Starting phenix.real_space_refine on Wed Sep 25 06:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/09_2024/6sgs_10183.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 143 5.16 5 C 17266 2.51 5 N 4430 2.21 5 O 4979 1.98 5 H 27338 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54156 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1044, 16027 Classifications: {'peptide': 1044} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 998} Conformer: "B" Number of residues, atoms: 1044, 16027 Classifications: {'peptide': 1044} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 998} bond proxies already assigned to first conformer: 16164 Chain: "B" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "D" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2336 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2287 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 3, 'TRANS': 148} Chain: "F" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 601 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "G" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 590 Classifications: {'peptide': 36} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 601 Classifications: {'peptide': 37} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Time building chain proxies: 24.68, per 1000 atoms: 0.46 Number of scatterers: 54156 At special positions: 0 Unit cell: (154.78, 135.16, 144.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 O 4979 8.00 N 4430 7.00 C 17266 6.00 H 27338 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.46 Conformation dependent library (CDL) restraints added in 4.2 seconds 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6448 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 24 sheets defined 60.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.957A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.563A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.898A pdb=" N VAL A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.824A pdb=" N GLN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 312 through 317 Proline residue: A 315 - end of helix No H-bonds generated for 'chain 'A' and resid 312 through 317' Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.904A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 386 removed outlier: 3.878A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix removed outlier: 3.906A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.272A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 3.656A pdb=" N GLN A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 463 through 494 removed outlier: 3.588A pdb=" N TYR A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.867A pdb=" N GLY A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 535 Processing helix chain 'A' and resid 537 through 558 removed outlier: 4.082A pdb=" N TYR A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 removed outlier: 3.540A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 691 through 707 Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.513A pdb=" N ALA A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.601A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.752A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 893 removed outlier: 3.639A pdb=" N LEU A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.358A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 920 removed outlier: 3.886A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 955 removed outlier: 3.740A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 972 through 991 Proline residue: A 988 - end of helix removed outlier: 3.516A pdb=" N ILE A 991 " --> pdb=" O MET A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1033 removed outlier: 4.172A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.727A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.794A pdb=" N PHE B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 210 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.925A pdb=" N PHE B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 359 removed outlier: 3.555A pdb=" N VAL B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 387 removed outlier: 4.005A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 5.053A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 458 removed outlier: 5.638A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.018A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.193A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 511 through 535 Processing helix chain 'B' and resid 538 through 558 removed outlier: 4.173A pdb=" N LEU B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 602 removed outlier: 3.514A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 642 Processing helix chain 'B' and resid 643 through 657 removed outlier: 3.976A pdb=" N GLN B 657 " --> pdb=" O ARG B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 708 removed outlier: 3.553A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 782 through 788 removed outlier: 4.289A pdb=" N GLY B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 849 removed outlier: 3.594A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 869 removed outlier: 3.622A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 893 removed outlier: 3.619A pdb=" N LEU B 876 " --> pdb=" O GLN B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.309A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 919 removed outlier: 3.743A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 915 " --> pdb=" O GLY B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 removed