Starting phenix.real_space_refine on Fri May 16 13:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.map" model { file = "/net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fux_50781/05_2025/9fux_50781.cif" } resolution = 2.49 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= -0.001 sd= 0.908 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 95 5.16 5 C 9239 2.51 5 N 2472 2.21 5 O 2748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14556 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10357 Classifications: {'peptide': 1286} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1235} Chain breaks: 4 Chain: "C" Number of atoms: 927 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Conformer: "B" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} bond proxies already assigned to first conformer: 924 Chain: "D" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 861 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1591 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 2 Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 818 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} 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 8874 SG CYS A1236 74.668 72.251 38.143 1.00 30.25 S ATOM 8897 SG CYS A1239 74.485 75.323 40.610 1.00 34.30 S ATOM 8524 SG CYS A1191 55.646 77.046 29.002 1.00 21.90 S ATOM 10084 SG CYS A1428 59.856 76.179 28.728 1.00 48.19 S ATOM 10090 SG CYS A1429 57.696 75.232 31.337 1.00 32.05 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASN C 486 " occ=0.26 ... (14 atoms not shown) pdb=" ND2BASN C 486 " occ=0.74 Time building chain proxies: 9.95, per 1000 atoms: 0.68 Number of scatterers: 14556 At special positions: 0 Unit cell: (93.4784, 102.242, 191.339, 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 95 16.00 O 2748 8.00 N 2472 7.00 C 9239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS F 512 " distance=2.03 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: 3.09 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 A1236 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1239 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1428 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1191 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1429 " Number of angles added : 1 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3466 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 63.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.874A pdb=" N ILE A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.680A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.560A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 166 through 188 removed outlier: 3.553A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.542A pdb=" N ARG A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.829A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.398A pdb=" N VAL A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 325 removed outlier: 3.897A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.609A pdb=" N PHE A 359 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 389 through 410 removed outlier: 3.747A 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 487 removed outlier: 3.575A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 511 removed outlier: 3.519A pdb=" N ASN A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.617A pdb=" N TYR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 731 through 746 removed outlier: 4.858A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 761 Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.728A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix removed outlier: 3.546A pdb=" N ASN A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 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: 3.688A 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: 3.610A pdb=" N ILE A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1126 Processing helix chain 'A' and resid 1126 through 1138 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.771A pdb=" N VAL A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A1160 " --> pdb=" O PRO A1156 " (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 1220 through 1224 Processing helix chain 'A' and resid 1236 through 1242 Processing helix chain 'A' and resid 1291 through 1309 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1393 through 1398 Processing helix chain 'A' and resid 1400 through 1407 Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.615A pdb=" N AASN C 486 " --> pdb=" O ASP C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.663A pdb=" N ASP C 505 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 507 through 541 removed outlier: 4.119A pdb=" N GLY C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN C 539 " --> pdb=" O HIS C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 