0) REVERT: A 512 ASP cc_start: 0.7858 (t0) cc_final: 0.7514 (t0) REVERT: A 520 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7894 (mtt) REVERT: A 537 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (p) REVERT: A 726 PHE cc_start: 0.8386 (m-80) cc_final: 0.7620 (t80) REVERT: A 730 TRP cc_start: 0.8552 (m100) cc_final: 0.8000 (m100) REVERT: A 732 TYR cc_start: 0.8206 (t80) cc_final: 0.7689 (t80) REVERT: A 740 GLU cc_start: 0.8007 (tp30) cc_final: 0.7484 (tp30) REVERT: A 743 ASP cc_start: 0.7189 (t0) cc_final: 0.6836 (t0) REVERT: A 798 ILE cc_start: 0.7866 (mt) cc_final: 0.7518 (mm) REVERT: A 799 GLU cc_start: 0.7639 (tt0) cc_final: 0.7186 (tm-30) REVERT: A 822 ASN cc_start: 0.8313 (t0) cc_final: 0.8013 (t0) REVERT: A 840 GLN cc_start: 0.7932 (tp40) cc_final: 0.7435 (tm-30) REVERT: A 845 ASN cc_start: 0.8205 (p0) cc_final: 0.7997 (p0) REVERT: A 851 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7872 (mtmt) REVERT: A 853 GLU cc_start: 0.7098 (pt0) cc_final: 0.6751 (pp20) REVERT: A 864 GLU cc_start: 0.7551 (tp30) cc_final: 0.7142 (tp30) REVERT: A 876 ASN cc_start: 0.8567 (t0) cc_final: 0.8123 (t0) REVERT: A 885 SER cc_start: 0.8609 (t) cc_final: 0.8204 (p) REVERT: A 891 TYR cc_start: 0.8193 (t80) cc_final: 0.7757 (t80) REVERT: A 893 LYS cc_start: 0.8499 (mppt) cc_final: 0.8087 (mppt) REVERT: A 907 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8430 (tttp) REVERT: A 939 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 954 LYS cc_start: 0.8895 (tppt) cc_final: 0.8674 (mmtt) REVERT: A 957 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: A 984 ASP cc_start: 0.7511 (p0) cc_final: 0.7254 (p0) REVERT: A 1047 ASP cc_start: 0.7566 (p0) cc_final: 0.7138 (p0) REVERT: A 1064 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 1080 ILE cc_start: 0.8773 (tp) cc_final: 0.8435 (tp) REVERT: A 1090 LYS cc_start: 0.8079 (mttt) cc_final: 0.7837 (mttt) REVERT: A 1092 LEU cc_start: 0.8179 (mt) cc_final: 0.7757 (tp) REVERT: A 1206 GLU cc_start: 0.7781 (tp30) cc_final: 0.7411 (tp30) REVERT: A 1220 ASP cc_start: 0.6411 (t0) cc_final: 0.6185 (t0) REVERT: A 1241 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 1327 ASN cc_start: 0.6883 (p0) cc_final: 0.6633 (p0) REVERT: A 1336 ILE cc_start: 0.9074 (tp) cc_final: 0.8798 (tp) REVERT: A 1431 LYS cc_start: 0.8329 (pttm) cc_final: 0.8054 (pttm) REVERT: A 1438 GLN cc_start: 0.8397 (pt0) cc_final: 0.7890 (pp30) REVERT: F 542 GLU cc_start: 0.5719 (mp0) cc_final: 0.5283 (mp0) outliers start: 37 outliers final: 28 residues processed: 369 average time/residue: 0.1328 time to fit residues: 66.2177 Evaluate side-chains 376 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 0.9990 chunk 90 optimal weight: 0.0170 chunk 59 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120638 restraints weight = 19865.120| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.41 r_work: 0.3486 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12815 Z= 0.159 Angle : 0.637 10.207 17311 Z= 0.323 Chirality : 0.042 0.176 1997 Planarity : 0.004 0.053 2201 Dihedral : 3.970 26.513 1707 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 2.65 % Allowed : 18.06 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.80 (0.22), residues: 1565 helix: 2.28 (0.17), residues: 959 sheet: 0.36 (0.53), residues: 95 loop : -0.78 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1082 