Starting phenix.real_space_refine on Thu Jun 12 16:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ir3_60799/06_2025/9ir3_60799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ir3_60799/06_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_60799/06_2025/9ir3_60799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ir3_60799/06_2025/9ir3_60799.map" model { file = "/net/cci-nas-00/data/ceres_data/9ir3_60799/06_2025/9ir3_60799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ir3_60799/06_2025/9ir3_60799.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.48, per 1000 atoms: 0.59 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.49 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: 4.26 Time building geometry restraints manager: 3.95 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.910 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (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 TRP 0.029 0.002 TRP A 754 HIS 0.006 0.001 HIS A 792 PHE 0.014 0.001 PHE A 914 TYR 0.015 0.002 TYR A 529 ARG 0.013 0.001 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.13549 ( 763) hydrogen bonds : angle 4.78038 ( 2196) metal coordination : bond 0.21059 ( 7) metal coordination : angle 1.65100 ( 1) covalent geometry : bond 0.00369 (12808) covalent geometry : angle 0.63560 (17310) *********************** 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 : 1.406 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: 0.8352 (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 318 GLU cc_start: 0.7793 (tp30) cc_final: 0.7590 (tp30) 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: 0.6857 (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: 0.7686 (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: 0.8032 (mm) REVERT: A 1327 ASN cc_start: 0.7291 (p0) cc_final: 0.7000 (p0) REVERT: A 1336 ILE cc_start: 0.8945 (tp) cc_final: 0.8651 (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: 0.3207 time to fit residues: 158.0644 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 : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 65 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** A1376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122285 restraints weight = 19765.745| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.42 r_work: 0.3503 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12815 Z= 0.166 Angle : 0.594 7.966 17311 Z= 0.310 Chirality : 0.043 0.185 1997 Planarity : 0.004 0.069 2201 Dihedral : 4.009 27.292 1707 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 1.22 % Allowed : 10.61 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1565 helix: 2.29 (0.18), residues: 960 sheet: 0.33 (0.54), residues: 99 loop : -0.63 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 754 HIS 0.005 0.001 HIS A 792 PHE 0.017 0.002 PHE A1107 TYR 0.011 0.001 TYR A 529 ARG 0.008 0.000 ARG A 761 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 763) hydrogen bonds : angle 3.96176 ( 2196) metal coordination : bond 0.02572 ( 7) metal coordination : angle 1.49749 ( 1) covalent geometry : bond 0.00362 (12808) covalent geometry : angle 0.59349 (17310) *********************** 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 364 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 2.185 Fit side-chains REVERT: A 31 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7242 (mp0) REVERT: A 57 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8138 (tppt) REVERT: A 112 LYS cc_start: 0.8364 (mttt) cc_final: 0.8155 (mtmm) REVERT: A 179 GLU cc_start: 0.8281 (tp30) cc_final: 0.7891 (tp30) REVERT: A 189 LYS cc_start: 0.8482 (pptt) cc_final: 0.8207 (pptt) REVERT: A 197 CYS cc_start: 0.8506 (t) cc_final: 0.7963 (p) REVERT: A 207 GLU cc_start: 0.7351 (mp0) cc_final: 0.7090 (mp0) REVERT: A 240 ASP cc_start: 0.7705 (m-30) cc_final: 0.7348 (m-30) REVERT: A 246 MET cc_start: 0.8073 (ttp) cc_final: 0.7742 (ttp) REVERT: A 259 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 262 ILE cc_start: 0.8207 (mt) cc_final: 0.7916 (mt) REVERT: A 282 ARG cc_start: 0.8590 (mtt90) cc_final: 0.8255 (mmm-85) REVERT: A 315 CYS cc_start: 0.7851 (m) cc_final: 0.7569 (m) REVERT: A 321 GLN cc_start: 0.8257 (tt0) cc_final: 0.8054 (tp40) REVERT: A 355 GLU cc_start: 0.8055 (tp30) cc_final: 0.7683 (tp30) REVERT: A 376 LYS cc_start: 0.8133 (tppt) cc_final: 0.7840 (tppp) REVERT: A 423 HIS cc_start: 0.8151 (p-80) cc_final: 0.7614 (p-80) REVERT: A 469 MET cc_start: 0.7557 (pmm) cc_final: 0.7249 (pmm) REVERT: A 512 ASP cc_start: 0.7607 (t0) cc_final: 0.7170 (t0) REVERT: A 726 PHE cc_start: 0.8324 (m-80) cc_final: 0.7616 (t80) REVERT: A 732 TYR cc_start: 0.8181 (t80) cc_final: 0.7531 (t80) REVERT: A 740 GLU cc_start: 0.8003 (tp30) cc_final: 0.7383 (tp30) REVERT: A 777 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7660 (tptp) REVERT: A 822 ASN cc_start: 0.8112 (t0) cc_final: 0.7807 (t0) REVERT: A 843 HIS cc_start: 0.7945 (t-90) cc_final: 0.7733 (t-90) REVERT: A 864 GLU cc_start: 0.7548 (tp30) cc_final: 0.7107 (tp30) REVERT: A 876 ASN cc_start: 0.8523 (t0) cc_final: 0.8111 (t0) REVERT: A 885 SER cc_start: 0.8454 (t) cc_final: 0.8092 (p) REVERT: A 891 TYR cc_start: 0.8166 (t80) cc_final: 0.7763 (t80) REVERT: A 939 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 984 ASP cc_start: 0.7483 (p0) cc_final: 0.7113 (p0) REVERT: A 1041 MET cc_start: 0.8442 (mtp) cc_final: 0.8158 (mtt) REVERT: A 1047 ASP cc_start: 0.7521 (p0) cc_final: 0.7058 (p0) REVERT: A 1206 GLU cc_start: 0.7773 (tp30) cc_final: 0.7432 (tp30) REVERT: A 1241 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 1300 ILE cc_start: 0.8463 (mm) cc_final: 0.8123 (mm) REVERT: A 1327 ASN cc_start: 0.7365 (p0) cc_final: 0.7084 (p0) REVERT: A 1336 ILE cc_start: 0.9139 (tp) cc_final: 0.8855 (tp) REVERT: A 1396 MET cc_start: 0.7519 (mmp) cc_final: 0.7214 (mmt) REVERT: A 1431 LYS cc_start: 0.8329 (pttm) cc_final: 0.8016 (pttm) REVERT: A 1438 GLN cc_start: 0.8411 (pt0) cc_final: 0.7902 (pp30) REVERT: F 542 GLU cc_start: 0.5705 (mp0) cc_final: 0.5335 (mp0) outliers