578 removed outlier: 3.709A pdb=" N ILE C 547 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 548 " --> pdb=" O PRO C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'D' and resid 479 through 485 Processing helix chain 'D' and resid 489 through 502 removed outlier: 3.547A pdb=" N HIS D 499 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS D 502 " --> pdb=" O TYR D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 506 removed outlier: 3.617A pdb=" N TYR D 506 " --> pdb=" O LEU D 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 507 through 538 removed outlier: 3.535A pdb=" N ILE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 541 No H-bonds generated for 'chain 'D' and resid 539 through 541' Processing helix chain 'D' and resid 542 through 573 removed outlier: 3.681A pdb=" N SER D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'E' and resid 502 through 506 removed outlier: 3.539A pdb=" N ASP E 505 " --> pdb=" O HIS E 502 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 506' Processing helix chain 'E' and resid 507 through 540 removed outlier: 3.575A pdb=" N VAL E 516 " --> pdb=" O CYS E 512 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 517 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 573 removed outlier: 3.704A pdb=" N ASN E 548 " --> pdb=" O PRO E 544 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS E 549 " --> pdb=" O LYS E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 607 removed outlier: 3.695A pdb=" N SER E 607 " --> pdb=" O GLU E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 638 removed outlier: 3.648A pdb=" N ILE E 638 " --> pdb=" O GLU E 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 635 through 638' Processing helix chain 'E' and resid 657 through 672 Processing helix chain 'E' and resid 676 through 687 Processing helix chain 'E' and resid 690 through 706 removed outlier: 3.527A pdb=" N ASN E 699 " --> pdb=" O GLN E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 484 Processing helix chain 'F' and resid 489 through 504 removed outlier: 3.595A pdb=" N ARG F 495 " --> pdb=" O HIS F 491 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS F 502 " --> pdb=" O TYR F 498 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY F 504 " --> pdb=" O ALA F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 541 removed outlier: 3.505A pdb=" N SER F 515 " --> pdb=" O LEU F 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 516 " --> pdb=" O CYS F 512 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 520 " --> pdb=" O VAL F 516 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 521 " --> pdb=" O LEU F 517 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN F 539 " --> pdb=" O HIS F 535 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS F 541 " --> pdb=" O GLU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 574 removed outlier: 3.671A pdb=" N SER F 573 " --> pdb=" O GLY F 569 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.895A pdb=" N ILE A 21 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 556 removed outlier: 7.269A pdb=" N VAL A 537 " --> pdb=" O TYR A 765 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA A 767 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR A 539 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.934A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA A 837 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA9, first strand: chain 'A' and resid 1225 through 1230 Processing sheet with id=AB1, first strand: chain 'E' and resid 609 through 610 823 hydrogen bonds defined for protein. 2355 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: 5.13 Time building geometry restraints manager: 3.72 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: 4777 1.34 - 1.46: 2375 1.46 - 1.58: 7520 1.58 - 1.70: 0 1.70 - 1.82: 158 Bond restraints: 14830 Sorted by residual: bond pdb=" CG LEU A 242 " pdb=" CD1 LEU A 242 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.29e+00 bond pdb=" C VAL E 653 " pdb=" N PRO E 654 " ideal model delta sigma weight residual 1.335 1.322 0.013 8.70e-03 1.32e+04 2.25e+00 bond pdb=" CB ARG A 561 " pdb=" CG ARG A 561 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB ARG A 408 " pdb=" CG ARG A 408 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" C GLY A1060 " pdb=" O GLY A1060 " ideal model delta sigma weight residual 1.239 1.229 0.010 7.10e-03 1.98e+04 1.83e+00 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 19865 2.89 - 5.78: 167 5.78 - 8.67: 6 8.67 - 11.56: 2 11.56 - 14.45: 3 Bond angle restraints: 20043 Sorted by residual: angle pdb=" CA LEU A 242 " pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 116.30 101.85 14.45 3.50e+00 8.16e-02 1.70e+01 angle pdb=" N VAL A1366 " pdb=" CA VAL A1366 " pdb=" C VAL A1366 " ideal model delta sigma weight residual 113.42 109.08 4.34 