outlier: 3.652A pdb=" N LEU B 932 " --> pdb=" O GLN B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 991 removed outlier: 4.800A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 996 through 1033 removed outlier: 4.161A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B1016 " --> pdb=" O VAL B1012 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.798A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.726A pdb=" N ASP C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 3.943A pdb=" N GLN C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.647A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.734A pdb=" N LYS C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.640A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 386 removed outlier: 4.213A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.747A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix removed outlier: 3.500A pdb=" N PHE C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.501A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 4.025A pdb=" N GLY C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 494 removed outlier: 3.629A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 511 through 536 removed outlier: 3.625A pdb=" N ARG C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.717A pdb=" N LEU C 546 " --> pdb=" O LEU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 removed outlier: 3.560A pdb=" N ARG C 637 " --> pdb=" O TRP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 656 removed outlier: 3.904A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 675 removed outlier: 4.052A pdb=" N GLY C 675 " --> pdb=" O VAL C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 707 Processing helix chain 'C' and resid 732 through 739 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 836 through 848 removed outlier: 3.703A pdb=" N ALA C 840 " --> pdb=" O SER C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 893 removed outlier: 3.830A pdb=" N ALA C 873 " --> pdb=" O SER C 869 " (cutoff:3.500A) Proline residue: C 874 - end of helix removed outlier: 3.844A pdb=" N ILE C 879 " --> pdb=" O SER C 875 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 902 removed outlier: 3.755A pdb=" N PHE C 899 " --> pdb=" O TRP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 919 removed outlier: 4.413A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 956 removed outlier: 3.727A pdb=" N VAL C 929 " --> pdb=" O VAL C 925 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 992 removed outlier: 5.341A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix removed outlier: 3.843A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 998 through 1017 removed outlier: 4.026A pdb=" N ALA C1002 " --> pdb=" O GLY C 998 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR C1013 " --> pdb=" O GLY C1009 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.913A pdb=" N LYS D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.585A pdb=" N ASN D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.548A pdb=" N ASN D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.998A pdb=" N VAL D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 49 through 58 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.627A pdb=" N LEU E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.562A pdb=" N VAL E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 123 removed outlier: 3.700A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'F' and resid 2 through 36 Proline residue: F 16 - end of helix Processing helix chain 'G' and resid 2 through 35 Proline residue: G 16 - end of helix Processing helix chain 'H' and resid 2 through 37 Proline residue: H 16 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.773A pdb=" N GLN A 89 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 80 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR A 93 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 12.251A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 826 " --> pdb=" O ASN A 719 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 830 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER A 715 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.773A pdb=" N GLN A 89 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 80 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 91 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET A 78 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR A 93 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 12.251A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.473A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.630A pdb=" N ALA A 286 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.017A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 219 removed outlier: 6.432A pdb=" N SER A 233 " --> pdb=" O PHE B 727 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE B 729 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.830A pdb=" N LYS A 252 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.488A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.049A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 822 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.049A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 822 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 178 removed outlier: 3.594A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 178 removed outlier: 3.594A pdb=" N GLY B 288 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 271 removed outlier: 4.128A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 219 removed outlier: 4.225A pdb=" N