start: 17 outliers final: 14 residues processed: 355 average time/residue: 0.4098 time to fit residues: 197.8972 Evaluate side-chains 346 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 332 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 556 MET 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 137 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 123 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.142523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123004 restraints weight = 20141.988| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.46 r_work: 0.3517 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12815 Z= 0.129 Angle : 0.551 7.225 17311 Z= 0.286 Chirality : 0.041 0.166 1997 Planarity : 0.004 0.058 2201 Dihedral : 3.869 23.803 1707 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 1.94 % Allowed : 12.90 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1565 helix: 2.43 (0.18), residues: 959 sheet: 0.31 (0.53), residues: 99 loop : -0.67 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1248 HIS 0.003 0.001 HIS A 887 PHE 0.013 0.001 PHE A1107 TYR 0.010 0.001 TYR A1316 ARG 0.007 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 763) hydrogen bonds : angle 3.72602 ( 2196) metal coordination : bond 0.01029 ( 7) metal coordination : angle 1.75728 ( 1) covalent geometry : bond 0.00275 (12808) covalent geometry : angle 0.55116 (17310) *********************** 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 370 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 343 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.6928 (t0) cc_final: 0.6648 (t0) REVERT: A 57 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8065 (tppt) REVERT: A 112 LYS cc_start: 0.8330 (mttt) cc_final: 0.8123 (mtmm) REVERT: A 128 MET cc_start: 0.8729 (ttp) cc_final: 0.8529 (ttm) REVERT: A 150 GLU cc_start: 0.7948 (tp30) cc_final: 0.7303 (tp30) REVERT: A 179 GLU cc_start: 0.8237 (tp30) cc_final: 0.7844 (tp30) REVERT: A 207 GLU cc_start: 0.7457 (mp0) cc_final: 0.7253 (mp0) REVERT: A 240 ASP cc_start: 0.7643 (m-30) cc_final: 0.7275 (m-30) REVERT: A 259 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 319 MET cc_start: 0.7985 (mmm) cc_final: 0.7595 (ttp) REVERT: A 321 GLN cc_start: 0.8240 (tt0) cc_final: 0.8037 (tp40) REVERT: A 339 ASP cc_start: 0.7707 (t0) cc_final: 0.7361 (t0) REVERT: A 355 GLU cc_start: 0.8076 (tp30) cc_final: 0.7683 (tp30) REVERT: A 376 LYS cc_start: 0.8268 (tppt) cc_final: 0.7980 (tppt) REVERT: A 423 HIS cc_start: 0.8073 (p-80) cc_final: 0.7566 (p-80) REVERT: A 512 ASP cc_start: 0.7608 (t0) cc_final: 0.7142 (t0) REVERT: A 726 PHE cc_start: 0.8346 (m-80) cc_final: 0.7718 (t80) REVERT: A 732 TYR cc_start: 0.8111 (t80) cc_final: 0.7472 (t80) REVERT: A 740 GLU cc_start: 0.8025 (tp30) cc_final: 0.7412 (tp30) REVERT: A 777 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7573 (tptp) REVERT: A 799 GLU cc_start: 0.7561 (tt0) cc_final: 0.7232 (tm-30) REVERT: A 822 ASN cc_start: 0.8164 (t0) cc_final: 0.7847 (t0) REVERT: A 864 GLU cc_start: 0.7510 (tp30) cc_final: 0.7067 (tp30) REVERT: A 876 ASN cc_start: 0.8546 (t0) cc_final: 0.8098 (t0) REVERT: A 885 SER cc_start: 0.8459 (t) cc_final: 0.8106 (p) REVERT: A 891 TYR cc_start: 0.8161 (t80) cc_final: 0.7734 (t80) REVERT: A 893 LYS cc_start: 0.8516 (mppt) cc_final: 0.8167 (mppt) REVERT: A 984 ASP cc_start: 0.7496 (p0) cc_final: 0.7135 (p0) REVERT: A 1041 MET cc_start: 0.8450 (mtp) cc_final: 0.8133 (mtt) REVERT: A 1047 ASP cc_start: 0.7536 (p0) cc_final: 0.7044 (p0) REVERT: A 1064 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7543 (t0) REVERT: A 1090 LYS cc_start: 0.8068 (mttt) cc_final: 0.7842 (mttt) REVERT: A 1206 GLU cc_start: 0.7768 (tp30) cc_final: 0.7470 (tp30) REVERT: A 1220 ASP cc_start: 0.6769 (t70) cc_final: 0.6543 (t70) REVERT: A 1241 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7851 (tm-30) REVERT: A 1300 ILE cc_start: 0.8484 (mm) cc_final: 0.8111 (mm) REVERT: A 1302 THR cc_start: 0.8762 (t) cc_final: 0.8534 (p) REVERT: A 1327 ASN cc_start: 0.7229 (p0) cc_final: 0.6964 (p0) REVERT: A 1336 ILE cc_start: 0.9119 (tp) cc_final: 0.8840 (tp) REVERT: A 1378 ASP cc_start: 0.6878 (p0) cc_final: 0.6678 (p0) REVERT: A 1400 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 1431 LYS cc_start: 0.8313 (pttm) cc_final: 0.8013 (pttm) REVERT: A 1438 GLN cc_start: 0.8354 (pt0) cc_final: 0.7856 (pp30) REVERT: F 542 GLU cc_start: 0.5431 (mp0) cc_final: 0.5118 (mp0) outliers start: 27 outliers final: 13 residues processed: 357 average time/residue: 0.3724 time to fit residues: 178.5509 Evaluate side-chains 352 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 337 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 CYS 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 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE 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 F residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 0.1980 chunk 150 optimal weight: 0.0270 chunk 73 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3922 r_free = 0.3922 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123398 restraints weight = 19973.894| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.46 r_work: 0.3516 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12815 Z= 0.128 Angle : 0.559 7.638 17311 Z= 0.287 Chirality : 0.041 0.171 1997 Planarity : 0.004 0.055 2201 Dihedral : 3.843 25.757 1707 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.15 % Allowed : 13.76 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.22), residues: 1565 helix: 2.46 (0.18), residues: 953 sheet: 0.25 (0.52), residues: 99 loop : -0.68 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1248 HIS 0.004 0.001 HIS A 843 PHE 0.011 0.001 PHE A 889 TYR 0.012 0.001 TYR A 529 ARG 0.008 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 763) hydrogen bonds : angle 3.63810 ( 2196) metal coordination : bond 0.01002 ( 7) metal coordination : angle 1.23221 ( 1) covalent geometry : bond 0.00276 (12808) covalent geometry : angle 0.55871 (17310) *********************** 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 378 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 348 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8034 (tppp) REVERT: A 112 LYS cc_start: 0.8341 (mttt) cc_final: 0.8140 (mtmm) REVERT: A 128 MET cc_start: 0.8749 (ttp) cc_final: 0.8548 (ttm) REVERT: A 150 GLU cc_start: 0.7926 (tp30) cc_final: 0.7229 (tp30) REVERT: A 179 GLU cc_start: 0.8194 (tp30) cc_final: 0.7819 (tp30) REVERT: A 197 CYS cc_start: 0.8510 (t) cc_final: 0.8272 (t) REVERT: A 207 GLU cc_start: 0.7465 (mp0) cc_final: 0.7219 (mp0) REVERT: A 240 ASP cc_start: 0.7598 (m-30) cc_final: 0.7234 (m-30) REVERT: A 259 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 315 CYS cc_start: 0.7826 (m) cc_final: 0.7536 (m) REVERT: A 339 ASP cc_start: 0.7734 (t0) cc_final: 0.7393 (t0) REVERT: A 355 GLU cc_start: 0.8121 (tp30) cc_final: 0.7749 (tp30) REVERT: A 376 LYS cc_start: 0.8280 (tppt) cc_final: 0.7985 (tppt) REVERT: A 423 HIS cc_start: 0.8056 (p-80) cc_final: 0.7499 (p-80) REVERT: A 430 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6454 (mtm110) REVERT: A 459 MET cc_start: 0.8242 (mmt) cc_final: 0.8019 (mmm) REVERT: A 470 TYR cc_start: 0.7769 (m-80) cc_final: 0.7535 (m-80) REVERT: A 482 GLU cc_start: 0.7752 (pm20) cc_final: 0.7466 (mp0) REVERT: A 512 ASP cc_start: 0.7781 (t0) cc_final: 0.7356 (t0) REVERT: A 537 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8052 (p) REVERT: A 726 PHE cc_start: 0.8327 (m-80) cc_final: 0.7833 (t80) REVERT: A 732 TYR cc_start: 0.8083 (t80) cc_final: 0.7455 (t80) REVERT: A 740 GLU cc_start: 0.8022 (tp30) cc_final: 0.7448 (tp30) REVERT: A 799 GLU cc_start: 0.7550 (tt0) cc_final: 0.7203 (tm-30) REVERT: A 822 ASN cc_start: 0.8186 (t0) cc_final: 0.7869 (t0) REVERT: A 843 HIS cc_start: 0.7907 (t-90) cc_final: 0.7700 (t-90) REVERT: A 851 LYS cc_start: 0.8064 (mtpp) cc_final: 0.7598 (mtmm) REVERT: A 864 GLU cc_start: 0.7488 (tp30) cc_final: 0.7093 (tp30) REVERT: A 876 ASN cc_start: 0.8581 (t0) cc_final: 0.8126 (t0) REVERT: A 885 SER cc_start: 0.8473 (t) cc_final: 0.8137 (p) REVERT: A 891 TYR cc_start: 0.8160 (t80) cc_final: 0.7779 (t80) REVERT: A 907 LYS cc_start: 0.8423 (tttp) cc_final: 0.8174 (ttmm) REVERT: A 984 ASP cc_start: 0.7508 (p0) cc_final: 0.7180 (p0) REVERT: A 1041 MET cc_start: 0.8396 (mtp) cc_final: 0.8079 (mtt) REVERT: A 1047 ASP cc_start: 0.7538 (p0) cc_final: 0.7072 (p0) REVERT: A 1064 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7537 (t0) REVERT: A 1090 LYS cc_start: 0.8062 (mttt) cc_final: 0.7827 (mttt) REVERT: A 1206 GLU cc_start: 0.7801 (tp30) cc_final: 0.7356 (tp30) REVERT: A 1220 ASP cc_start: 0.6824 (t70) cc_final: 0.6618 (t70) REVERT: A 1241 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8017 (tm-30) REVERT: A 1300 ILE cc_start: 0.8537 (mm) cc_final: 0.8141 (mm) REVERT: A 1302 THR cc_start: 0.8765 (t) cc_final: 0.8537 (p) REVERT: A 1327 ASN cc_start: 0.7202 (p0) cc_final: 0.6920 (p0) REVERT: A 1336 ILE cc_start: 0.9139 (tp) cc_final: 0.8862 (tp) REVERT: A 1378 ASP cc_start: 0.6852 (p0) cc_final: 0.6554 (p0) REVERT: A 1396 MET cc_start: 0.7473 (mmp) cc_final: 0.7181 (mmt) REVERT: A 1431 LYS cc_start: 0.8321 (pttm) cc_final: 0.8048 (pttm) REVERT: A 1438 GLN cc_start: 0.8371 (pt0) cc_final: 0.7851 (pp30) REVERT: F 542 GLU cc_start: 0.5513 (mp0) cc_final: 0.5176 (mp0) outliers start: 30 outliers final: 19 residues processed: 361 average time/residue: 0.3520 time to fit residues: 173.8679 Evaluate side-chains 361 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 340 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 537 VAL 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 1175 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 0.0980 chunk 9 optimal weight: 0.0970 chunk 115 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 137 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 A 981 ASN A1364 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123561 restraints weight = 19905.175| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.45 r_work: 0.3527 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12815 Z= 0.125 Angle : 0.554 7.469 17311 Z= 0.284 Chirality : 0.040 0.174 1997 Planarity : 0.004 0.057 2201 Dihedral : 3.801 24.475 1707 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 2.15 % Allowed : 15.27 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1565 helix: 2.53 (0.18), residues: 951 sheet: 0.27 (0.53), residues: 99 loop : -0.65 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1248 HIS 0.003 0.001 HIS A 887 PHE 0.011 0.001 PHE A 889 TYR 0.012 0.001 TYR A 801 ARG 0.008 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 763) hydrogen bonds : angle 3.58069 ( 2196) metal coordination : bond 0.00978 ( 7) metal coordination : angle 1.17361 ( 1) covalent geometry : bond 0.00272 (12808) covalent geometry : angle 0.55353 (17310) *********************** 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 375 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 345 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8468 (tt) cc_final: 0.8189 (mm) REVERT: A 57 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8028 (tppp) REVERT: A 112 LYS cc_start: 0.8326 (mttt) cc_final: 0.8126 (mtmm) REVERT: A 150 GLU cc_start: 0.7949 (tp30) cc_final: 0.7231 (tp30) REVERT: A 179 GLU cc_start: 0.8187 (tp30) cc_final: 0.7934 (tp30) REVERT: A 197 CYS cc_start: 0.8557 (t) cc_final: 0.8298 (t) REVERT: A 207 GLU cc_start: 0.7466 (mp0) cc_final: 0.7180 (mp0) REVERT: A 240 ASP cc_start: 0.7577 (m-30) cc_final: 0.7257 (m-30) REVERT: A 289 MET cc_start: 0.7933 (tpp) cc_final: 0.7716 (tpp) REVERT: A 315 CYS cc_start: 0.7849 (m) cc_final: 0.7542 (m) REVERT: A 319 MET cc_start: 0.8032 (mmm) cc_final: 0.7611 (ttp) REVERT: A 339 ASP cc_start: 0.7729 (t0) cc_final: 0.7390 (t0) REVERT: A 355 GLU cc_start: 0.8059 (tp30) cc_final: 0.7695 (tp30) REVERT: A 376 LYS cc_start: 0.8217 (tppt) cc_final: 0.7907 (tppt) REVERT: A 423 HIS cc_start: 0.8023 (p-80) cc_final: 0.7460 (p-80) REVERT: A 430 ARG