TYR 0.010 0.001 TYR A1320 PHE 0.013 0.001 PHE A 889 TRP 0.007 0.001 TRP A 754 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00360 (12808) covalent geometry : angle 0.63748 (17310) hydrogen bonds : bond 0.04787 ( 763) hydrogen bonds : angle 3.77874 ( 2196) metal coordination : bond 0.00924 ( 7) metal coordination : angle 0.57074 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 344 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8519 (tt) cc_final: 0.8309 (mm) REVERT: A 14 GLU cc_start: 0.7114 (pm20) cc_final: 0.6772 (pm20) REVERT: A 57 LYS cc_start: 0.8392 (mmtt) cc_final: 0.8025 (tppp) REVERT: A 150 GLU cc_start: 0.8015 (tp30) cc_final: 0.7263 (tp30) REVERT: A 179 GLU cc_start: 0.8178 (tp30) cc_final: 0.7806 (tp30) REVERT: A 193 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7515 (mtt90) REVERT: A 233 GLU cc_start: 0.7219 (pp20) cc_final: 0.6932 (pp20) REVERT: A 240 ASP cc_start: 0.7658 (m-30) cc_final: 0.7350 (m-30) REVERT: A 307 LEU cc_start: 0.8311 (mt) cc_final: 0.8107 (mt) REVERT: A 315 CYS cc_start: 0.7879 (m) cc_final: 0.7633 (m) REVERT: A 339 ASP cc_start: 0.7743 (t0) cc_final: 0.7438 (t0) REVERT: A 355 GLU cc_start: 0.7995 (tp30) cc_final: 0.7655 (tp30) REVERT: A 376 LYS cc_start: 0.8253 (tppt) cc_final: 0.7954 (tppt) REVERT: A 423 HIS cc_start: 0.8079 (p-80) cc_final: 0.7778 (p-80) REVERT: A 430 ARG cc_start: 0.6886 (mtm110) cc_final: 0.6507 (mtm110) REVERT: A 459 MET cc_start: 0.8217 (mmm) cc_final: 0.7985 (mmt) REVERT: A 469 MET cc_start: 0.7589 (pmm) cc_final: 0.7260 (pmm) REVERT: A 507 ASP cc_start: 0.8021 (t70) cc_final: 0.7767 (t0) REVERT: A 512 ASP cc_start: 0.7835 (t0) cc_final: 0.7467 (t0) REVERT: A 520 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7857 (mtt) REVERT: A 537 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 726 PHE cc_start: 0.8340 (m-80) cc_final: 0.7579 (t80) REVERT: A 730 TRP cc_start: 0.8559 (m100) cc_final: 0.8020 (m100) REVERT: A 732 TYR cc_start: 0.8182 (t80) cc_final: 0.7614 (t80) REVERT: A 740 GLU cc_start: 0.7996 (tp30) cc_final: 0.7489 (tp30) REVERT: A 743 ASP cc_start: 0.7178 (t0) cc_final: 0.6818 (t0) REVERT: A 798 ILE cc_start: 0.7898 (mt) cc_final: 0.7541 (mm) REVERT: A 799 GLU cc_start: 0.7535 (tt0) cc_final: 0.7189 (tm-30) REVERT: A 822 ASN cc_start: 0.8306 (t0) cc_final: 0.8008 (t0) REVERT: A 853 GLU cc_start: 0.7106 (pt0) cc_final: 0.6765 (pp20) REVERT: A 864 GLU cc_start: 0.7553 (tp30) cc_final: 0.7141 (tp30) REVERT: A 876 ASN cc_start: 0.8561 (t0) cc_final: 0.8114 (t0) REVERT: A 885 SER cc_start: 0.8602 (t) cc_final: 0.8198 (p) REVERT: A 891 TYR cc_start: 0.8192 (t80) cc_final: 0.7753 (t80) REVERT: A 893 LYS cc_start: 0.8490 (mppt) cc_final: 0.8084 (mppt) REVERT: A 907 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8431 (tttp) REVERT: A 939 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 954 LYS cc_start: 0.8898 (tppt) cc_final: 0.8685 (mmtt) REVERT: A 957 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: A 984 ASP cc_start: 0.7499 (p0) cc_final: 0.7251 (p0) REVERT: A 1047 ASP cc_start: 0.7545 (p0) cc_final: 0.7117 (p0) REVERT: A 1064 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7533 (t0) REVERT: A 1090 LYS cc_start: 0.8087 (mttt) cc_final: 0.7836 (mttt) REVERT: A 1092 LEU cc_start: 0.8179 (mt) cc_final: 0.7768 (tp) REVERT: A 1206 GLU cc_start: 0.7778 (tp30) cc_final: 