Starting phenix.real_space_refine on Sun Mar 10 21:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/03_2024/6sgs_10183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/03_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_10183/03_2024/6sgs_10183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/03_2024/6sgs_10183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/03_2024/6sgs_10183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgs_10183/03_2024/6sgs_10183.pdb" } 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.14, per 1000 atoms: 0.39 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: 32.81 Conformation dependent library (CDL) restraints added in 5.2 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: 3.42 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: 20.27 Time building geometry restraints manager: 34.67 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: 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 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: 0.010 Normalize map: mean=0, sd=1: 0.980 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: 7.600 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 136.930 Find NCS groups from input model: 2.100 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 151.610 ------------------------------------------------------------------------------- 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 : 2.994 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: 0.7584 time to fit residues: 961.9015 Evaluate side-chains 531 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 530 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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: 0.4980 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 273 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 112 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 747 ASN C 923 ASN D 36 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4094 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= 0.338 Angle : 0.737 11.899 37101 Z= 0.393 Chirality : 0.047 0.263 4379 Planarity : 0.006 0.061 4746 Dihedral : 4.630 45.984 3734 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.78 % Allowed : 8.46 % Favored : 89.76 % 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: -1.12 (0.14), residues: 3513 helix: 0.04 (0.11), residues: 1995 sheet: -1.03 (0.23), residues: 438 loop : -1.93 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 187 HIS 0.007 0.001 HIS D 85 PHE 0.025 0.002 PHE A 281 TYR 0.023 0.002 TYR A 541 ARG 0.008 0.001 ARG A 185 *********************** 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 636 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 585 time to evaluate : 2.994 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: A 76 MET cc_start: 0.7725 (mtp) cc_final: 0.7465 (mtp) REVERT: A 150 THR cc_start: 0.7129 (t) cc_final: 0.6583 (t) REVERT: A 417 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7992 (mm-30) REVERT: A 470 PHE cc_start: 0.8355 (m-80) cc_final: 0.8134 (m-10) REVERT: A 498 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6901 (ptmm) REVERT: A 575 MET cc_start: 0.5829 (mmm) cc_final: 0.5449 (mmm) REVERT: A 774 MET cc_start: 0.8713 (ttt) cc_final: 0.8475 (ttt) REVERT: A 825 MET cc_start: 0.8463 (mmt) cc_final: 0.8205 (mmt) REVERT: A 980 LEU cc_start: 0.7718 (tp) cc_final: 0.7188 (mt) REVERT: B 115 MET cc_start: 0.8851 (mmm) cc_final: 0.8316 (mmt) REVERT: B 356 TYR cc_start: 0.8448 (t80) cc_final: 0.7837 (t80) REVERT: B 414 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6974 (tm-30) REVERT: C 37 THR cc_start: 0.7950 (m) cc_final: 0.7702 (m) REVERT: C 69 MET cc_start: 0.8690 (mmm) cc_final: 0.8250 (mmt) REVERT: C 259 ARG cc_start: 0.6108 (mtp85) cc_final: 0.5840 (mmm-85) REVERT: C 353 LEU cc_start: 0.8405 (mm) cc_final: 0.8000 (tt) REVERT: C 672 VAL cc_start: 0.7513 (t) cc_final: 0.7300 (t) REVERT: D 36 ASN cc_start: 0.6017 (OUTLIER) cc_final: 0.5160 (m-40) REVERT: D 68 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7235 (tppt) REVERT: E 27 ASP cc_start: 0.5987 (m-30) cc_final: 0.5192 (m-30) REVERT: F 13 ILE cc_start: 0.7449 (mm) cc_final: 0.7207 (mm) REVERT: H 14 MET cc_start: 0.7412 (mmm) cc_final: 0.7066 (mmp) outliers start: 51 outliers final: 25 residues processed: 614 average time/residue: 0.6899 time to fit residues: 680.5229 Evaluate side-chains 522 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 496 time to evaluate : 3.040 ------------------------------------------------------------------------------- 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 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 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 1033 PHE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 135 SER 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 583 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 114 ILE 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: 3.9990 chunk 263 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 314 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 254 optimal weight: 3.9990 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 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 176 GLN B 284 GLN B 360 GLN B 737 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 27321 Z= 0.250 Angle : 0.541 8.074 37101 Z= 0.286 Chirality : 0.041 0.152 4379 Planarity : 0.004 0.051 4746 Dihedral : 4.268 38.999 3734 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.29 % Allowed : 10.94 % Favored : 87.77 % 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: 0.75 (0.12), residues: 2000 sheet: -0.85 (0.24), residues: 433 loop : -1.61 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 754 HIS 0.005 0.001 HIS B 526 PHE 0.019 0.001 PHE A 682 TYR 0.017 0.001 TYR C 541 ARG 0.012 0.000 ARG C 263 *********************** 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 534 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 497 time to evaluate : 3.179 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: A 76 MET cc_start: 0.8009 (mtp) cc_final: 0.7670 (mtp) REVERT: A 112 GLN cc_start: 0.7640 (tp40) cc_final: 0.7285 (mm110) REVERT: A 150 THR cc_start: 0.6894 (t) cc_final: 0.6531 (t) REVERT: A 470 PHE cc_start: 0.8543 (m-80) cc_final: 0.8304 (m-10) REVERT: A 498 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7085 (ptmm) REVERT: A 575 MET cc_start: 0.5952 (mmm) cc_final: 0.5750 (mmm) REVERT: A 902 MET cc_start: 0.8615 (mmm) cc_final: 0.8343 (mmm) REVERT: A 980 LEU cc_start: 0.7944 (tp) cc_final: 0.7439 (mt) REVERT: B 356 TYR cc_start: 0.8419 (t80) cc_final: 0.7951 (t80) REVERT: B 417 GLU cc_start: 0.7604 (tp30) cc_final: 0.7182 (tp30) REVERT: B 497 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8416 (mp) REVERT: B 815 ARG cc_start: 0.8129 (ptm-80) cc_final: 0.7806 (ttp-170) REVERT: C 422 GLU cc_start: 0.5692 (mt-10) cc_final: 0.5431 (mt-10) REVERT: C 552 MET cc_start: 0.7384 (ptm) cc_final: 0.7109 (ptm) REVERT: D 36 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.5934 (m-40) REVERT: E 27 ASP cc_start: 0.5944 (m-30) cc_final: 0.5264 (m-30) REVERT: F 13 ILE cc_start: 0.7498 (mm) cc_final: 0.7249 (mm) outliers start: 37 outliers final: 25 residues processed: 517 average time/residue: 0.7251 time to fit residues: 603.4608 Evaluate side-chains 481 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 454 time to evaluate : 3.048 ------------------------------------------------------------------------------- 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 391 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain C residue 83 ASP 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 456 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 112 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: 1.9990 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 298 ASN A 737 GLN A 846 GLN B 194 ASN ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 584 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 27321 Z= 0.297 Angle : 0.603 8.102 37101 Z= 0.320 Chirality : 0.043 0.256 4379 Planarity : 0.005 0.107 4746 Dihedral : 4.305 31.278 3734 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.82 % Allowed : 11.53 % Favored : 86.65 % 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: 0.95 (0.12), residues: 1994 sheet: -0.77 (0.24), residues: 447 loop : -1.48 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 809 HIS 0.006 0.001 HIS B 526 PHE 0.032 0.002 PHE A 513 TYR 0.022 