cc_start: 0.6929 (mtm110) cc_final: 0.6417 (mtm110) REVERT: A 459 MET cc_start: 0.8291 (mmt) cc_final: 0.8086 (mmm) REVERT: A 482 GLU cc_start: 0.7801 (pm20) cc_final: 0.7454 (mp0) REVERT: A 512 ASP cc_start: 0.7807 (t0) cc_final: 0.7364 (t0) REVERT: A 537 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 726 PHE cc_start: 0.8327 (m-80) cc_final: 0.7816 (t80) REVERT: A 727 CYS cc_start: 0.8438 (m) cc_final: 0.8213 (p) REVERT: A 732 TYR cc_start: 0.8084 (t80) cc_final: 0.7448 (t80) REVERT: A 740 GLU cc_start: 0.8028 (tp30) cc_final: 0.7439 (tp30) REVERT: A 799 GLU cc_start: 0.7548 (tt0) cc_final: 0.7180 (tm-30) REVERT: A 822 ASN cc_start: 0.8281 (t0) cc_final: 0.7945 (t0) REVERT: A 853 GLU cc_start: 0.7038 (pt0) cc_final: 0.6685 (pp20) REVERT: A 864 GLU cc_start: 0.7514 (tp30) cc_final: 0.7113 (tp30) REVERT: A 876 ASN cc_start: 0.8579 (t0) cc_final: 0.8132 (t0) REVERT: A 885 SER cc_start: 0.8461 (t) cc_final: 0.8118 (p) REVERT: A 891 TYR cc_start: 0.8159 (t80) cc_final: 0.7753 (t80) REVERT: A 893 LYS cc_start: 0.8521 (mppt) cc_final: 0.8110 (mppt) REVERT: A 907 LYS cc_start: 0.8558 (tttp) cc_final: 0.8257 (ttmm) REVERT: A 984 ASP cc_start: 0.7521 (p0) cc_final: 0.7199 (p0) REVERT: A 1041 MET cc_start: 0.8385 (mtp) cc_final: 0.8058 (mtt) REVERT: A 1047 ASP cc_start: 0.7532 (p0) cc_final: 0.7085 (p0) REVERT: A 1064 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7532 (t0) REVERT: A 1090 LYS cc_start: 0.8055 (mttt) cc_final: 0.7818 (mttt) REVERT: A 1206 GLU cc_start: 0.7764 (tp30) cc_final: 0.7328 (tp30) REVERT: A 1220 ASP cc_start: 0.6836 (t70) cc_final: 0.6606 (t70) REVERT: A 1241 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 1300 ILE cc_start: 0.8527 (mm) cc_final: 0.8113 (mm) REVERT: A 1313 GLU cc_start: 0.7220 (mp0) cc_final: 0.6995 (mp0) REVERT: A 1327 ASN cc_start: 0.6942 (p0) cc_final: 0.6682 (p0) REVERT: A 1336 ILE cc_start: 0.9108 (tp) cc_final: 0.8823 (tp) REVERT: A 1378 ASP cc_start: 0.6801 (p0) cc_final: 0.6561 (p0) REVERT: A 1396 MET cc_start: 0.7503 (mmp) cc_final: 0.7222 (mmt) REVERT: A 1431 LYS cc_start: 0.8321 (pttm) cc_final: 0.8038 (pttm) REVERT: A 1438 GLN cc_start: 0.8360 (pt0) cc_final: 0.7833 (pp30) REVERT: F 542 GLU cc_start: 0.5561 (mp0) cc_final: 0.5164 (mp0) outliers start: 30 outliers final: 17 residues processed: 358 average time/residue: 0.3436 time to fit residues: 164.5366 Evaluate side-chains 364 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 345 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 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 537 VAL 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 1166 ASP Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1225 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 0.0050 chunk 130 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 133 optimal weight: 0.0170 chunk 137 optimal weight: 0.5980 chunk 96 optimal weight: 0.0470 chunk 50 optimal weight: 0.7980 overall best weight: 0.2130 ------------------------------------------------------------------------------- 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 981 ASN 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 = 0.3933 r_free = 0.3933 target = 0.143760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124259 restraints weight = 20040.641| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.47 r_work: 0.3537 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12815 Z= 0.118 Angle : 0.566 8.071 17311 Z= 0.289 Chirality : 0.040 0.171 1997 Planarity : 0.004 0.056 2201 Dihedral : 3.770 24.816 1707 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 16.63 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1565 helix: 2.58 (0.18), residues: 952 sheet: 0.26 (0.53), residues: 99 loop : -0.63 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1248 HIS 0.004 0.001 HIS A 843 PHE 0.010 0.001 PHE A 889 TYR 0.030 0.001 TYR A 801 ARG 0.010 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 763) hydrogen bonds : angle 3.51380 ( 2196) metal coordination : bond 0.00892 ( 7) metal coordination : angle 1.01085 ( 1) covalent geometry : bond 0.00255 (12808) covalent geometry : angle 0.56553 (17310) *********************** 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 373 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 345 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8480 (tt) cc_final: 0.8218 (mm) REVERT: A 57 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8009 (tppp) REVERT: A 128 MET cc_start: 0.8846 (ttm) cc_final: 0.8618 (ttp) REVERT: A 150 GLU cc_start: 0.7950 (tp30) cc_final: 0.7550 (tm-30) REVERT: A 197 CYS cc_start: 0.8550 (t) cc_final: 0.8270 (t) REVERT: A 207 GLU cc_start: 0.7461 (mp0) cc_final: 0.7152 (mp0) REVERT: A 240 ASP cc_start: 0.7547 (m-30) cc_final: 0.7220 (m-30) REVERT: A 249 GLU cc_start: 0.7816 (tp30) cc_final: 0.7575 (tp30) REVERT: A 259 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 289 MET cc_start: 0.7920 (tpp) cc_final: 0.7693 (tpp) REVERT: A 315 CYS cc_start: 0.7835 (m) cc_final: 0.7529 (m) REVERT: A 319 MET cc_start: 0.7953 (mmm) cc_final: 0.7548 (ttp) REVERT: A 339 ASP cc_start: 0.7754 (t0) cc_final: 0.7415 (t0) REVERT: A 355 GLU cc_start: 0.8067 (tp30) cc_final: 0.7673 (tp30) REVERT: A 376 LYS cc_start: 0.8234 (tppt) cc_final: 0.7936 (tppt) REVERT: A 423 HIS cc_start: 0.7971 (p-80) cc_final: 0.7396 (p-80) REVERT: A 430 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6541 (mtm110) REVERT: A 482 GLU cc_start: 0.7722 (pm20) cc_final: 0.7396 (mp0) REVERT: A 512 ASP cc_start: 0.7800 (t0) cc_final: 0.7365 (t0) REVERT: A 560 MET cc_start: 0.8168 (tpp) cc_final: 0.7911 (mmt) REVERT: A 726 PHE cc_start: 0.8325 (m-80) cc_final: 0.7870 (t80) REVERT: A 732 TYR cc_start: 0.8017 (t80) cc_final: 0.7755 (t80) REVERT: A 740 GLU cc_start: 0.7925 (tp30) cc_final: 0.7343 (tp30) REVERT: A 786 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6214 (tp30) REVERT: A 799 GLU cc_start: 0.7450 (tt0) cc_final: 0.7099 (tm-30) REVERT: A 822 ASN cc_start: 0.8241 (t0) cc_final: 0.7945 (t0) REVERT: A 853 GLU cc_start: 