0.7416 (tp30) REVERT: A 1241 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 1327 ASN cc_start: 0.6906 (p0) cc_final: 0.6631 (p0) REVERT: A 1336 ILE cc_start: 0.9077 (tp) cc_final: 0.8807 (tp) REVERT: A 1431 LYS cc_start: 0.8327 (pttm) cc_final: 0.8055 (pttm) REVERT: A 1438 GLN cc_start: 0.8344 (pt0) cc_final: 0.7859 (pp30) REVERT: F 542 GLU cc_start: 0.5735 (mp0) cc_final: 0.5288 (mp0) outliers start: 37 outliers final: 28 residues processed: 365 average time/residue: 0.1444 time to fit residues: 70.5748 Evaluate side-chains 375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.139140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120298 restraints weight = 20033.641| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.37 r_work: 0.3474 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12815 Z= 0.172 Angle : 0.663 10.867 17311 Z= 0.334 Chirality : 0.043 0.176 1997 Planarity : 0.004 0.053 2201 Dihedral : 4.009 26.485 1707 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.65 % Allowed : 17.92 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.76 (0.22), residues: 1565 helix: 2.29 (0.17), residues: 952 sheet: 0.17 (0.51), residues: 99 loop : -0.81 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1082 TYR 0.010 0.001 TYR A1320 PHE 0.014 0.001 PHE A 889 TRP 0.008 0.001 TRP A 754 HIS 0.003 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00392 (12808) covalent geometry : angle 0.66314 (17310) hydrogen bonds : bond 0.04875 ( 763) hydrogen bonds : angle 3.79173 ( 2196) metal coordination : bond 0.00935 ( 7) metal coordination : angle 0.06403 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 348 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7126 (pm20) cc_final: 0.6774 (pm20) REVERT: A 57 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8048 (tppp) REVERT: A 150 GLU cc_start: 0.7989 (tp30) cc_final: 0.7248 (tp30) REVERT: A 179 GLU cc_start: 0.8158 (tp30) cc_final: 0.7939 (tp30) REVERT: A 193 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7495 (mtt90) REVERT: A 240 ASP cc_start: 0.7663 (m-30) cc_final: 0.7352 (m-30) REVERT: A 315 CYS cc_start: 0.7865 (m) cc_final: 0.7613 (m) REVERT: A 319 MET cc_start: 0.7997 (mmm) cc_final: 0.7617 (ttp) REVERT: A 336 MET cc_start: 0.7522 (tpp) cc_final: 0.7284 (tpp) REVERT: A 339 ASP cc_start: 0.7789 (t0) cc_final: 0.7498 (t0) REVERT: A 355 GLU cc_start: 0.7982 (tp30) cc_final: 0.7652 (tp30) REVERT: A 376 LYS cc_start: 0.8246 (tppt) cc_final: 0.7950 (tppt) REVERT: A 423 HIS cc_start: 0.8104 (p-80) cc_final: 0.7805 (p-80) REVERT: A 459 MET cc_start: 0.8151 (mmm) cc_final: 0.7926 (mmt) REVERT: A 469 MET cc_start: 0.7599 (pmm) cc_final: 0.7276 (pmm) REVERT: A 507 ASP cc_start: 0.8092 (t70) cc_final: 0.7828 (t0) REVERT: A 512 ASP cc_start: 0.7816 (t0) cc_final: 0.7464 (t0) REVERT: A 520 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7824 (mtt) REVERT: A 537 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8127 (p) REVERT: A 726 PHE cc_start: 0.8302 (m-80) cc_final: 0.7563 (t80) REVERT: A 730 TRP cc_start: 0.8568 (m100) cc_final: 0.8040 (m100) REVERT: A 732 TYR cc_start: 0.8175 (t80) cc_final: 0.7704 (t80) REVERT: A 740 GLU cc_start: 0.8002 (tp30) cc_final: 0.7365 (tp30) REVERT: A 743 ASP cc_start: 0.7167 (t0) cc_final: 0.6797 (t0) REVERT: A 744 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 798 ILE