Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 06:43:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/07_2023/6sgs_10183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/07_2023/6sgs_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_10183/07_2023/6sgs_10183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/07_2023/6sgs_10183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/07_2023/6sgs_10183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/07_2023/6sgs_10183.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B ARG 765": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 795": "OD1" <-> "OD2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 20.47, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 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: 33.98 Conformation dependent library (CDL) restraints added in 4.3 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: 1.48 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: 22.21 Time building geometry restraints manager: 35.89 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: 98.69 - 105.76: 601 105.76 - 112.83: 65303 112.83 - 119.90: 14022 119.90 - 126.97: 18999 126.97 - 134.04: 254 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: 19338 17.64 - 35.27: 1844 35.27 - 52.91: 310 52.91 - 70.54: 79 70.54 - 88.18: 44 Dihedral angle restraints: 21615 sinusoidal: 10013 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 21612 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 1.850 nonbonded pdb=" OD2 ASP A 568 " pdb="HH12 ARG A 637 " model vdw 1.602 1.850 nonbonded pdb=" OE1 GLN A 255 " pdb=" H GLN A 255 " model vdw 1.606 1.850 nonbonded pdb=" OD1 ASP D 143 " pdb=" H LYS D 147 " model vdw 1.608 1.850 nonbonded pdb=" HH TYR A 527 " pdb=" O ILE A1019 " model vdw 1.612 1.850 ... (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 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.610 Extract box with map and model: 9.100 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 135.010 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.170 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.590 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.997 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 outliers start: 4 outliers final: 1 residues processed: 807 average time/residue: 0.7801 time to fit residues: 993.0665 Evaluate side-chains 527 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 526 time to evaluate : 2.990 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4815 time to fit residues: 4.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 146 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 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: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 27321 Z= 0.338 Angle : 0.713 10.806 37101 Z= 0.380 Chirality : 0.047 0.419 4379 Planarity : 0.005 0.063 4746 Dihedral : 4.575 21.479 3732 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.89 % 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: -1.27 (0.13), residues: 3513 helix: -0.06 (0.11), residues: 1995 sheet: -1.08 (0.23), residues: 438 loop : -2.05 (0.18), residues: 1080 *********************** 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 638 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 584 time to evaluate : 3.236 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 outliers start: 54 outliers final: 30 residues processed: 616 average time/residue: 0.6925 time to fit residues: 685.4705 Evaluate side-chains 526 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 496 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5146 time to fit residues: 33.0711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 263 optimal weight: 0.1980 chunk 215 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 317 optimal weight: 8.9990 chunk 342 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 846 GLN B 68 ASN B 176 GLN B 284 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 27321 Z= 0.160 Angle : 0.513 8.675 37101 Z= 0.267 Chirality : 0.040 0.149 4379 Planarity : 0.004 0.046 4746 Dihedral : 4.134 20.746 3732 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.66 % 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: -0.29 (0.14), residues: 3513 helix: 0.74 (0.12), residues: 2004 sheet: -0.79 (0.24), residues: 435 loop : -1.62 (0.18), residues: 1074 *********************** 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 525 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 506 time to evaluate : 3.079 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 outliers start: 19 outliers final: 12 residues processed: 514 average time/residue: 0.7208 time to fit residues: 599.4824 Evaluate side-chains 471 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 459 time to evaluate : 3.005 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5234 time to fit residues: 15.5406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 846 GLN B 194 ASN B 737 GLN C 584 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.125 27321 Z= 0.320 Angle : 0.650 12.103 37101 Z= 0.344 Chirality : 0.044 0.208 4379 Planarity : 0.005 0.087 4746 Dihedral : 4.398 27.137 3732 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.26 % 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: -0.16 (0.14), residues: 3513 helix: 0.87 (0.12), residues: 1994 sheet: -0.81 (0.24), residues: 446 loop : -1.54 (0.18), residues: 1073 *********************** 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 535 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 499 time to evaluate : 3.031 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 outliers start: 36 outliers final: 18 residues processed: 522 average time/residue: 0.7723 time to fit residues: 632.6870 Evaluate side-chains 442 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 424 time to evaluate : 3.051 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5003 time to fit residues: 20.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 287 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 605 ASN A 737 GLN A 846 GLN C 469 GLN E 89 HIS E 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 27321 Z= 0.262 Angle : 0.552 8.239 37101 Z= 0.289 Chirality : 0.042 0.219 4379 Planarity : 0.004 0.061 4746 Dihedral : 4.189 22.395 3732 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.91 % 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: 0.21 (0.14), residues: 3513 helix: 1.16 (0.12), residues: 1993 sheet: -0.73 (0.24), residues: 452 loop : -1.34 (0.18), residues: 1068 *********************** 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 489 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 463 time to evaluate : 3.082 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 outliers start: 26 outliers final: 14 residues processed: 480 average time/residue: 0.7583 time to fit residues: 578.5444 Evaluate side-chains 443 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 429 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5311 time to fit residues: 17.