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA LEU A 210 " pdb=" CB LEU A 210 " pdb=" CG LEU A 210 " ideal model delta sigma weight residual 116.30 128.81 -12.51 3.50e+00 8.16e-02 1.28e+01 angle pdb=" CA LEU A1138 " pdb=" CB LEU A1138 " pdb=" CG LEU A1138 " ideal model delta sigma weight residual 116.30 128.11 -11.81 3.50e+00 8.16e-02 1.14e+01 angle pdb=" CG1 ILE A1145 " pdb=" CB ILE A1145 " pdb=" CG2 ILE A1145 " ideal model delta sigma weight residual 110.70 100.59 10.11 3.00e+00 1.11e-01 1.14e+01 ... (remaining 20038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 8135 17.31 - 34.62: 789 34.62 - 51.94: 115 51.94 - 69.25: 33 69.25 - 86.56: 10 Dihedral angle restraints: 9082 sinusoidal: 3753 harmonic: 5329 Sorted by residual: dihedral pdb=" CA LEU A 919 " pdb=" C LEU A 919 " pdb=" N VAL A 920 " pdb=" CA VAL A 920 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE A1379 " pdb=" C PHE A1379 " pdb=" N ARG A1380 " pdb=" CA ARG A1380 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA MET A 755 " pdb=" C MET A 755 " pdb=" N HIS A 756 " pdb=" CA HIS A 756 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1794 0.056 - 0.112: 437 0.112 - 0.167: 44 0.167 - 0.223: 1 0.223 - 0.279: 1 Chirality restraints: 2277 Sorted by residual: chirality pdb=" CB ILE A1145 " pdb=" CA ILE A1145 " pdb=" CG1 ILE A1145 " pdb=" CG2 ILE A1145 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 367 " pdb=" CA ILE A 367 " pdb=" CG1 ILE A 367 " pdb=" CG2 ILE A 367 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL A1218 " pdb=" N VAL A1218 " pdb=" C VAL A1218 " pdb=" CB VAL A1218 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 2274 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 529 " 0.031 2.00e-02 2.50e+03 2.56e-02 1.32e+01 pdb=" CG TYR A 529 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 529 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 529 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 529 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 529 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 529 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 529 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1379 " -0.019 2.00e-02 2.50e+03 1.92e-02 6.47e+00 pdb=" CG PHE A1379 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A1379 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A1379 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A1379 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1379 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1379 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 911 " -0.216 9.50e-02 1.11e+02 9.68e-02 5.97e+00 pdb=" NE ARG A 911 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 911 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 911 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 911 " -0.005 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 95 2.57 - 3.16: 11716 3.16 - 3.74: 23247 3.74 - 4.32: 33900 4.32 - 4.90: 54426 Nonbonded interactions: 123384 Sorted by model distance: nonbonded pdb=" OG SER A 916 " pdb=" OD1 ASN A 929 " model vdw 1.993 3.040 nonbonded pdb=" OH TYR A 897 " pdb=" OE1 GLN A1259 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR A 972 " pdb=" OD1 ASP A 974 " model vdw 2.180 3.040 nonbonded pdb=" O ILE A1072 " pdb=" OG1 THR A1076 " model vdw 2.181 3.040 nonbonded pdb=" NE2 GLN A 139 " pdb=" OD2 ASP A 143 " model vdw 2.189 3.120 ... (remaining 123379 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 'C' and (resid 480 through 485 or resid 487 through 580)) selection = (chain 'D' and (resid 480 through 485 or resid 487 through 580)) selection = (chain 'F' and (resid 480 through 485 or resid 487 through 580)) } 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=0.26 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: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.230 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 0.083 14838 Z= 0.235 Angle : 0.701 14.447 20046 Z= 0.364 Chirality : 0.046 0.279 2277 Planarity : 0.006 0.098 2565 Dihedral : 13.846 86.562 5613 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.20), residues: 1792 helix: 0.64 (0.16), residues: 1041 sheet: 0.34 (0.53), residues: 92 loop : -0.56 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 754 HIS 0.007 0.001 HIS D 570 PHE 0.044 0.002 PHE A1379 TYR 0.062 0.003 TYR A 529 ARG 0.008 0.001 ARG A 911 Details of bonding type rmsd hydrogen bonds : bond 0.18932 ( 823) hydrogen bonds : angle 6.30269 ( 2355) metal coordination : bond 0.00700 ( 7) metal coordination : angle 1.61346 ( 1) SS BOND : bond 0.00126 ( 1) SS BOND : angle 0.91147 ( 2) covalent geometry : bond 0.00565 (14830) covalent geometry : angle 0.70092 (20043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 503 ARG cc_start: 0.6400 (ttm110) cc_final: 0.6013 (pmm150) REVERT: A 1075 ILE cc_start: 0.7937 (mp) cc_final: 0.7721 (mp) REVERT: C 