SER B 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.965A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 12.265A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 12.265A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP C 681 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.298A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.298A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 608 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N GLY C 616 " --> pdb=" O GLN C 622 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N GLN C 622 " --> pdb=" O GLY C 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 267 through 272 removed outlier: 8.219A pdb=" N TYR C 182 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 770 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.175A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 790 through 792 1761 hydrogen bonds defined for protein. 5118 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: 19.92 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 27332 1.03 - 1.23: 14 1.23 - 1.42: 10998 1.42 - 1.61: 16035 1.61 - 1.81: 280 Bond restraints: 54659 Sorted by residual: bond pdb=" C SER A 805 " pdb=" O SER A 805 " ideal model delta sigma weight residual 1.234 1.139 0.095 1.34e-02 5.57e+03 5.00e+01 bond pdb=" C THR A 431 " pdb=" O THR A 431 " ideal model delta sigma weight residual 1.236 1.157 0.080 1.15e-02 7.56e+03 4.80e+01 bond pdb=" C ARG C 637 " pdb=" N PRO C 638 " ideal model delta sigma weight residual 1.329 1.406 -0.076 1.25e-02 6.40e+03 3.73e+01 bond pdb=" C LEU A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 1.329 1.384 -0.055 1.18e-02 7.18e+03 2.17e+01 bond pdb=" C PRO A 427 " pdb=" O PRO A 427 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.33e-02 5.65e+03 1.66e+01 ... (remaining 54654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 97574 1.63 - 3.26: 1446 3.26 - 4.89: 141 4.89 - 6.52: 13 6.52 - 8.15: 5 Bond angle restraints: 99179 Sorted by residual: angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 120.38 127.00 -6.62 1.03e+00 9.43e-01 4.13e+01 angle pdb=" CA SER A 805 " pdb=" C SER A 805 " pdb=" O SER A 805 " ideal model delta sigma weight residual 121.78 114.51 7.27 1.28e+00 6.10e-01 3.23e+01 angle pdb=" CA PHE B 801 " pdb=" C PHE B 801 " pdb=" O PHE B 801 " ideal model delta sigma weight residual 120.63 114.52 6.11 1.08e+00 8.57e-01 3.20e+01 angle pdb=" CA LEU A 425 " pdb=" C LEU A 425 " pdb=" N PRO A 426 " ideal model delta sigma weight residual 117.79 123.49 -5.70 1.08e+00 8.57e-01 2.78e+01 angle pdb=" C SER A 805 " pdb=" N SER A 806 " pdb=" CA SER A 806 " ideal model delta sigma weight residual 122.29 130.44 -8.15 1.65e+00 3.67e-01 2.44e+01 ... (remaining 99174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 22663 17.64 - 35.27: 2152 35.27 - 52.91: 582 52.91 - 70.54: 168 70.54 - 88.18: 44 Dihedral angle restraints: 25609 sinusoidal: 14007 harmonic: 11602 Sorted by residual: dihedral pdb=" CA GLN C 437 " pdb=" C GLN C 437 " pdb=" N ILE C 438 " pdb=" CA ILE C 438 " ideal model delta harmonic sigma weight residual -180.00 -157.77 -22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLN B 437 " pdb=" C GLN B 437 " pdb=" N ILE B 438 " pdb=" CA ILE B 438 " ideal model delta harmonic sigma weight residual 180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG A 971 " pdb=" C ARG A 971 " pdb=" N LEU A 972 " pdb=" CA LEU A 972 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 25606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3474 0.045 - 0.090: 695 0.090 - 0.135: 198 0.135 - 0.180: 10 0.180 - 0.224: 2 Chirality restraints: 4379 Sorted by residual: chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL C 741 " pdb=" N VAL C 741 " pdb=" C VAL C 741 " pdb=" CB VAL C 741 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG A 971 " pdb=" N ARG A 971 " pdb=" C ARG A 971 " pdb=" CB ARG A 971 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 4376 not shown) Planarity restraints: 8123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 928 " 0.186 2.00e-02 2.50e+03 2.07e-01 6.41e+02 pdb=" CD GLN B 928 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN B 928 " -0.179 2.00e-02 2.50e+03 pdb=" NE2 GLN B 928 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 928 " -0.306 2.00e-02 2.50e+03 pdb="HE22 GLN B 928 " 0.311 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 797 " 0.183 2.00e-02 2.50e+03 2.01e-01 6.05e+02 pdb=" CD GLN C 797 " -0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN C 797 " -0.172 2.00e-02 2.50e+03 pdb=" NE2 GLN C 797 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN C 797 " -0.295 2.00e-02 2.50e+03 pdb="HE22 GLN C 797 " 0.303 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 928 " -0.056 2.00e-02 2.50e+03 5.49e-02 4.51e+01 pdb=" CD GLN C 928 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN C 928 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 GLN C 928 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 928 " 0.076 2.00e-02 2.50e+03 pdb="HE22 GLN C 928 " -0.083 2.00e-02 2.50e+03 ... (remaining 8120 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.20: 3282 2.20 - 2.80: 113696 2.80 - 3.40: 148971 3.40 - 4.00: 199306 4.00 - 4.60: 315424 Nonbonded interactions: 780679 Sorted by model distance: nonbonded pdb=" OD1 ASP C 795 " pdb=" H ASP C 795 " model vdw 1.595 2.450 nonbonded pdb=" OD2 ASP A 568 " pdb="HH12 ARG A 637 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLN A 255 " pdb=" H GLN A 255 " model vdw 1.606 2.450 nonbonded pdb=" OD1 ASP D 143 " pdb=" H LYS D 147 " model vdw 1.608 2.450 nonbonded pdb=" HH TYR A 527 " pdb=" O