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 337 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 737 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 27321 Z= 0.217 Angle : 0.522 6.835 37101 Z= 0.272 Chirality : 0.040 0.154 4379 Planarity : 0.004 0.070 4746 Dihedral : 4.045 20.861 3732 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.59 % 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: 0.56 (0.14), residues: 3513 helix: 1.43 (0.12), residues: 2001 sheet: -0.57 (0.24), residues: 451 loop : -1.18 (0.19), residues: 1061 *********************** 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 465 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 448 time to evaluate : 3.064 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 outliers start: 17 outliers final: 7 residues processed: 459 average time/residue: 0.7669 time to fit residues: 551.0226 Evaluate side-chains 422 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 415 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4630 time to fit residues: 10.0926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 191 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 205 optimal weight: 0.0000 chunk 155 optimal weight: 6.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 213 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN A 846 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 27321 Z= 0.234 Angle : 0.524 6.834 37101 Z= 0.274 Chirality : 0.041 0.150 4379 Planarity : 0.004 0.066 4746 Dihedral : 4.017 20.993 3732 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.38 % 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: 0.68 (0.14), residues: 3513 helix: 1.54 (0.12), residues: 1996 sheet: -0.52 (0.24), residues: 451 loop : -1.15 (0.19), residues: 1066 *********************** 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 452 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 441 time to evaluate : 3.117 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 outliers start: 11 outliers final: 4 residues processed: 444 average time/residue: 0.7842 time to fit residues: 544.6404 Evaluate side-chains 420 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5464 time to fit residues: 7.8139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 229 optimal weight: 0.4980 chunk 166 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 737 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.8222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 27321 Z= 0.165 Angle : 0.495 6.831 37101 Z= 0.256 Chirality : 0.040 0.147 4379 Planarity : 0.003 0.044 4746 Dihedral : 3.881 20.977 3732 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.52 % 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: 1.01 (0.15), residues: 3513 helix: 1.78 (0.12), residues: 1998 sheet: -0.45 (0.24), residues: 443 loop : -0.91 (0.19), residues: 1072 *********************** 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 446 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 431 time to evaluate : 3.145 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 outliers start: 15 outliers final: 7 residues processed: 440 average time/residue: 0.7672 time to fit residues: 534.2105 Evaluate side-chains 423 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 416 time to evaluate : 3.099 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4851 time to fit residues: 10.3862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 294 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 296 optimal weight: 0.0470 chunk 312 optimal weight: 9.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 737 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.8485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 27321 Z= 0.261 Angle : 0.536 8.793 37101 Z= 0.281 Chirality : 0.041 0.167 4379 Planarity : 0.004 0.049 4746 Dihedral : 3.969 21.496 3732 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.31 % 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: 0.97 (0.14), residues: 3513 helix: 1.73 (0.12), residues: 2000 sheet: -0.35 (0.24), residues: 440 loop : -0.97 (0.19), residues: 1073 *********************** 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 439 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 430 time to evaluate : 3.080 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 outliers start: 9 outliers final: 4 residues processed: 435 average time/residue: 0.7931 time to fit residues: 543.1195 Evaluate side-chains 428 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 424 time to evaluate : 3.130 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.6106 time to fit residues: 8.1109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 0.6980 chunk 331 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 347 optimal weight: 0.7980 chunk 320 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 737 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.8638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 27321 Z= 0.202 Angle : 0.507 6.740 37101 Z= 0.264 Chirality : 0.040 0.146 4379 Planarity : 0.004 0.074 4746 Dihedral : 3.905 19.834 3732 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.14 % 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: 1.14 (0.15), residues: 3513 helix: 1.87 (0.12), residues: 1996 sheet: -0.37 (0.24), residues: 446 loop : -0.84 (0.19), residues: 1071 ********************** 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 426 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 422 time to evaluate : 3.121 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 outliers start: 4 outliers final: 0 residues processed: 424 average time/residue: 0.8160 time to fit residues: 542.8880 Evaluate side-chains 411 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 737 GLN ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.099672 restraints weight = 109755.239| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.63 r_work: 0.2861 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.8871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 27321 Z= 0.314 Angle : 0.556 6.631 37101 Z= 0.292 Chirality : 0.042 0.149 4379 Planarity : 0.004 0.055 4746 Dihedral : 4.049 21.888 3732 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.38 % 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: 1.73 (0.12), residues: 1994 sheet: -0.32 (0.25), residues: 436 loop : -0.94 (0.19), residues: 1083 =============================================================================== Job complete usr+sys time: 11406.31 seconds wall clock time: 197 minutes 26.54 seconds (11846.54 seconds total)