0.002 TYR A 541 ARG 0.006 0.000 ARG A 185 *********************** 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 553 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 501 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.7681 (tp40) cc_final: 0.7381 (mm-40) REVERT: A 468 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7482 (ttp80) REVERT: A 470 PHE cc_start: 0.8705 (m-80) cc_final: 0.8420 (m-80) REVERT: A 498 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7468 (ptmm) REVERT: A 980 LEU cc_start: 0.8383 (tp) cc_final: 0.7883 (mt) REVERT: B 356 TYR cc_start: 0.8515 (t80) cc_final: 0.8160 (t80) REVERT: B 417 GLU cc_start: 0.7753 (tp30) cc_final: 0.7422 (tp30) REVERT: B 497 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 815 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.8000 (ttp-170) REVERT: C 20 MET cc_start: 0.7588 (mtt) cc_final: 0.7363 (mtt) REVERT: C 182 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8761 (m-10) REVERT: C 414 GLU cc_start: 0.7037 (tp30) cc_final: 0.6825 (tm-30) REVERT: C 415 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8278 (t0) REVERT: C 418 ARG cc_start: 0.8049 (tmm160) cc_final: 0.7819 (ttp-170) REVERT: C 422 GLU cc_start: 0.6287 (mt-10) cc_final: 0.6032 (mt-10) REVERT: C 737 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7451 (tm-30) REVERT: D 145 PHE cc_start: 0.7296 (m-80) cc_final: 0.6692 (m-80) REVERT: E 36 ASN cc_start: 0.7928 (t0) cc_final: 0.7577 (t0) outliers start: 52 outliers final: 33 residues processed: 540 average time/residue: 0.7433 time to fit residues: 630.7907 Evaluate side-chains 474 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 438 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 182 TYR 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 82 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 757 SER 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 87 THR Chi-restraints excluded: chain C residue 135 SER 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 456 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 37 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 233 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 302 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN C 415 ASN C 469 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6947 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= 0.172 Angle : 0.508 6.848 37101 Z= 0.265 Chirality : 0.040 0.154 4379 Planarity : 0.004 0.053 4746 Dihedral : 4.058 28.776 3734 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.33 % Allowed : 12.30 % Favored : 86.37 % 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: 0.45 (0.14), residues: 3513 helix: 1.37 (0.12), residues: 1992 sheet: -0.70 (0.24), residues: 444 loop : -1.23 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.004 0.001 HIS B 526 PHE 0.018 0.001 PHE A 682 TYR 0.014 0.001 TYR A 541 ARG 0.008 0.000 ARG C 259 *********************** 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 498 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 460 time to evaluate : 3.016 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 108 GLN cc_start: 0.8265 (tt0) cc_final: 0.8032 (tt0) REVERT: A 112 GLN cc_start: 0.7636 (tp40) cc_final: 0.7319 (mm-40) REVERT: A 124 GLN cc_start: 0.8027 (mt0) cc_final: 0.7742 (mt0) REVERT: A 138 MET cc_start: 0.8810 (ptm) cc_final: 0.8532 (ptm) REVERT: A 342 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7670 (mmtm) REVERT: A 468 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7444 (ttp80) REVERT: A 470 PHE cc_start: 0.8666 (m-80) cc_final: 0.8390 (m-80) REVERT: A 498 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7482 (ptmm) REVERT: A 798 MET cc_start: 0.8296 (mmm) cc_final: 0.7988 (mmt) REVERT: A 980 LEU cc_start: 0.8372 (tp) cc_final: 0.7886 (mt) REVERT: B 356 TYR cc_start: 0.8337 (t80) cc_final: 0.7992 (t80) REVERT: B 417 GLU cc_start: 0.7749 (tp30) cc_final: 0.7422 (tp30) REVERT: B 620 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6788 (ttp-110) REVERT: B 730 ASP cc_start: 0.7893 (m-30) cc_final: 0.7567 (m-30) REVERT: B 815 ARG cc_start: 0.8332 (ptm-80) cc_final: 0.8043 (ttp-170) REVERT: C 20 MET cc_start: 0.7589 (mtt) cc_final: 0.7259 (mtt) REVERT: C 182 