0.7053 (pt0) cc_final: 0.6700 (pp20) REVERT: A 864 GLU cc_start: 0.7494 (tp30) cc_final: 0.7110 (tp30) REVERT: A 876 ASN cc_start: 0.8584 (t0) cc_final: 0.8146 (t0) REVERT: A 885 SER cc_start: 0.8441 (t) cc_final: 0.8089 (p) REVERT: A 891 TYR cc_start: 0.8161 (t80) cc_final: 0.7765 (t80) REVERT: A 893 LYS cc_start: 0.8509 (mppt) cc_final: 0.8125 (mppt) REVERT: A 907 LYS cc_start: 0.8605 (tttp) cc_final: 0.8063 (ttmm) REVERT: A 984 ASP cc_start: 0.7517 (p0) cc_final: 0.7207 (p0) REVERT: A 1041 MET cc_start: 0.8409 (mtp) cc_final: 0.8049 (mtt) REVERT: A 1047 ASP cc_start: 0.7522 (p0) cc_final: 0.7087 (p0) REVERT: A 1064 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7519 (t0) REVERT: A 1080 ILE cc_start: 0.8744 (tp) cc_final: 0.8380 (tp) REVERT: A 1090 LYS cc_start: 0.8062 (mttt) cc_final: 0.7826 (mttt) REVERT: A 1206 GLU cc_start: 0.7743 (tp30) cc_final: 0.7488 (tp30) REVERT: A 1220 ASP cc_start: 0.6741 (t70) cc_final: 0.6517 (t70) REVERT: A 1241 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 1300 ILE cc_start: 0.8538 (mm) cc_final: 0.8118 (mm) REVERT: A 1327 ASN cc_start: 0.6937 (p0) cc_final: 0.6674 (p0) REVERT: A 1336 ILE cc_start: 0.9100 (tp) cc_final: 0.8821 (tp) REVERT: A 1378 ASP cc_start: 0.6702 (p0) cc_final: 0.6467 (p0) REVERT: A 1431 LYS cc_start: 0.8302 (pttm) cc_final: 0.8019 (pttm) REVERT: A 1438 GLN cc_start: 0.8360 (pt0) cc_final: 0.7826 (pp30) REVERT: F 542 GLU cc_start: 0.5582 (mp0) cc_final: 0.5175 (mp0) outliers start: 28 outliers final: 19 residues processed: 358 average time/residue: 0.3220 time to fit residues: 153.5278 Evaluate side-chains 362 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 342 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 533 GLU 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 1166 ASP Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1264 HIS 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 567 ILE Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 562 THR 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 3 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 0.0070 chunk 1 optimal weight: 0.0670 chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN A1165 HIS A1364 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.122326 restraints weight = 20049.196| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.44 r_work: 0.3501 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12815 Z= 0.156 Angle : 0.603 10.118 17311 Z= 0.305 Chirality : 0.042 0.178 1997 Planarity : 0.004 0.057 2201 Dihedral : 3.846 25.494 1707 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 2.44 % Allowed : 16.99 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.22), residues: 1565 helix: 2.53 (0.17), residues: 951 sheet: 0.25 (0.53), residues: 99 loop : -0.65 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1204 HIS 0.004 0.001 HIS A 792 PHE 0.014 0.001 PHE A 889 TYR 0.012 0.001 TYR A 801 ARG 0.011 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 763) hydrogen bonds : angle 3.62815 ( 2196) metal coordination : bond 0.01055 ( 7) metal coordination : angle 1.31337 ( 1) covalent geometry : bond 0.00350 (12808) covalent geometry : angle 0.60331 (17310) *********************** 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 379 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 345 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8523 (tt) cc_final: 0.8289 (mm) REVERT: A 57 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8064 (tppp) REVERT: A 150 GLU cc_start: 0.7977 (tp30) cc_final: 0.7228 (tp30) REVERT: A 193 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7627 (mtt90) REVERT: A 197 CYS cc_start: 0.8549 (t) cc_final: 0.8254 (t) REVERT: A 198 ILE cc_start: 0.8680 (tt) cc_final: 0.8476 (pt) REVERT: A 207 GLU cc_start: 0.7485 (mp0) cc_final: 0.7181 (mp0) REVERT: A 240 ASP cc_start: 0.7632 (m-30) cc_final: 0.7308 (m-30) REVERT: A 289 MET cc_start: 0.7907 (tpp) cc_final: 0.7690 (tpp) REVERT: A 315 CYS cc_start: 0.7832 (m) cc_final: 0.7547 (m) REVERT: A 319 MET cc_start: 0.7947 (mmm) cc_final: 0.7581 (ttp) REVERT: A 339 ASP cc_start: 0.7782 (t0) cc_final: 0.7418 (t0) REVERT: A 355 GLU cc_start: 0.8084 (tp30) cc_final: 0.7698 (tp30) REVERT: A 376 LYS cc_start: 0.8220 (tppt) cc_final: 0.7920 (tppt) REVERT: A 430 ARG cc_start: 0.6934 (mtm110) cc_final: 0.6575 (mtm110) REVERT: A 459 MET cc_start: 0.8294 (mmm) cc_final: 0.8029 (mmt) REVERT: A 460 GLU cc_start: 0.7402 (tp30) cc_final: 0.7187 (tp30) REVERT: A 482 GLU cc_start: 0.7745 (pm20) cc_final: 0.7416 (mp0) REVERT: A 507 ASP cc_start: 0.7961 (t70) cc_final: 0.7716 (t0) REVERT: A 512 ASP cc_start: 0.7837 (t0) cc_final: 0.7426 (t0) REVERT: A 520 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: A 537 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8012 (p) REVERT: A 560 MET cc_start: 0.8195 (tpp) cc_final: 0.7979 (mmt) REVERT: A 726 PHE cc_start: 0.8311 (m-80) cc_final: 0.7808 (t80) REVERT: A 732 TYR cc_start: 0.8160 (t80) cc_final: 0.7531 (t80) REVERT: A 740 GLU cc_start: 0.8049 (tp30) cc_final: 0.7461 (tp30) REVERT: A 786 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6455 (tp30) REVERT: A 822 ASN cc_start: 0.8294 (t0) cc_final: 0.8006 (t0) REVERT: A 853 GLU cc_start: 0.7138 (pt0) cc_final: 0.6772 (pp20) REVERT: A 864 GLU cc_start: 0.7539 (tp30) cc_final: 0.7126 (tp30) REVERT: A 876 ASN cc_start: 0.8582 (t0) cc_final: 0.8192 (t0) REVERT: A 885 SER cc_start: 0.8572 (t) cc_final: 0.8149 (p) REVERT: A 891 TYR cc_start: 0.8190 (t80) cc_final: 0.7793 (t80) REVERT: A 907 LYS cc_start: 0.8619 (tttp) cc_final: 0.8050 (ttmm) REVERT: A 909 MET cc_start: 0.8353 (mmm) cc_final: 0.8068 (tpp) REVERT: A 984 ASP cc_start: 0.7553 (p0) cc_final: 0.7251 (p0) REVERT: A 1041 MET cc_start: 0.8419 (mtp) cc_final: 0.8049 (mtt) REVERT: A 1047 ASP cc_start: 0.7532 (p0) cc_final: 0.7095 (p0) REVERT: A 1090 LYS cc_start: 0.8069 (mttt) cc_final: 0.7838 (mttt) REVERT: A 1092 LEU cc_start: 0.8159 (mt) cc_final: 0.7724 (tp) REVERT: A 1122 ILE cc_start: 0.8625 (tt) cc_final: 0.8317 (mt) REVERT: A 