ILE A1019 " model vdw 1.612 2.450 ... (remaining 780674 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 'A' and (resid 1 through 196 or resid 198 through 1033)) selection = (chain 'B' and (resid 1 through 196 or resid 198 through 1033)) selection = (chain 'C' and (resid 1 through 196 or resid 198 through 1033)) } ncs_group { reference = (chain 'D' and ((resid 15 and (name N or name CA or name C or name O or name HA2 \ or name HA3)) or resid 16 through 166)) selection = chain 'E' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = chain 'G' selection = (chain 'H' and resid 1 through 36) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.730 Extract box with map and model: 1.870 Check model and map are aligned: 0.380 Set scattering table: 0.470 Process input model: 96.560 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 0.004 0.095 27321 Z= 0.283 Angle : 0.637 8.152 37101 Z= 0.396 Chirality : 0.040 0.224 4379 Planarity : 0.004 0.060 4746 Dihedral : 13.195 85.179 9850 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.14 % Allowed : 1.15 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -3.26 (0.12), residues: 3513 helix: -1.67 (0.10), residues: 1974 sheet: -1.73 (0.23), residues: 425 loop : -2.97 (0.15), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 515 HIS 0.004 0.001 HIS B 526 PHE 0.021 0.001 PHE A 948 TYR 0.017 0.001 TYR A 49 ARG 0.007 0.000 ARG C 637 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 804 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 THR cc_start: 0.6109 (t) cc_final: 0.5896 (t) REVERT: A 357 LEU cc_start: 0.8316 (tp) cc_final: 0.8055 (mt) REVERT: A 375 VAL cc_start: 0.7563 (t) cc_final: 0.7118 (t) REVERT: A 391 ASN cc_start: 0.7139 (p0) cc_final: 0.6124 (p0) REVERT: A 774 MET cc_start: 0.8097 (ttt) cc_final: 0.7861 (ttt) REVERT: B 115 MET cc_start: 0.7749 (mmm) cc_final: 0.7394 (mmt) REVERT: B 356 TYR cc_start: 0.8145 (t80) cc_final: 0.7423 (t80) REVERT: B 415 ASN cc_start: 0.8306 (t0) cc_final: 0.8076 (t0) REVERT: B 598 TYR cc_start: 0.7524 (m-80) cc_final: 0.7231 (m-10) REVERT: C 37 THR cc_start: 0.7176 (m) cc_final: 0.6889 (m) REVERT: C 83 ASP cc_start: 0.6757 (m-30) cc_final: 0.6405 (m-30) REVERT: C 259 ARG cc_start: 0.5968 (mtp85) cc_final: 0.5728 (mtp180) REVERT: C 353 LEU cc_start: 0.8248 (mm) cc_final: 0.7954 (tt) REVERT: C 672 VAL cc_start: 0.7368 (t) cc_final: 0.7147 (t) REVERT: C 741 VAL cc_start: 0.7222 (t) cc_final: 0.6974 (t) REVERT: E 27 ASP cc_start: 0.6081 (m-30) cc_final: 0.5523 (m-30) REVERT: E 69 ASN cc_start: 0.6152 (m110) cc_final: 0.5828 (t0) REVERT: F 13 ILE cc_start: 0.7506 (mm) cc_final: 0.7280 (mm) outliers start: 4 outliers final: 1 residues processed: 807 average time/residue: 0.7781 time to fit residues: 989.3539 Evaluate side-chains 531 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 530 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 795 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 273 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 517 ASN A 569 GLN A 605 ASN A 642 ASN A 709 HIS A 846 GLN B 161 ASN B 360 GLN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 181 GLN C 415 ASN C 577 GLN C 923 ASN D 36 ASN D 112 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27321 Z= 0.347 Angle : 0.747 11.054 37101 Z= 0.401 Chirality : 0.047 0.291 4379 Planarity : 0.006 0.070 4746 Dihedral : 4.700 47.980 3734 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.71 % Allowed : 8.25 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.20 (0.14), residues: 3513 helix: -0.03 (0.11), residues: 1999 sheet: -1.15 (0.23), residues: 438 loop : -1.92 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 187 HIS 0.009 0.001 HIS D 85 PHE 0.026 0.002 PHE B 572 TYR 0.024 0.002 TYR A 541 ARG 0.018 0.001 ARG B 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 583 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7792 (mtp) cc_final: 0.7562 (mtp) REVERT: A 108 GLN cc_start: 0.8303 (tt0) cc_final: 0.8090 (tt0) REVERT: A 417 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 470 PHE cc_start: 0.8421 (m-80) cc_final: 0.8201 (m-10) REVERT: A 498 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6906 (ptmm) REVERT: A 575 MET cc_start: 0.5859 (mmm) cc_final: 0.5483 (mmm) REVERT: A 774 MET cc_start: 0.8740 (ttt) cc_final: 0.8474 (ttt) REVERT: A 980 LEU cc_start: 0.7828 (tp) cc_final: 0.7303 (mt) REVERT: B 356 TYR cc_start: 0.8448 (t80) cc_final: 0.7899 (t80) REVERT: B 395 MET cc_start: 0.7439 (mmm) cc_final: 0.7127 (mmm) REVERT: B 414 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7007 (tm-30) REVERT: C 37 THR cc_start: 0.8007 (m) cc_final: 0.7766 (m) REVERT: C 56 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7137 (m) REVERT: C 672 VAL cc_start: 0.7700 (t) cc_final: 0.7455 (t) REVERT: C 681 ASP cc_start: 0.7270 (t70) cc_final: 0.6917 (t70) REVERT: D 36 ASN cc_start: 0.6071 (OUTLIER) cc_final: 0.5245 (m-40) REVERT: D 68 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7233 (tppt) REVERT: E 27 ASP cc_start: 0.6033 (m-30) cc_final: 0.5264 (m-30) REVERT: F 13 ILE cc_start: 0.7466 (mm) cc_final: 0.7223 (mm) REVERT: H 14 MET cc_start: 0.7383 (mmm) cc_final: 0.7037 (mmp) outliers start: 49 outliers final: 23 residues processed: 608 average time/residue: 0.7063 time to fit residues: 693.5017 Evaluate side-chains 519 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 494 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1033 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 773 VAL Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 36 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 317 