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8712 (m-10) REVERT: C 422 GLU cc_start: 0.6210 (mt-10) cc_final: 0.5904 (mt-10) REVERT: C 795 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6288 (p0) REVERT: D 145 PHE cc_start: 0.7318 (m-80) cc_final: 0.6816 (m-80) REVERT: E 36 ASN cc_start: 0.7939 (t0) cc_final: 0.7636 (t0) REVERT: F 31 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7456 (mt-10) outliers start: 38 outliers final: 28 residues processed: 486 average time/residue: 0.7606 time to fit residues: 579.8934 Evaluate side-chains 473 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 443 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 391 ASN 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 B residue 82 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 87 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 140 VAL 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 456 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 795 ASP Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 37 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 0.9980 chunk 303 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 337 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 27321 Z= 0.255 Angle : 0.526 5.862 37101 Z= 0.277 Chirality : 0.041 0.160 4379 Planarity : 0.004 0.056 4746 Dihedral : 4.056 26.647 3734 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.64 % Allowed : 12.44 % Favored : 85.91 % 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: 0.55 (0.14), residues: 3513 helix: 1.42 (0.12), residues: 2000 sheet: -0.63 (0.24), residues: 446 loop : -1.16 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 809 HIS 0.003 0.001 HIS E 52 PHE 0.019 0.001 PHE A 682 TYR 0.015 0.001 TYR C 541 ARG 0.012 0.001 ARG C 263 *********************** 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 499 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 452 time to evaluate : 3.065 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: A 108 GLN cc_start: 0.8325 (tt0) cc_final: 0.8079 (tt0) REVERT: A 112 GLN cc_start: 0.7680 (tp40) cc_final: 0.7365 (mm-40) REVERT: A 124 GLN cc_start: 0.8036 (mt0) cc_final: 0.7782 (mt0) REVERT: A 138 MET cc_start: 0.8896 (ptm) cc_final: 0.8662 (ptm) REVERT: A 468 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7510 (ttp80) REVERT: A 470 PHE cc_start: 0.8700 (m-80) cc_final: 0.8431 (m-10) REVERT: A 498 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7521 (ptmm) REVERT: A 980 LEU cc_start: 0.8468 (tp) cc_final: 0.7953 (mt) REVERT: B 356 TYR cc_start: 0.8428 (t80) cc_final: 0.8091 (t80) REVERT: B 417 GLU cc_start: 0.7837 (tp30) cc_final: 0.7485 (tp30) REVERT: B 620 ARG cc_start: 0.7219 (ttm-80) cc_final: 0.7018 (ttp-110) REVERT: B 730 ASP cc_start: 0.7837 (m-30) cc_final: 0.7599 (m-30) REVERT: B 815 ARG cc_start: 0.8415 (ptm-80) cc_final: 0.8111 (ttp-170) REVERT: C 182 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8759 (m-10) REVERT: C 737 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7223 (mm-40) REVERT: E 36 ASN cc_start: 0.8098 (t0) cc_final: 0.7820 (t0) REVERT: E 81 SER cc_start: 0.8230 (m) cc_final: 0.7672 (p) REVERT: F 31 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7487 (mt-10) outliers start: 47 outliers final: 38 residues processed: 487 average time/residue: 0.7574 time to fit residues: 580.3525 Evaluate side-chains 465 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 426 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASN 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 A residue 686 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 194 ASN 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 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 87 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 135 SER 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 250 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 37 SER 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: 0.0050 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: 4.9990 chunk 336 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN C 415 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27321 Z= 0.199 Angle : 0.500 5.691 37101 Z= 0.260 Chirality : 0.040 0.148 4379 Planarity : 