1206 GLU cc_start: 0.7761 (tp30) cc_final: 0.7348 (tp30) REVERT: A 1241 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 1327 ASN cc_start: 0.6911 (p0) cc_final: 0.6640 (p0) REVERT: A 1336 ILE cc_start: 0.9079 (tp) cc_final: 0.8803 (tp) REVERT: A 1378 ASP cc_start: 0.6647 (p0) cc_final: 0.6344 (p0) REVERT: A 1431 LYS cc_start: 0.8317 (pttm) cc_final: 0.8036 (pttm) REVERT: A 1438 GLN cc_start: 0.8362 (pt0) cc_final: 0.7825 (pp30) REVERT: F 542 GLU cc_start: 0.5604 (mp0) cc_final: 0.5158 (mp0) outliers start: 34 outliers final: 21 residues processed: 361 average time/residue: 0.3134 time to fit residues: 151.3398 Evaluate side-chains 366 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 343 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 556 MET 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 1166 ASP Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1225 MET 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 556 VAL Chi-restraints excluded: chain F residue 562 THR 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 108 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 119 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 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 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 GLN A1364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121882 restraints weight = 20081.227| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.45 r_work: 0.3493 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12815 Z= 0.167 Angle : 0.619 8.432 17311 Z= 0.314 Chirality : 0.042 0.179 1997 Planarity : 0.004 0.058 2201 Dihedral : 3.911 25.818 1707 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 2.44 % Allowed : 17.20 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.22), residues: 1565 helix: 2.42 (0.17), residues: 952 sheet: 0.22 (0.52), residues: 99 loop : -0.72 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.005 0.001 HIS A 423 PHE 0.014 0.001 PHE A 889 TYR 0.013 0.001 TYR A 801 ARG 0.012 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 763) hydrogen bonds : angle 3.67848 ( 2196) metal coordination : bond 0.00968 ( 7) metal coordination : angle 0.22706 ( 1) covalent geometry : bond 0.00375 (12808) covalent geometry : angle 0.61912 (17310) *********************** 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 379 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 345 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8525 (tt) cc_final: 0.8302 (mm) REVERT: A 57 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8062 (tppp) REVERT: A 150 GLU cc_start: 0.7982 (tp30) cc_final: 0.7591 (tm-30) REVERT: A 193 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7655 (mtt90) REVERT: A 197 CYS cc_start: 0.8564 (t) cc_final: 0.8203 (p) REVERT: A 207 GLU cc_start: 0.7509 (mp0) cc_final: 0.7207 (mp0) REVERT: A 233 GLU cc_start: 0.7268 (pp20) cc_final: 0.6944 (pp20) REVERT: A 240 ASP cc_start: 0.7659 (m-30) cc_final: 0.7335 (m-30) REVERT: A 289 MET cc_start: 0.7924 (tpp) cc_final: 0.7700 (tpp) REVERT: A 315 CYS cc_start: 0.7831 (m) cc_final: 0.7555 (m) REVERT: A 319 MET cc_start: 0.7942 (mmm) cc_final: 0.7570 (ttp) REVERT: A 336 MET cc_start: 0.7456 (tpp) cc_final: 0.7219 (tpp) REVERT: A 339 ASP cc_start: 0.7789 (t0) cc_final: 0.7463 (t0) REVERT: A 355 GLU cc_start: 0.8071 (tp30) cc_final: 0.7713 (tp30) REVERT: A 376 LYS cc_start: 0.8218 (tppt) cc_final: 0.7911 (tppt) REVERT: A 430 ARG cc_start: 0.6914 (mtm110) cc_final: 0.6547 (mtm110) REVERT: A 459 MET cc_start: 0.8301 (mmm) cc_final: 0.8032 (mmt) REVERT: A 482 GLU cc_start: 0.7774 (pm20) cc_final: 0.7438 (mp0) REVERT: A 507 ASP cc_start: 0.7980 (t70) cc_final: 0.7726 (t0) REVERT: A 512 ASP cc_start: 0.7844 (t0) cc_final: 0.7465 (t0) REVERT: A 520 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7786 (mtt) REVERT: A 537 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8040 (p) REVERT: A 726 PHE cc_start: 0.8296 (m-80) cc_final: 0.7799 (t80) REVERT: A 732 TYR cc_start: 0.8197 (t80) cc_final: 0.7593 (t80) REVERT: A 740 GLU cc_start: 0.7997 (tp30) cc_final: 0.7472 (tp30) REVERT: A 743 ASP cc_start: 0.7254 (t0) cc_final: 0.6974 (t0) REVERT: A 786 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6873 (tp30) REVERT: A 799 GLU cc_start: 0.7447 (tt0) cc_final: 0.7180 (tm-30) REVERT: A 822 ASN cc_start: 0.8268 (t0) cc_final: 0.7980 (t0) REVERT: A 853 GLU cc_start: 0.7155 (pt0) cc_final: 0.6802 (pp20) REVERT: A 864 GLU cc_start: 0.7516 (tp30) cc_final: 0.7116 (tp30) REVERT: A 876 ASN cc_start: 0.8583 (t0) cc_final: 0.8131 (t0) REVERT: A 885 SER cc_start: 0.8585 (t) cc_final: 0.8163 (p) REVERT: A 891 TYR cc_start: 0.8208 (t80) cc_final: 0.7796 (t80) REVERT: A 907 LYS cc_start: 0.8681 (tttp) cc_final: 0.8104 (ttmm) REVERT: A 909 MET cc_start: 0.8353 (mmm) cc_final: 0.8053 (tpp) REVERT: A 984 ASP cc_start: 0.7556 (p0) cc_final: 0.7275 (p0) REVERT: A 1039 LYS cc_start: 0.8381 (mttt) cc_final: 0.8039 (mttm) REVERT: A 1041 MET cc_start: 0.8442 (mtp) cc_final: 0.8054 (mtt) REVERT: A 1047 ASP cc_start: 0.7556 (p0) cc_final: 0.7123 (p0) REVERT: A 1090 LYS cc_start: 0.8065 (mttt) cc_final: 0.7830 (mttt) REVERT: A 1092 LEU cc_start: 0.8183 (mt) cc_final: 0.7766 (tp) REVERT: A 1122 ILE cc_start: 0.8629 (tt) cc_final: 0.8396 (mt) REVERT: A 1206 GLU cc_start: 0.7814 (tp30) cc_final: 0.7406 (tp30) REVERT: A 1220 ASP cc_start: 0.6768 (t0) cc_final: 0.6501 (t70) REVERT: A 1241 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8092 (tm-30) REVERT: A 1300 ILE cc_start: 0.8452 (mm) cc_final: 0.8123 (mm) REVERT: A 1327 ASN cc_start: 0.6927 (p0) cc_final: 0.6649 (p0) REVERT: A 1336 ILE cc_start: 0.9075 (tp) cc_final: 0.8811 (tp) REVERT: A 1378 ASP cc_start: 0.6633 (p0) cc_final: 0.6332 (p0) REVERT: A 1431 LYS cc_start: 0.8319 (pttm) cc_final: 0.8062 (pttm) REVERT: A 1438 GLN cc_start: 0.8360 (pt0) cc_final: 0.7835 (pp30) REVERT: F 542 GLU cc_start: 0.5675 (mp0) cc_final: 0.5067 (mp0) outliers start: 34 outliers final: 25 residues processed: 363 average time/residue: 0.3309 time to fit residues: 162.0981 