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 314 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 846 GLN B 68 ASN B 161 ASN B 176 GLN B 284 GLN B 737 GLN C 70 ASN C 517 ASN C 605 ASN D 36 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 27321 Z= 0.228 Angle : 0.543 8.952 37101 Z= 0.286 Chirality : 0.041 0.155 4379 Planarity : 0.004 0.048 4746 Dihedral : 4.243 20.411 3732 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.36 % Allowed : 10.59 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.36 (0.14), residues: 3513 helix: 0.71 (0.12), residues: 1997 sheet: -0.88 (0.24), residues: 438 loop : -1.64 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 754 HIS 0.005 0.001 HIS A 692 PHE 0.020 0.001 PHE A 682 TYR 0.015 0.001 TYR C 157 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 503 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7996 (mtp) cc_final: 0.7753 (mtp) REVERT: A 112 GLN cc_start: 0.7649 (tp40) cc_final: 0.7305 (mm110) REVERT: A 470 PHE cc_start: 0.8549 (m-80) cc_final: 0.8306 (m-10) REVERT: A 498 LYS cc_start: 0.7307 (mtpt) cc_final: 0.6975 (ptmm) REVERT: A 575 MET cc_start: 0.5906 (mmm) cc_final: 0.5706 (mmm) REVERT: A 902 MET cc_start: 0.8623 (mmm) cc_final: 0.8341 (mmm) REVERT: A 980 LEU cc_start: 0.7879 (tp) cc_final: 0.7398 (mt) REVERT: B 356 TYR cc_start: 0.8448 (t80) cc_final: 0.7993 (t80) REVERT: B 417 GLU cc_start: 0.7544 (tp30) cc_final: 0.7165 (tp30) REVERT: B 815 ARG cc_start: 0.8183 (ptm-80) cc_final: 0.7675 (ttp-170) REVERT: C 259 ARG cc_start: 0.6307 (mtp85) cc_final: 0.5979 (mtp180) REVERT: C 712 MET cc_start: 0.7286 (ttm) cc_final: 0.7044 (tpp) REVERT: D 36 ASN cc_start: 0.6136 (OUTLIER) cc_final: 0.5876 (m-40) REVERT: E 27 ASP cc_start: 0.5958 (m-30) cc_final: 0.5344 (m-30) REVERT: E 36 ASN cc_start: 0.7646 (t0) cc_final: 0.7255 (t0) REVERT: E 107 ASN cc_start: 0.8138 (t0) cc_final: 0.7719 (t0) REVERT: F 13 ILE cc_start: 0.7491 (mm) cc_final: 0.7226 (mm) outliers start: 39 outliers final: 23 residues processed: 521 average time/residue: 0.7249 time to fit residues: 613.2868 Evaluate side-chains 481 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 457 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain D residue 36 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 298 ASN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 161 ASN C 81 ASN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27321 Z= 0.323 Angle : 0.622 7.390 37101 Z= 0.330 Chirality : 0.043 0.199 4379 Planarity : 0.005 0.050 4746 Dihedral : 4.384 21.673 3732 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.85 % Allowed : 11.11 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.17 (0.14), residues: 3513 helix: 0.89 (0.12), residues: 1989 sheet: -0.91 (0.23), residues: 450 loop : -1.55 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 809 HIS 0.008 0.001 HIS B 526 PHE 0.043 0.002 PHE A 513 TYR 0.023 0.002 TYR B 157 ARG 0.011 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 498 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7729 (tp40) cc_final: 0.7413 (mm-40) REVERT: A 342 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7742 (mmtm) REVERT: A 468 ARG cc_start: 0.7915 (ttm110) cc_final: 0.7546 (ttp80) REVERT: A 470 PHE cc_start: 0.8754 (m-80) cc_final: 0.8494 (m-80) REVERT: A 498 LYS cc_start: 0.7690 (mtpt) cc_final: 0.7463 (ptmm) REVERT: A 575 MET cc_start: 0.6336 (mmm) cc_final: 0.6112 (mmm) REVERT: A 980 LEU cc_start: 0.8386 (tp) cc_final: 0.7844 (mt) REVERT: B 356 TYR cc_start: 0.8532 (t80) cc_final: 0.8205 (t80) REVERT: B 417 GLU cc_start: 0.7733 (tp30) cc_final: 0.7404 (tp30) REVERT: B 497 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8668 (mp) REVERT: B 801 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: B 815 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.8007 (ttp-170) REVERT: C 20 MET cc_start: 0.7539 (mtt) cc_final: 0.7325 (mtt) REVERT: C 182 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8728 (m-10) REVERT: C 659 LYS cc_start: 0.8391 (mmtm) cc_final: 0.7968 (tptp) REVERT: C 702 LEU cc_start: 0.8568 (tp) cc_final: 0.8352 (mt) REVERT: C 737 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7401 (mm-40) REVERT: D 145 PHE cc_start: 0.7282 (m-80) cc_final: 0.7046 (m-80) REVERT: E 36 ASN cc_start: 0.7969 (t0) cc_final: 0.7742 (t0) outliers start: 53 outliers final: 34 residues processed: 532 average time/residue: 0.8392 time to fit residues: 719.1917 Evaluate side-chains 467 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 430 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 8 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN C 622 GLN D 36 ASN D 59 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27321 Z= 0.344 Angle : 0.592 7.623 37101 Z= 0.314 Chirality : 0.043 0.154 4379 Planarity : 0.004 0.070 4746 Dihedral : 4.332 19.322 3732 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 12.34 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.05 (0.14), residues: 3513 helix: 1.04 (0.12), residues: 1989 sheet: -0.68 (0.24), residues: 445 loop : -1.49 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.006 0.001 HIS E 125 PHE 0.022 0.002 PHE A 682 TYR 0.018 0.002 TYR C 49 ARG 0.006 0.001 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 447 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7737 (tp40) cc_final: 0.7455 (mm-40) REVERT: A 138 MET cc_start: 0.8948 (ptm) cc_final: 0.8723 (ptm) REVERT: A 254 ASN cc_start: 0.7299 (m-40) cc_final: 0.6886 (m-40) REVERT: A 468 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7590 (ttp80) REVERT: A 470 PHE cc_start: 0.8760 (m-80) cc_final: 0.8469 (m-10) REVERT: A 