531 MET cc_start: 0.7274 (mmt) cc_final: 0.6773 (mpt) REVERT: D 531 MET cc_start: 0.6135 (mtt) cc_final: 0.5900 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 239 average time/residue: 1.5027 time to fit residues: 389.5413 Evaluate side-chains 201 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 139 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1094 HIS A1374 ASN A1394 GLN A1438 GLN E 632 GLN ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 535 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141800 restraints weight = 23938.662| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.16 r_work: 0.3464 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14838 Z= 0.163 Angle : 0.622 13.171 20046 Z= 0.320 Chirality : 0.043 0.203 2277 Planarity : 0.005 0.048 2565 Dihedral : 4.781 25.604 1951 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.65 % Rotamer: Outliers : 1.16 % Allowed : 7.60 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1792 helix: 1.23 (0.16), residues: 1050 sheet: 0.85 (0.52), residues: 83 loop : -0.47 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 754 HIS 0.008 0.001 HIS D 570 PHE 0.028 0.002 PHE A1379 TYR 0.028 0.002 TYR A 529 ARG 0.008 0.001 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 823) hydrogen bonds : angle 4.65161 ( 2355) metal coordination : bond 0.00389 ( 7) metal coordination : angle 1.55742 ( 1) SS BOND : bond 0.00170 ( 1) SS BOND : angle 1.24388 ( 2) covalent geometry : bond 0.00374 (14830) covalent geometry : angle 0.62214 (20043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 218 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 503 ARG cc_start: 0.6880 (ttm110) cc_final: 0.5769 (pmm150) REVERT: A 911 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6536 (ptt-90) REVERT: A 1096 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7022 (mttp) REVERT: C 531 MET cc_start: 0.7209 (mmt) cc_final: 0.6647 (mpt) REVERT: D 531 MET cc_start: 0.5967 (mtt) cc_final: 0.5747 (OUTLIER) REVERT: E 548 ASN cc_start: 0.6905 (m-40) cc_final: 0.6361 (t160) REVERT: E 575 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8367 (mtt) REVERT: E 694 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7024 (pt) outliers start: 19 outliers final: 3 residues processed: 226 average time/residue: 1.4713 time to fit residues: 361.9985 Evaluate side-chains 208 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain E residue 575 MET Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain F residue 557 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 143 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 156 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 858 GLN A1394 GLN E 632 GLN F 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.193586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142003 restraints weight = 14608.357| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.02 r_work: 0.3546 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14838 Z= 0.169 Angle : 0.599 13.377 20046 Z= 0.308 Chirality : 0.043 0.173 2277 Planarity : 0.004 0.053 2565 Dihedral : 4.695 24.647 1951 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.59 % Rotamer: Outliers : 1.46 % Allowed : 9.67 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.06 (0.20), residues: 1792 helix: 1.45 (0.16), residues: 1050 sheet: 0.34 (0.49), residues: 91 loop : -0.38 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 754 HIS 0.005 0.001 HIS D 570 PHE 0.025 0.002 PHE A 399 TYR 0.019 0.002 TYR A 529 ARG 0.003 0.000 ARG A1117 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 823) hydrogen bonds : angle 4.47233 ( 2355) metal coordination : bond 0.00451 ( 7) metal coordination : angle 0.94858 ( 1) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.99456 ( 2) covalent geometry : bond 0.00395 (14830) covalent geometry : angle 0.59923 (20043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7451 (tpt90) REVERT: A 503 ARG cc_start: 0.7007 (ttm110) cc_final: 0.6087 (pmm150) REVERT: A 911 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6571 (ptt-90) REVERT: A 1082 ARG cc_start: 0.7146 (ttm110) cc_final: 0.6838 (ttp-110) REVERT: A 1096 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7021 (mttp) REVERT: C 531 MET cc_start: 0.7266 (mmt) cc_final: 0.6695 (mpt) REVERT: D 531 MET cc_start: 0.6166 (mtt) cc_final: 0.5921 (tpp) REVERT: D 575 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: E 575 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: E 641 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: E 694 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7082 (pt) REVERT: F 535 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6052 (m170) outliers start: 24 outliers final: 4 residues processed: 221 average time/residue: 1.5354 time to fit residues: 368.8602 Evaluate side-chains 223 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1331 