Evaluate side-chains 362 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 335 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1051 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 1166 ASP Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1185 LEU 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 E residue 575 MET 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 564 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 46 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 134 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN F 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120932 restraints weight = 19971.389| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.45 r_work: 0.3481 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12815 Z= 0.180 Angle : 0.632 9.847 17311 Z= 0.321 Chirality : 0.043 0.181 1997 Planarity : 0.004 0.062 2201 Dihedral : 3.996 25.518 1707 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.15 % Allowed : 18.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.22), residues: 1565 helix: 2.34 (0.17), residues: 958 sheet: 0.30 (0.53), residues: 95 loop : -0.77 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 806 HIS 0.003 0.001 HIS A1165 PHE 0.014 0.001 PHE A 889 TYR 0.012 0.001 TYR A 801 ARG 0.013 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 763) hydrogen bonds : angle 3.72362 ( 2196) metal coordination : bond 0.01030 ( 7) metal coordination : angle 0.16488 ( 1) covalent geometry : bond 0.00405 (12808) covalent geometry : angle 0.63159 (17310) *********************** 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 371 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8538 (tt) cc_final: 0.8306 (mm) REVERT: A 57 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8063 (tppp) REVERT: A 76 ASN cc_start: 0.8470 (m-40) cc_final: 0.7575 (m110) REVERT: A 128 MET cc_start: 0.8842 (ttm) cc_final: 0.8607 (ttp) REVERT: A 150 GLU cc_start: 0.7993 (tp30) cc_final: 0.7583 (tm-30) REVERT: A 193 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7592 (mtt90) REVERT: A 207 GLU cc_start: 0.7531 (mp0) cc_final: 0.7212 (mp0) REVERT: A 233 GLU cc_start: 0.7286 (pp20) cc_final: 0.6958 (pp20) REVERT: A 240 ASP cc_start: 0.7678 (m-30) cc_final: 0.7365 (m-30) REVERT: A 289 MET cc_start: 0.7948 (tpp) cc_final: 0.7713 (tpp) REVERT: A 315 CYS cc_start: 0.7901 (m) cc_final: 0.7623 (m) REVERT: A 336 MET cc_start: 0.7517 (tpp) cc_final: 0.7263 (tpp) REVERT: A 339 ASP cc_start: 0.7786 (t0) cc_final: 0.7445 (t0) REVERT: A 355 GLU cc_start: 0.8074 (tp30) cc_final: 0.7730 (tp30) REVERT: A 376 LYS cc_start: 0.8216 (tppt) cc_final: 0.7909 (tppt) REVERT: A 430 ARG cc_start: 0.6902 (mtm110) cc_final: 0.6531 (mtm110) REVERT: A 459 MET cc_start: 0.8334 (mmm) cc_final: 0.8057 (mmt) REVERT: A 482 GLU cc_start: 0.7872 (pm20) cc_final: 0.7524 (mp0) REVERT: A 507 ASP cc_start: 0.7999 (t70) cc_final: 0.7736 (t0) REVERT: A 512 ASP cc_start: 0.7873 (t0) cc_final: 0.7569 (t0) REVERT: A 520 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7811 (mtt) REVERT: A 537 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 726 PHE cc_start: 0.8428 (m-80) cc_final: 0.7886 (t80) REVERT: A 727 CYS cc_start: 0.8240 (p) cc_final: 0.7888 (t) REVERT: A 732 TYR cc_start: 0.8250 (t80) cc_final: 0.7666 (t80) REVERT: A 740 GLU cc_start: 0.8011 (tp30) cc_final: 0.7501 (tp30) REVERT: A 743 ASP cc_start: 0.7235 (t0) cc_final: 0.6898 (t0) REVERT: A 777 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7690 (tptp) REVERT: A 786 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6898 (tp30) REVERT: A 822 ASN cc_start: 0.8284 (t0) cc_final: 0.7996 (t0) REVERT: A 853 GLU cc_start: 0.7164 (pt0) cc_final: 0.6805 (pp20) REVERT: A 864 GLU cc_start: 0.7529 (tp30) cc_final: 0.7119 (tp30) REVERT: A 876 ASN cc_start: 0.8599 (t0) cc_final: 0.8135 (t0) REVERT: A 885 SER cc_start: 0.8588 (t) cc_final: 0.8161 (p) REVERT: A 891 TYR cc_start: 0.8216 (t80) cc_final: 0.7794 (t80) REVERT: A 907 LYS cc_start: 0.8687 (tttp) cc_final: 0.8093 (ttmm) REVERT: A 984 ASP cc_start: 0.7553 (p0) cc_final: 0.7279 (p0) REVERT: A 1041 MET cc_start: 0.8432 (mtp) cc_final: 0.8064 (mtt) REVERT: A 1047 ASP cc_start: 0.7571 (p0) cc_final: 0.7142 (p0) REVERT: A 1080 ILE cc_start: 0.8778 (tp) cc_final: 0.8419 (tp) REVERT: A 1090 LYS cc_start: 0.8080 (mttt) cc_final: 0.7837 (mttt) REVERT: A 1092 LEU cc_start: 0.8196 (mt) cc_final: 0.7775 (tp) REVERT: A 1122 ILE cc_start: 0.8620 (tt) cc_final: 0.8397 (mt) REVERT: A 1206 GLU cc_start: 0.7795 (tp30) cc_final: 0.7540 (tp30) REVERT: A 1220 ASP cc_start: 0.6810 (t0) cc_final: 0.6558 (t70) REVERT: A 1241 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 1300 ILE cc_start: 0.8450 (mm) cc_final: 0.8120 (mm) REVERT: A 1327 ASN cc_start: 0.6936 (p0) cc_final: 0.6650 (p0) REVERT: A 1336 ILE cc_start: 0.9082 (tp) cc_final: 0.8830 (tp) REVERT: A 1378 ASP cc_start: 0.6671 (p0) cc_final: 0.6332 (p0) REVERT: A 1431 LYS cc_start: 0.8318 (pttm) cc_final: 0.8057 (pttm) REVERT: A 1438 GLN cc_start: 0.8376 (pt0) cc_final: 0.7850 (pp30) REVERT: F 542 GLU cc_start: 0.5670 (mp0) cc_final: 0.5206 (mp0) outliers start: 30 outliers final: 26 residues processed: 355 average time/residue: 0.3228 time to fit residues: 153.4601 Evaluate side-chains 364 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 336 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 279 MET 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 811 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1051 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 1166 ASP Chi-restraints excluded: chain A residue 1175 LYS Chi-restraints excluded: chain A residue 1185 LEU 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 E residue 575 MET Chi-restraints excluded: chain F residue 539 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 117 optimal weight: 0.0030 chunk 18 optimal weight: 0.0270 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 ASN F 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122388 restraints weight = 