498 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7546 (ptmm) REVERT: A 980 LEU cc_start: 0.8635 (tp) cc_final: 0.8014 (mt) REVERT: B 156 ASP cc_start: 0.7487 (t0) cc_final: 0.7287 (t0) REVERT: B 356 TYR cc_start: 0.8487 (t80) cc_final: 0.8204 (t80) REVERT: B 417 GLU cc_start: 0.7829 (tp30) cc_final: 0.7488 (tp30) REVERT: B 730 ASP cc_start: 0.7939 (m-30) cc_final: 0.7730 (m-30) REVERT: B 791 VAL cc_start: 0.9076 (m) cc_final: 0.8798 (t) REVERT: B 801 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 815 ARG cc_start: 0.8462 (ptm-80) cc_final: 0.7968 (ttt180) REVERT: C 32 VAL cc_start: 0.8581 (m) cc_final: 0.8330 (t) REVERT: C 83 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: C 182 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8784 (m-10) REVERT: C 414 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7290 (tp30) REVERT: C 737 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7481 (mm-40) REVERT: D 32 ILE cc_start: 0.7599 (mt) cc_final: 0.7372 (mt) REVERT: D 155 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7060 (m-40) REVERT: E 36 ASN cc_start: 0.8271 (t0) cc_final: 0.8052 (t0) REVERT: F 31 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7401 (mt-10) outliers start: 49 outliers final: 31 residues processed: 482 average time/residue: 0.7524 time to fit residues: 572.3718 Evaluate side-chains 462 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 427 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain F residue 8 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 280 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.7872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27321 Z= 0.181 Angle : 0.514 7.047 37101 Z= 0.269 Chirality : 0.040 0.152 4379 Planarity : 0.004 0.050 4746 Dihedral : 4.106 19.240 3732 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.50 % Allowed : 13.07 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.47 (0.14), residues: 3513 helix: 1.37 (0.12), residues: 1997 sheet: -0.52 (0.24), residues: 435 loop : -1.30 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 789 HIS 0.003 0.001 HIS E 52 PHE 0.018 0.001 PHE A 682 TYR 0.014 0.001 TYR A 541 ARG 0.006 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 438 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7681 (tp40) cc_final: 0.7417 (mm-40) REVERT: A 138 MET cc_start: 0.8937 (ptm) cc_final: 0.8697 (ptm) REVERT: A 254 ASN cc_start: 0.7260 (m-40) cc_final: 0.6896 (m-40) REVERT: A 468 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7548 (ttp80) REVERT: A 470 PHE cc_start: 0.8704 (m-80) cc_final: 0.8423 (m-10) REVERT: A 498 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7547 (ptmm) REVERT: A 980 LEU cc_start: 0.8492 (tp) cc_final: 0.7960 (mt) REVERT: B 156 ASP cc_start: 0.7621 (t0) cc_final: 0.7343 (t0) REVERT: B 248 LYS cc_start: 0.8714 (mttp) cc_final: 0.8284 (mtpp) REVERT: B 356 TYR cc_start: 0.8407 (t80) cc_final: 0.8101 (t80) REVERT: B 417 GLU cc_start: 0.7786 (tp30) cc_final: 0.7451 (tp30) REVERT: B 730 ASP cc_start: 0.7895 (m-30) cc_final: 0.7681 (m-30) REVERT: B 761 ASP cc_start: 0.8226 (m-30) cc_final: 0.8008 (m-30) REVERT: B 791 VAL cc_start: 0.9079 (m) cc_final: 0.8822 (t) REVERT: B 815 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.8018 (ttt180) REVERT: C 83 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: C 120 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7158 (tp40) REVERT: C 414 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 737 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7452 (mm-40) REVERT: E 36 ASN cc_start: 0.8186 (t0) cc_final: 0.7977 (t0) REVERT: F 31 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7409 (mt-10) REVERT: H 19 MET cc_start: 0.6688 (tpp) cc_final: 0.6477 (tpp) outliers start: 43 outliers final: 30 residues processed: 465 average time/residue: 0.7479 time to fit residues: 553.0799 Evaluate side-chains 447 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 415 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain F residue 8 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 336 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.8335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27321 Z= 0.298 Angle : 0.561 7.145 37101 Z= 0.295 Chirality : 0.042 0.154 4379 Planarity : 0.004 0.057 4746 Dihedral : 4.172 20.729 3732 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.54 % Allowed : 13.42 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.48 (0.14), residues: 3513 helix: 1.37 (0.12), residues: 2001 sheet: -0.53 (0.24), residues: 441 loop : -1.26 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.004 0.001 HIS E 125 PHE 0.020 0.001 PHE C 11 TYR 0.019 0.002 TYR C 157 ARG 0.006 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 440 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7761 (tp40) cc_final: 0.7461 (mm-40) REVERT: A 138 MET cc_start: 0.8970 (ptm) cc_final: 0.8725 (ptm) REVERT: A 254 ASN cc_start: 0.7237 (m-40) cc_final: 0.6895 (m-40) REVERT: A 468 ARG cc_start: 0.7852 (ttm110) cc_final: 0.7627 (ttp80) REVERT: A 470 PHE cc_start: 0.8746 (m-80) cc_final: 0.8458 (m-10) REVERT: A 498 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7632 (ptmm) REVERT: A 980 LEU cc_start: 0.8658 (tp) cc_final: 0.8005 (mt) REVERT: B 156 ASP cc_start: 0.7678 (t0) cc_final: 0.7424 (t0) REVERT: B 248 LYS cc_start: 0.8740 (mttp) cc_final: 0.8322 (mtpp) REVERT: B 356 TYR cc_start: 0.8488 (t80) cc_final: 0.8195 (t80) REVERT: B 414 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 417 GLU cc_start: 0.7831 (tp30) cc_final: 0.7470 (tp30) REVERT: B 467 TYR cc_start: 0.8815 (m-80) cc_final: 