ASP Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 575 MET Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain E residue 641 GLU Chi-restraints excluded: chain E residue 676 GLU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain F residue 535 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 46 optimal weight: 0.0370 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.0040 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A 904 GLN A1083 ASN A1394 GLN E 632 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.196240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144966 restraints weight = 23870.489| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 4.15 r_work: 0.3497 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14838 Z= 0.118 Angle : 0.537 11.511 20046 Z= 0.277 Chirality : 0.040 0.157 2277 Planarity : 0.004 0.052 2565 Dihedral : 4.441 22.589 1951 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.82 % Allowed : 10.95 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.39 (0.20), residues: 1792 helix: 1.75 (0.16), residues: 1052 sheet: 0.49 (0.50), residues: 91 loop : -0.34 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1248 HIS 0.003 0.001 HIS F 499 PHE 0.022 0.001 PHE A 399 TYR 0.013 0.001 TYR A 732 ARG 0.004 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 823) hydrogen bonds : angle 4.25058 ( 2355) metal coordination : bond 0.00247 ( 7) metal coordination : angle 0.08319 ( 1) SS BOND : bond 0.00182 ( 1) SS BOND : angle 0.92158 ( 2) covalent geometry : bond 0.00257 (14830) covalent geometry : angle 0.53707 (20043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.6698 (p0) cc_final: 0.6466 (p0) REVERT: A 141 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7418 (tpt90) REVERT: A 587 ASP cc_start: 0.5652 (p0) cc_final: 0.5426 (p0) REVERT: A 803 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7471 (tp40) REVERT: A 1082 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6700 (ttp-110) REVERT: A 1096 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6964 (mttp) REVERT: A 1442 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: C 531 MET cc_start: 0.7174 (mmt) cc_final: 0.6603 (mpt) REVERT: D 575 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8445 (mtm) REVERT: E 577 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7260 (tmm) REVERT: E 694 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7000 (pt) REVERT: F 518 MET cc_start: 0.5958 (ptm) cc_final: 0.5677 (ptm) REVERT: F 535 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.5967 (m170) outliers start: 30 outliers final: 8 residues processed: 238 average time/residue: 1.4577 time to fit residues: 377.0194 Evaluate side-chains 222 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 822 ASN Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 577 MET Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 676 GLU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain F residue 535 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 126 optimal weight: 0.0470 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 ASN A 929 ASN A1327 ASN A1394 GLN D 535 HIS E 632 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.195417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144880 restraints weight = 19155.257| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.30 r_work: 0.3496 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14838 Z= 0.131 Angle : 0.553 12.016 20046 Z= 0.282 Chirality : 0.041 0.154 2277 Planarity : 0.004 0.051 2565 Dihedral : 4.414 21.866 1951 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 1.82 % Allowed : 12.65 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.49 (0.20), residues: 1792 helix: 1.84 (0.16), residues: 1052 sheet: 0.49 (0.50), residues: 91 loop : -0.32 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 754 HIS 0.003 0.001 HIS A 396 PHE 0.024 0.001 PHE A 399 TYR 0.016 0.001 TYR A 470 ARG 0.007 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 823) hydrogen bonds : angle 4.20151 ( 2355) metal coordination : bond 0.00311 ( 7) metal coordination : angle 0.73235 ( 1) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.80138 ( 2) covalent geometry : bond 0.00299 (14830) covalent geometry : angle 0.55247 (20043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7402 (tpt90) REVERT: A 803 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7402 (tp40) REVERT: A 911 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6531 (ptt-90) REVERT: A 1082 ARG cc_start: 0.7036 (ttm110) cc_final: 0.6652 (ttp-110) REVERT: A 1096 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.6814 (mttp) REVERT: A 1132 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6978 (mt-10) REVERT: A 1161 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7485 (ttt90) REVERT: A 1442 