0.004 0.053 4746 Dihedral : 3.922 19.553 3732 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.68 % Allowed : 12.62 % Favored : 85.70 % 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: 0.78 (0.15), residues: 3513 helix: 1.62 (0.12), residues: 1989 sheet: -0.60 (0.24), residues: 439 loop : -1.02 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.003 0.001 HIS E 52 PHE 0.018 0.001 PHE A 682 TYR 0.012 0.001 TYR C 49 ARG 0.011 0.000 ARG C 263 *********************** 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 486 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 438 time to evaluate : 3.076 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: A 108 GLN cc_start: 0.8365 (tt0) cc_final: 0.8104 (tt0) REVERT: A 112 GLN cc_start: 0.7648 (tp40) cc_final: 0.7351 (mm-40) REVERT: A 124 GLN cc_start: 0.7941 (mt0) cc_final: 0.7704 (mt0) REVERT: A 138 MET cc_start: 0.8919 (ptm) cc_final: 0.8698 (ptm) REVERT: A 414 GLU cc_start: 0.7589 (tp30) cc_final: 0.7354 (tp30) REVERT: A 468 ARG cc_start: 0.7796 (ttm110) cc_final: 0.7467 (ttp80) REVERT: A 470 PHE cc_start: 0.8668 (m-80) cc_final: 0.8392 (m-10) REVERT: A 498 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7543 (ptmm) REVERT: A 980 LEU cc_start: 0.8514 (tp) cc_final: 0.8014 (mt) REVERT: B 248 LYS cc_start: 0.8531 (mttp) cc_final: 0.8127 (mtpp) REVERT: B 280 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: B 356 TYR cc_start: 0.8229 (t80) cc_final: 0.7925 (t80) REVERT: B 417 GLU cc_start: 0.7781 (tp30) cc_final: 0.7506 (tp30) REVERT: B 554 TYR cc_start: 0.8212 (t80) cc_final: 0.7616 (t80) REVERT: B 558 ARG cc_start: 0.7535 (mtp-110) cc_final: 0.7333 (ttm170) REVERT: B 730 ASP cc_start: 0.7758 (m-30) cc_final: 0.7493 (m-30) REVERT: B 815 ARG cc_start: 0.8408 (ptm-80) cc_final: 0.8032 (ttt180) REVERT: C 20 MET cc_start: 0.7927 (mtt) cc_final: 0.7689 (mtt) REVERT: C 120 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7121 (tp40) REVERT: C 422 GLU cc_start: 0.6428 (mt-10) cc_final: 0.6136 (mt-10) REVERT: C 737 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7275 (mm-40) REVERT: E 36 ASN cc_start: 0.8074 (t0) cc_final: 0.7790 (t0) REVERT: E 81 SER cc_start: 0.8284 (m) cc_final: 0.7608 (p) outliers start: 48 outliers final: 35 residues processed: 470 average time/residue: 0.7760 time to fit residues: 567.0384 Evaluate side-chains 453 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 416 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 280 GLU 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 813 SER 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 87 THR Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 135 SER 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 562 SER Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 ASN 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: 0.8980 chunk 200 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 229 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 ASN C 81 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27321 Z= 0.144 Angle : 0.476 5.850 37101 Z= 0.246 Chirality : 0.039 0.150 4379 Planarity : 0.004 0.060 4746 Dihedral : 3.767 19.193 3732 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.26 % Allowed : 13.53 % Favored : 85.21 % 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: 1.09 (0.15), residues: 3513 helix: 1.83 (0.12), residues: 1994 sheet: -0.48 (0.24), residues: 445 loop : -0.83 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 789 HIS 0.002 0.000 HIS E 52 PHE 0.017 0.001 PHE A 682 TYR 0.012 0.001 TYR B 182 ARG 0.011 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 477 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 441 time to evaluate : 3.055 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 108 GLN cc_start: 0.8338 (tt0) cc_final: 0.8077 (tt0) REVERT: A 112 GLN cc_start: 0.7671 (tp40) cc_final: 0.7368 (mm-40) REVERT: A 124 GLN cc_start: 0.7943 (mt0) cc_final: 0.7723 (mt0) REVERT: A 138 MET cc_start: 0.8911 (ptm) cc_final: 0.8690 (ptm) REVERT: A 414 GLU cc_start: 0.7559 (tp30) cc_final: 0.7358 (tp30) REVERT: A 468 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7491 (ttp80) REVERT: A 470 PHE cc_start: 0.8618 (m-80) cc_final: 0.8352 (m-10) REVERT: A 498 LYS cc_start: 