19955.257| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.45 r_work: 0.3503 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2307 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= 0.140 Angle : 0.628 8.032 17311 Z= 0.318 Chirality : 0.042 0.170 1997 Planarity : 0.004 0.065 2201 Dihedral : 3.970 26.703 1707 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.51 % Allowed : 19.50 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1565 helix: 2.41 (0.17), residues: 954 sheet: 0.23 (0.52), residues: 99 loop : -0.78 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.003 0.001 HIS A 792 PHE 0.011 0.001 PHE A 889 TYR 0.011 0.001 TYR A 470 ARG 0.014 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 763) hydrogen bonds : angle 3.64399 ( 2196) metal coordination : bond 0.00786 ( 7) metal coordination : angle 0.77699 ( 1) covalent geometry : bond 0.00314 (12808) covalent geometry : angle 0.62770 (17310) ********************** 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 364 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 343 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.8532 (tt) cc_final: 0.8258 (mm) REVERT: A 12 TYR cc_start: 0.8092 (m-10) cc_final: 0.7712 (m-80) REVERT: A 57 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8030 (tppp) REVERT: A 150 GLU cc_start: 0.7974 (tp30) cc_final: 0.7574 (tm-30) REVERT: A 193 ARG cc_start: 0.7806 (mtt90) cc_final: 0.7561 (mtt90) REVERT: A 207 GLU cc_start: 0.7529 (mp0) cc_final: 0.7211 (mp0) REVERT: A 233 GLU cc_start: 0.7217 (pp20) cc_final: 0.6890 (pp20) REVERT: A 240 ASP cc_start: 0.7650 (m-30) cc_final: 0.7343 (m-30) REVERT: A 289 MET cc_start: 0.7935 (tpp) cc_final: 0.7720 (tpp) REVERT: A 315 CYS cc_start: 0.7820 (m) cc_final: 0.7549 (m) REVERT: A 336 MET cc_start: 0.7540 (tpp) cc_final: 0.7278 (tpp) REVERT: A 339 ASP cc_start: 0.7817 (t0) cc_final: 0.7481 (t0) REVERT: A 355 GLU cc_start: 0.8016 (tp30) cc_final: 0.7646 (tp30) REVERT: A 376 LYS cc_start: 0.8218 (tppt) cc_final: 0.7911 (tppt) REVERT: A 430 ARG cc_start: 0.6891 (mtm110) cc_final: 0.6411 (mtt90) REVERT: A 455 PHE cc_start: 0.8186 (m-80) cc_final: 0.7538 (m-80) REVERT: A 459 MET cc_start: 0.8282 (mmm) cc_final: 0.8011 (mmt) REVERT: A 482 GLU cc_start: 0.7871 (pm20) cc_final: 0.7510 (mp0) REVERT: A 507 ASP cc_start: 0.8011 (t70) cc_final: 0.7744 (t0) REVERT: A 512 ASP cc_start: 0.7864 (t0) cc_final: 0.7536 (t0) REVERT: A 520 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (mtt) REVERT: A 726 PHE cc_start: 0.8282 (m-80) cc_final: 0.7772 (t80) REVERT: A 732 TYR cc_start: 0.8165 (t80) cc_final: 0.7652 (t80) REVERT: A 740 GLU cc_start: 0.8022 (tp30) cc_final: 0.7485 (tp30) REVERT: A 743 ASP cc_start: 0.7214 (t0) cc_final: 0.6894 (t0) REVERT: A 777 LYS cc_start: 0.7897 (mmmt) cc_final: 0.7639 (tptp) REVERT: A 822 ASN cc_start: 0.8285 (t0) cc_final: 0.8050 (t0) REVERT: A 853 GLU cc_start: 0.7128 (pt0) cc_final: 0.6762 (pp20) REVERT: A 864 GLU cc_start: 0.7486 (tp30) cc_final: 0.7086 (tp30) REVERT: A 876 ASN cc_start: 0.8603 (t0) cc_final: 0.8136 (t0) REVERT: A 885 SER cc_start: 0.8473 (t) cc_final: 0.8149 (p) REVERT: A 891 TYR cc_start: 0.8189 (t80) cc_final: 0.7775 (t80) REVERT: A 907 LYS cc_start: 0.8669 (tttp) cc_final: 0.8102 (ttmm) REVERT: A 984 ASP cc_start: 0.7499 (p0) cc_final: 0.7226 (p0) REVERT: A 1041 MET cc_start: 0.8417 (mtp) cc_final: 0.8030 (mtt) REVERT: A 1047 ASP cc_start: 0.7530 (p0) cc_final: 0.7132 (p0) REVERT: A 1080 ILE cc_start: 0.8734 (tp) cc_final: 0.8393 (tp) REVERT: A 1090 LYS cc_start: 0.8068 (mttt) cc_final: 0.7826 (mttt) REVERT: A 1092 LEU cc_start: 0.8166 (mt) cc_final: 0.7752 (tp) REVERT: A 1122 ILE cc_start: 0.8615 (tt) cc_final: 0.8357 (mt) REVERT: A 1206 GLU cc_start: 0.7814 (tp30) cc_final: 0.7410 (tp30) REVERT: A 1241 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 1300 ILE cc_start: 0.8477 (mm) cc_final: 0.8145 (mm) REVERT: A 1327 ASN cc_start: 0.6900 (p0) cc_final: 0.6626 (p0) REVERT: A 1336 ILE cc_start: 0.9085 (tp) cc_final: 0.8829 (tp) REVERT: A 1378 ASP cc_start: 0.6626 (p0) cc_final: 0.6303 (p0) REVERT: A 1396 MET cc_start: 0.7453 (mmp) cc_final: 0.7196 (mmt) REVERT: A 1431 LYS cc_start: 0.8299 (pttm) cc_final: 0.8054 (pttm) REVERT: A 1438 GLN cc_start: 0.8393 (pt0) cc_final: 0.7859 (pp30) REVERT: F 542 GLU cc_start: 0.5890 (mp0) cc_final: 0.5414 (mp0) outliers start: 21 outliers final: 19 residues processed: 352 average time/residue: 0.3277 time to fit residues: 154.2818 Evaluate side-chains 361 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 341 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 279 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 1051 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 1175 LYS 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 564 LEU Chi-restraints excluded: chain G residue 537 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 113 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.139835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120775 restraints weight = 20025.495| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.44 r_work: 0.3474 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12815 Z= 0.205 Angle : 0.669 11.084 17311 Z= 0.339 Chirality : 0.044 0.176 1997 Planarity : 0.004 0.066 2201 Dihedral : 4.100 27.111 1707 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 1.72 % Allowed : 19.71 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1565 helix: 2.26 (0.17), residues: 953 sheet: 0.21 (0.52), residues: 99 loop : -0.78 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 806 HIS 0.005 0.001 HIS A 320 PHE 0.016 0.002 PHE A 889 TYR 0.013 0.002 TYR A 12 ARG 0.014 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.05172 ( 763) hydrogen bonds : angle 3.82766 ( 2196) metal coordination : bond 0.01198 ( 7) metal coordination : angle 0.09943 ( 1) covalent geometry : bond 0.00463 (12808) covalent geometry : angle 0.66895 (17310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.76 seconds wall clock time: 119 minutes 0.47 seconds (7140.47 seconds total)