cc_start: 0.7925 (mt) cc_final: 0.7562 (mm) REVERT: A 799 GLU cc_start: 0.7556 (tt0) cc_final: 0.7196 (tm-30) REVERT: A 822 ASN cc_start: 0.8286 (t0) cc_final: 0.7985 (t0) REVERT: A 853 GLU cc_start: 0.7125 (pt0) cc_final: 0.6774 (pp20) REVERT: A 864 GLU cc_start: 0.7561 (tp30) cc_final: 0.7154 (tp30) REVERT: A 876 ASN cc_start: 0.8559 (t0) cc_final: 0.8160 (t0) REVERT: A 885 SER cc_start: 0.8600 (t) cc_final: 0.8214 (p) REVERT: A 891 TYR cc_start: 0.8192 (t80) cc_final: 0.7734 (t80) REVERT: A 893 LYS cc_start: 0.8496 (mppt) cc_final: 0.8096 (mppt) REVERT: A 907 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8433 (tttp) REVERT: A 939 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 957 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: A 984 ASP cc_start: 0.7532 (p0) cc_final: 0.7304 (p0) REVERT: A 1047 ASP cc_start: 0.7568 (p0) cc_final: 0.7150 (p0) REVERT: A 1064 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7531 (t0) REVERT: A 1080 ILE cc_start: 0.8783 (tp) cc_final: 0.8451 (tp) REVERT: A 1090 LYS cc_start: 0.8086 (mttt) cc_final: 0.7834 (mttt) REVERT: A 1092 LEU cc_start: 0.8197 (mt) cc_final: 0.7782 (tp) REVERT: A 1206 GLU cc_start: 0.7799 (tp30) cc_final: 0.7441 (tp30) REVERT: A 1241 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8076 (tm-30) REVERT: A 1327 ASN cc_start: 0.6945 (p0) cc_final: 0.6689 (p0) REVERT: A 1336 ILE cc_start: 0.9082 (tp) cc_final: 0.8810 (tp) REVERT: A 1431 LYS cc_start: 0.8338 (pttm) cc_final: 0.8063 (pttm) REVERT: A 1438 GLN cc_start: 0.8349 (pt0) cc_final: 0.7861 (pp30) REVERT: F 542 GLU cc_start: 0.5764 (mp0) cc_final: 0.5316 (mp0) outliers start: 37 outliers final: 31 residues processed: 369 average time/residue: 0.1424 time to fit residues: 70.3441 Evaluate side-chains 379 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1084 SER Chi-restraints excluded: chain A residue 1127 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1306 TRP Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 543 ILE Chi-restraints excluded: chain F residue 556 VAL Chi-restraints excluded: chain F residue 564 LEU Chi-restraints excluded: chain G residue 537 GLU Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1011 ASN A1364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119843 restraints weight = 19992.757| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.43 r_work: 0.3473 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12815 Z= 0.181 Angle : 0.666 10.072 17311 Z= 0.339 Chirality : 0.043 0.178 1997 Planarity : 0.004 0.058 2201 Dihedral : 4.046 26.518 1707 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 2.72 % Allowed : 18.49 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 1.70 (0.22), residues: 1565 helix: 2.24 (0.17), residues: 952 sheet: 0.21 (0.51), residues: 99 loop : -0.85 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1082 TYR 0.027 0.001 TYR A 801 PHE 0.014 0.001 PHE A 889 TRP 0.006 0.001 TRP A 754 HIS 0.005 0.001 HIS A1165 Details of bonding type rmsd covalent geometry : bond 0.00412 (12808) covalent geometry : angle 0.66556 (17310) hydrogen bonds : bond 0.04962 ( 763) hydrogen bonds : angle 3.84910 ( 2196) metal coordination : bond 0.00980 ( 7) metal coordination : angle 0.09305 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.08 seconds wall clock time: 53 minutes 48.07 seconds (3228.07 seconds total)