0.8445 (m-80) REVERT: B 761 ASP cc_start: 0.8266 (m-30) cc_final: 0.8052 (m-30) REVERT: B 791 VAL cc_start: 0.9005 (m) cc_final: 0.8736 (t) REVERT: B 815 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.7981 (ttt180) REVERT: C 20 MET cc_start: 0.8383 (mtm) cc_final: 0.8099 (mtt) REVERT: C 32 VAL cc_start: 0.8644 (m) cc_final: 0.8422 (t) REVERT: C 83 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: C 120 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7206 (tp40) REVERT: C 182 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: C 414 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 659 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7918 (tptp) REVERT: C 737 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7653 (mm-40) REVERT: D 155 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7279 (t0) REVERT: E 36 ASN cc_start: 0.8366 (t0) cc_final: 0.8148 (t0) REVERT: F 31 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7418 (mt-10) outliers start: 44 outliers final: 33 residues processed: 470 average time/residue: 0.7952 time to fit residues: 591.3748 Evaluate side-chains 448 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 411 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 35 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 264 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.8450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27321 Z= 0.187 Angle : 0.513 7.023 37101 Z= 0.268 Chirality : 0.040 0.150 4379 Planarity : 0.004 0.048 4746 Dihedral : 4.043 20.073 3732 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.47 % Allowed : 14.09 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.73 (0.14), residues: 3513 helix: 1.55 (0.12), residues: 2003 sheet: -0.43 (0.25), residues: 433 loop : -1.11 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.003 0.001 HIS E 52 PHE 0.018 0.001 PHE A 682 TYR 0.020 0.001 TYR A 541 ARG 0.006 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 425 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7711 (tp40) cc_final: 0.7408 (mm-40) REVERT: A 138 MET cc_start: 0.8956 (ptm) cc_final: 0.8719 (ptm) REVERT: A 254 ASN cc_start: 0.7119 (m-40) cc_final: 0.6830 (m-40) REVERT: A 468 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7603 (ttp80) REVERT: A 470 PHE cc_start: 0.8689 (m-80) cc_final: 0.8411 (m-10) REVERT: A 498 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7664 (ptmm) REVERT: A 558 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7341 (mtp85) REVERT: A 673 GLU cc_start: 0.6505 (mp0) cc_final: 0.6150 (mp0) REVERT: A 980 LEU cc_start: 0.8569 (tp) cc_final: 0.7994 (mt) REVERT: B 156 ASP cc_start: 0.7637 (t0) cc_final: 0.7382 (t0) REVERT: B 248 LYS cc_start: 0.8709 (mttp) cc_final: 0.8343 (mtpp) REVERT: B 359 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8019 (mt) REVERT: B 414 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 417 GLU cc_start: 0.7830 (tp30) cc_final: 0.7472 (tp30) REVERT: B 447 MET cc_start: 0.7873 (mmp) cc_final: 0.7641 (mmp) REVERT: B 467 TYR cc_start: 0.8790 (m-80) cc_final: 0.8575 (m-80) REVERT: B 761 ASP cc_start: 0.8221 (m-30) cc_final: 0.8014 (m-30) REVERT: B 791 VAL cc_start: 0.8990 (m) cc_final: 0.8730 (t) REVERT: B 815 ARG cc_start: 0.8381 (ptm-80) cc_final: 0.8007 (ttt180) REVERT: C 20 MET cc_start: 0.8362 (mtm) cc_final: 0.8130 (mtt) REVERT: C 83 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: C 120 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7155 (tp40) REVERT: C 182 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: C 395 MET cc_start: 0.8675 (mmp) cc_final: 0.7980 (mmp) REVERT: C 414 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7080 (tm-30) REVERT: C 659 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7921 (tptp) REVERT: C 737 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7643 (mm-40) REVERT: D 155 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7204 (t0) REVERT: E 36 ASN cc_start: 0.8317 (t0) cc_final: 0.8102 (t0) outliers start: 42 outliers final: 28 residues processed: 453 average time/residue: 0.7938 time to fit residues: 567.8545 Evaluate side-chains 446 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 413 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 35 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 313 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 296 optimal weight: 0.0030 chunk 312 optimal weight: 8.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 274 ASN D 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.8568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27321 Z= 0.191 Angle : 0.503 7.038 37101 Z= 0.262 Chirality : 0.040 0.147 4379 Planarity : 0.004 0.047 4746 Dihedral : 3.933 19.141 3732 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.54 % Allowed : 13.95 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.94 (0.14), residues: 3513 helix: 1.71 (0.12), residues: 2005 sheet: -0.39 (0.25), residues: 433 loop : -1.00 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 754 HIS 0.002 0.001 HIS E 52 PHE 0.018 0.001 PHE A 682 TYR 0.018 0.001 TYR A 541 ARG 0.007 0.000 ARG B 620 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 419 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7782 (tp40) cc_final: 0.7465 (mm-40) REVERT: A 138 MET cc_start: 0.8955 (ptm) cc_final: 0.8716 (ptm) REVERT: A 254 ASN cc_start: 0.7127 (m-40) cc_final: 0.6880 (m-40) REVERT: A 470 PHE cc_start: 0.8656 (m-80) cc_final: 0.8383 (m-10) REVERT: A 498 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7655 (ptmm) REVERT: A 673 GLU cc_start: 0.6396 (mp0) cc_final: 0.6144 (mp0) REVERT: A 980 LEU