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: C 531 MET cc_start: 0.7220 (mmt) cc_final: 0.6637 (mpt) REVERT: D 575 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8533 (mtm) REVERT: E 641 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6043 (tm-30) REVERT: F 518 MET cc_start: 0.5994 (ptm) cc_final: 0.5756 (ptm) REVERT: F 535 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6030 (m170) outliers start: 30 outliers final: 8 residues processed: 227 average time/residue: 1.4684 time to fit residues: 361.7355 Evaluate side-chains 221 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 641 GLU Chi-restraints excluded: chain F residue 535 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 64 optimal weight: 0.0870 chunk 48 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 ASN A 929 ASN A1394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.196871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149601 restraints weight = 28602.480| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.70 r_work: 0.3452 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14838 Z= 0.114 Angle : 0.524 11.067 20046 Z= 0.269 Chirality : 0.040 0.141 2277 Planarity : 0.004 0.050 2565 Dihedral : 4.282 21.825 1951 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % Rotamer: Outliers : 1.70 % Allowed : 13.75 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.70 (0.20), residues: 1792 helix: 2.00 (0.16), residues: 1053 sheet: 0.62 (0.52), residues: 91 loop : -0.23 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1248 HIS 0.006 0.001 HIS D 535 PHE 0.022 0.001 PHE A 399 TYR 0.013 0.001 TYR A 167 ARG 0.005 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 823) hydrogen bonds : angle 4.09132 ( 2355) metal coordination : bond 0.00313 ( 7) metal coordination : angle 0.28343 ( 1) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.80163 ( 2) covalent geometry : bond 0.00252 (14830) covalent geometry : angle 0.52368 (20043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7470 (tpt90) REVERT: A 469 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6915 (pmt) REVERT: A 803 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7514 (tp40) REVERT: A 911 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6484 (ptt-90) REVERT: A 1096 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7065 (mttp) REVERT: A 1132 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7102 (mt-10) REVERT: A 1442 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: C 531 MET cc_start: 0.7293 (mmt) cc_final: 0.6714 (mpt) REVERT: F 479 MET cc_start: 0.5964 (tmm) cc_final: 0.5329 (tmm) REVERT: F 518 MET cc_start: 0.6088 (ptm) cc_final: 0.5874 (ptm) REVERT: F 535 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6060 (m170) outliers start: 28 outliers final: 8 residues processed: 234 average time/residue: 1.4894 time to fit residues: 381.5674 Evaluate side-chains 223 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain F residue 535 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 858 GLN A 876 ASN A 929 ASN A1394 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.192298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139909 restraints weight = 21030.033| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.45 r_work: 0.3452 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14838 Z= 0.217 Angle : 0.648 14.118 20046 Z= 0.330 Chirality : 0.045 0.198 2277 Planarity : 0.005 0.046 2565 Dihedral : 4.666 23.302 1951 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.37 % Allowed : 13.69 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.24 (0.20), residues: 1792 helix: 1.63 (0.16), residues: 1052 sheet: 0.33 (0.50), residues: 91 loop : -0.38 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 754 HIS 0.006 0.001 HIS A 396 PHE 0.026 0.002 PHE A 399 TYR 0.022 0.002 TYR A 407 ARG 0.006 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 823) hydrogen bonds : angle 4.36362 ( 2355) metal coordination : bond 0.00751 ( 7) metal coordination : angle 1.59604 ( 1) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.74873 ( 2) covalent geometry : bond 0.00523 (14830) covalent geometry : angle 0.64815 (20043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7460 (tpt90) REVERT: A 469 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7038 (pmt) REVERT: A 803 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7585 (tp40) REVERT: A 911 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6636 (ptt-90) REVERT: A 969 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: A 1096 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6858 (mttp) REVERT: A 1132 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7031 (mt-10) REVERT: A 1161 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7592 (ttt90) REVERT: A 1442 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7195 (mm-30) REVERT: C 531 MET cc_start: 0.7253 (mmt) cc_final: 0.6679 (mpt) REVERT: D 575 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8578 (mtm) REVERT: E 531 MET cc_start: 0.7840 (ttp) cc_final: 0.7324 (tpt) REVERT: F 479 MET cc_start: 0.5973 (tmm) cc_final: 0.5650 (tmm) REVERT: F 518 MET cc_start: 0.6028 (ptm) cc_final: 0.5818 (ptm) outliers start: 39 outliers final: 9 residues processed: 232 average time/residue: 1.4807 time to fit residues: 372.6522 Evaluate side-chains 221 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 575 MET Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain F residue 562 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 48 optimal weight: 0.0570 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 858 GLN A 876 ASN A1394 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141151 restraints weight = 21137.404| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.48 r_work: 0.3453 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14838 Z= 0.160 Angle : 0.611 13.255 20046 Z= 0.310 Chirality : 0.042 0.220 2277 Planarity : 0.004 0.046 2565 Dihedral : 4.576 22.888 1951 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 14.72 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.34 (0.20), residues: 1792 helix: 1.73 (0.16), residues: 1047 sheet: 0.37 (0.50), residues: 91 loop : -0.37 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 754 HIS 0.004 0.001 HIS A 396 PHE 0.024 0.002 PHE A 399 TYR 0.014 0.002 TYR A 284 ARG 0.007 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 823) hydrogen bonds : angle 4.29322 ( 2355) metal coordination : bond 0.00451 ( 7) metal coordination : angle 0.90283 ( 1) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.80287 ( 2) covalent geometry : bond 0.00376 (14830) covalent geometry : angle 0.61085 (20043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7440 (tpt90) REVERT: A 204 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8094 (pptt) REVERT: A 469 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6952 (pmt) REVERT: A 803 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7540 (tp40) REVERT: A 911 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6573 (ptt-90) REVERT: A 969 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: A 1096 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6887 (mttp) REVERT: A 1132 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7065 (mt-10) REVERT: A 1161 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7562 (ttt90) REVERT: A 1442 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: C 531 MET cc_start: 0.7258 (mmt) cc_final: 0.6672 (mpt) REVERT: D 575 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8574 (mtm) REVERT: E 531 MET cc_start: 0.7802 (ttp) cc_final: 0.7308 (tpt) REVERT: F 479 MET cc_start: 0.5957 (tmm) cc_final: 0.5237 (mmm) REVERT: F 518 MET cc_start: 0.6041 (ptm) cc_final: 0.5826 (ptm) outliers start: 29 outliers final: 13 residues processed: 224 average time/residue: 1.5411 time to fit residues: 374.6975 Evaluate side-chains 224 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 503 ARG Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain D residue 575 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 155 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 858 GLN A 876 ASN A1394 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.195357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143417 restraints weight = 23979.357| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 4.30 r_work: 0.3477 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14838 Z= 0.128 Angle : 0.574 11.887 20046 Z= 0.291 Chirality : 0.041 0.178 2277 Planarity : 0.004 0.045 2565 Dihedral : 4.405 21.737 1951 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.40 % Allowed : 15.39 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.56 (0.20), residues: 1792 helix: 1.90 (0.16), residues: 1046 sheet: 0.52 (0.50), residues: 91 loop : -0.28 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 754 HIS 0.004 0.001 HIS A 16 PHE 0.024 0.001 PHE A 399 TYR 0.013 0.001 TYR A 732 ARG 0.007 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 823) hydrogen bonds : angle 4.16463 ( 2355) metal coordination : bond 0.00336 ( 7) metal coordination : angle 0.11310 ( 1) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.80081 ( 2) covalent geometry : bond 0.00293 (14830) covalent geometry : angle 0.57448 (20043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7444 (tpt90) REVERT: A 204 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (pptt) REVERT: A 469 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6916 (pmt) REVERT: A 803 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7578 (tp40) REVERT: A 911 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6475 (ptt-90) REVERT: A 969 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: A 1096 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7011 (mttp) REVERT: A 1161 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7560 (ttt90) REVERT: C 531 MET cc_start: 0.7251 (mmt) cc_final: 0.6674 (mpt) REVERT: D 518 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5398 (ttp) REVERT: D 575 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8457 (mtm) REVERT: E 689 GLU cc_start: 0.6549 (mp0) cc_final: 0.6341 (tp30) REVERT: F 479 MET cc_start: 0.5925 (tmm) cc_final: 0.5219 (mmm) REVERT: F 518 MET cc_start: 0.6021 (ptm) cc_final: 0.5798 (ptm) outliers start: 23 outliers final: 10 residues processed: 225 average time/residue: 1.4565 time to fit residues: 356.2457 Evaluate side-chains 226 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain D residue 575 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 876 ASN A1394 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.196263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144018 restraints weight = 20233.791| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.09 r_work: 0.3531 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14838 Z= 0.124 Angle : 0.569 11.506 20046 Z= 0.288 Chirality : 0.040 0.167 2277 Planarity : 0.004 0.046 2565 Dihedral : 4.317 22.149 1951 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 1.28 % Allowed : 15.57 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.64 (0.20), residues: 1792 helix: 1.98 (0.16), residues: 1053 sheet: 0.54 (0.50), residues: 91 loop : -0.28 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 754 HIS 0.005 0.001 HIS A 16 PHE 0.023 0.001 PHE A 399 TYR 0.018 0.001 TYR A 470 ARG 0.007 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 823) hydrogen bonds : angle 4.10793 ( 2355) metal coordination : bond 0.00344 ( 7) metal coordination : angle 0.17848 ( 1) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.78398 ( 2) covalent geometry : bond 0.00281 (14830) covalent geometry : angle 0.56925 (20043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7897 (mmtm) REVERT: A 141 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7410 (tpt90) REVERT: A 204 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (pptt) REVERT: A 469 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7009 (pmt) REVERT: A 587 ASP cc_start: 0.5500 (p0) cc_final: 0.5290 (p0) REVERT: A 803 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7425 (tp40) REVERT: A 911 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6500 (ptt-90) REVERT: A 969 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: A 1096 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6890 (mttp) REVERT: A 1161 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7513 (ttt90) REVERT: C 531 MET cc_start: 0.7266 (mmt) cc_final: 0.6680 (mpt) REVERT: D 518 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5308 (tmm) REVERT: E 689 GLU cc_start: 0.6524 (mp0) cc_final: 0.6290 (tp30) REVERT: F 479 MET cc_start: 0.5909 (tmm) cc_final: 0.5304 (mmm) REVERT: F 518 MET cc_start: 0.6036 (ptm) cc_final: 0.5811 (ptm) outliers start: 21 outliers final: 10 residues processed: 221 average time/residue: 1.4828 time to fit residues: 357.6782 Evaluate side-chains 219 residues out of total 1642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1096 LYS Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1260 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1329 ASP Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain D residue 518 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 113 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 876 ASN A1011 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1394 GLN ** D 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.196061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143857 restraints weight = 19230.261| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.93 r_work: 0.3532 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14838 Z= 0.128 Angle : 0.578 11.992 20046 Z= 0.291 Chirality : 0.041 0.211 2277 Planarity : 0.004 0.047 2565 Dihedral : 4.306 22.116 1951 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 1.52 % Allowed : 15.39 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.65 (0.20), residues: 1792 helix: 1.98 (0.16), residues: 1055 sheet: 0.52 (0.50), residues: 91 loop : -0.28 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 754 HIS 0.006 0.001 HIS A 380 PHE 0.024 0.001 PHE A 399 TYR 0.014 0.001 TYR A 167 ARG 0.008 0.000 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 823) hydrogen bonds : angle 4.12738 ( 2355) metal coordination : bond 0.00342 ( 7) metal coordination : angle 0.11065 ( 1) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.77975 ( 2) covalent geometry : bond 0.00295 (14830) covalent geometry : angle 0.57833 (20043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14480.08 seconds wall clock time: 249 minutes 15.09 seconds (14955.09 seconds total)