cc_start: 0.8431 (tp) cc_final: 0.7887 (mt) REVERT: B 156 ASP cc_start: 0.7682 (t0) cc_final: 0.7432 (t0) REVERT: B 248 LYS cc_start: 0.8687 (mttp) cc_final: 0.8356 (mtpp) REVERT: B 356 TYR cc_start: 0.8274 (t80) cc_final: 0.7985 (t80) REVERT: B 359 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 414 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 417 GLU cc_start: 0.7840 (tp30) cc_final: 0.7474 (tp30) REVERT: B 447 MET cc_start: 0.7880 (mmp) cc_final: 0.7643 (mmp) REVERT: B 791 VAL cc_start: 0.9027 (m) cc_final: 0.8763 (t) REVERT: B 815 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.8026 (ttt180) REVERT: C 20 MET cc_start: 0.8369 (mtm) cc_final: 0.8143 (mtt) REVERT: C 83 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: C 120 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7191 (tp40) REVERT: C 182 TYR cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (m-10) REVERT: C 395 MET cc_start: 0.8672 (mmp) cc_final: 0.7984 (mmp) REVERT: C 414 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7092 (tm-30) REVERT: C 659 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7915 (tptp) REVERT: C 737 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7671 (mm-40) REVERT: C 781 MET cc_start: 0.8719 (mmp) cc_final: 0.7869 (mmp) REVERT: D 155 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7144 (t0) REVERT: E 36 ASN cc_start: 0.8305 (t0) cc_final: 0.8077 (t0) outliers start: 44 outliers final: 30 residues processed: 449 average time/residue: 0.7960 time to fit residues: 564.7361 Evaluate side-chains 446 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 411 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain H residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.8738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27321 Z= 0.237 Angle : 0.518 6.787 37101 Z= 0.271 Chirality : 0.040 0.175 4379 Planarity : 0.004 0.046 4746 Dihedral : 3.963 19.830 3732 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.43 % Allowed : 13.91 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.98 (0.14), residues: 3513 helix: 1.74 (0.12), residues: 2004 sheet: -0.38 (0.25), residues: 435 loop : -0.96 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.003 0.001 HIS E 59 PHE 0.018 0.001 PHE C 948 TYR 0.020 0.001 TYR B 467 ARG 0.007 0.000 ARG B 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7026 Ramachandran restraints generated. 3513 Oldfield, 0 Emsley, 3513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 425 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7752 (tp40) cc_final: 0.7454 (mm-40) REVERT: A 138 MET cc_start: 0.8957 (ptm) cc_final: 0.8721 (ptm) REVERT: A 470 PHE cc_start: 0.8688 (m-80) cc_final: 0.8410 (m-10) REVERT: A 498 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7680 (ptmm) REVERT: A 673 GLU cc_start: 0.6395 (mp0) cc_final: 0.6148 (mp0) REVERT: A 980 LEU cc_start: 0.8617 (tp) cc_final: 0.7972 (mt) REVERT: B 156 ASP cc_start: 0.7816 (t0) cc_final: 0.7546 (t0) REVERT: B 248 LYS cc_start: 0.8714 (mttp) cc_final: 0.8398 (mtpp) REVERT: B 356 TYR cc_start: 0.8324 (t80) cc_final: 0.8052 (t80) REVERT: B 359 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8049 (mt) REVERT: B 414 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 417 GLU cc_start: 0.7881 (tp30) cc_final: 0.7512 (tp30) REVERT: B 447 MET cc_start: 0.7822 (mmp) cc_final: 0.7600 (mmp) REVERT: B 791 VAL cc_start: 0.9010 (m) cc_final: 0.8731 (t) REVERT: B 815 ARG cc_start: 0.8412 (ptm-80) cc_final: 0.8043 (ttt180) REVERT: C 20 MET cc_start: 0.8424 (mtm) cc_final: 0.8196 (mtt) REVERT: C 83 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: C 120 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7274 (tp40) REVERT: C 182 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8761 (m-10) REVERT: C 414 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7228 (tm-30) REVERT: C 558 ARG cc_start: 0.7115 (mtp180) cc_final: 0.6889 (ttt-90) REVERT: C 659 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7888 (tptp) REVERT: C 737 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7642 (mm-40) REVERT: D 155 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7189 (t0) REVERT: E 36 ASN cc_start: 0.8436 (t0) cc_final: 0.8200 (t0) outliers start: 41 outliers final: 32 residues processed: 454 average time/residue: 0.7700 time to fit residues: 553.6504 Evaluate side-chains 452 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 415 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain H residue 35 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 0.9980 chunk 294 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 255 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 277 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105592 restraints weight = 107603.100| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.54 r_work: 0.2915 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.8791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27321 Z= 0.154 Angle : 0.488 6.989 37101 Z= 0.253 Chirality : 0.040 0.148 4379 Planarity : 0.004 0.043 4746 Dihedral : 3.819 18.320 3732 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.36 % Allowed : 13.98 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.15), residues: 3513 helix: 1.93 (0.12), residues: 2004 sheet: -0.34 (0.25), residues: 433 loop : -0.77 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 754 HIS 0.002 0.000 HIS E 52 PHE 0.017 0.001 PHE A 682 TYR 0.013 0.001 TYR B 467 ARG 0.004 0.000 ARG C 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12245.32 seconds wall clock time: 215 minutes 20.01 seconds (12920.01 seconds total)