0.7820 (mtpt) cc_final: 0.7547 (ptmm) REVERT: A 980 LEU cc_start: 0.8496 (tp) cc_final: 0.8009 (mt) REVERT: B 248 LYS cc_start: 0.8481 (mttp) cc_final: 0.8126 (mtpp) REVERT: B 356 TYR cc_start: 0.8211 (t80) cc_final: 0.7828 (t80) REVERT: B 417 GLU cc_start: 0.7809 (tp30) cc_final: 0.7531 (tp30) REVERT: B 447 MET cc_start: 0.7980 (mmp) cc_final: 0.7728 (mmp) REVERT: B 467 TYR cc_start: 0.8709 (m-80) cc_final: 0.8432 (m-80) REVERT: B 730 ASP cc_start: 0.7707 (m-30) cc_final: 0.7422 (m-30) REVERT: B 791 VAL cc_start: 0.9055 (m) cc_final: 0.8780 (t) REVERT: B 815 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.8146 (ttt180) REVERT: C 20 MET cc_start: 0.7896 (mtt) cc_final: 0.7664 (mtt) REVERT: C 120 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7105 (tp40) REVERT: C 681 ASP cc_start: 0.7608 (t0) cc_final: 0.7393 (t0) REVERT: C 737 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7298 (mm-40) REVERT: E 81 SER cc_start: 0.8284 (m) cc_final: 0.7610 (p) outliers start: 36 outliers final: 27 residues processed: 465 average time/residue: 0.7785 time to fit residues: 565.4879 Evaluate side-chains 457 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 429 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 575 MET 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 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 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 924 ASP Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain F residue 26 ILE 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: 2.9990 chunk 313 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 296 optimal weight: 0.0020 chunk 312 optimal weight: 9.9990 overall best weight: 1.6132 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 760 ASN ** 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: 0.8129 moved from start: 0.8170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27321 Z= 0.213 Angle : 0.502 6.715 37101 Z= 0.261 Chirality : 0.040 0.179 4379 Planarity : 0.004 0.053 4746 Dihedral : 3.812 19.077 3732 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.40 % Allowed : 13.46 % Favored : 85.15 % 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: 1.16 (0.15), residues: 3513 helix: 1.89 (0.12), residues: 1995 sheet: -0.43 (0.24), residues: 450 loop : -0.81 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.002 0.001 HIS A 596 PHE 0.017 0.001 PHE A 682 TYR 0.014 0.001 TYR C 157 ARG 0.009 0.000 ARG C 263 *********************** 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 471 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 431 time to evaluate : 3.091 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: A 108 GLN cc_start: 0.8418 (tt0) cc_final: 0.8141 (tt0) REVERT: A 112 GLN cc_start: 0.7737 (tp40) cc_final: 0.7433 (mm-40) REVERT: A 124 GLN cc_start: 0.7905 (mt0) cc_final: 0.7702 (mt0) REVERT: A 138 MET cc_start: 0.8959 (ptm) cc_final: 0.8738 (ptm) REVERT: A 468 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7491 (ttp80) REVERT: A 470 PHE cc_start: 0.8648 (m-80) cc_final: 0.8378 (m-10) REVERT: A 498 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7577 (ptmm) REVERT: A 850 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8205 (mmmm) REVERT: A 980 LEU cc_start: 0.8603 (tp) cc_final: 0.8034 (mt) REVERT: B 248 LYS cc_start: 0.8571 (mttp) cc_final: 0.8223 (mtpp) REVERT: B 356 TYR cc_start: 0.8246 (t80) cc_final: 0.7947 (t80) REVERT: B 417 GLU cc_start: 0.7805 (tp30) cc_final: 0.7441 (tp30) REVERT: B 447 MET cc_start: 0.7954 (mmp) cc_final: 0.7716 (mmp) REVERT: B 554 TYR cc_start: 0.8321 (t80) cc_final: 0.7994 (t80) REVERT: B 657 GLN cc_start: 0.7701 (pp30) cc_final: 0.7470 (pp30) REVERT: B 730 ASP cc_start: 0.7874 (m-30) cc_final: 0.7618 (m-30) REVERT: B 815 ARG cc_start: 0.8435 (ptm-80) cc_final: 0.8093 (ttt180) REVERT: C 20 MET cc_start: 0.8017 (mtt) cc_final: 0.7778 (mtt) REVERT: C 32 VAL cc_start: 0.8494 (m) cc_final: 0.8201 (t) REVERT: C 120 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7008 (tp40) REVERT: C 182 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8782 (m-10) REVERT: C 737 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7432 (mm-40) REVERT: C 781 MET cc_start: 0.8823 (mmp) cc_final: 0.7997 (mmp) REVERT: E 81 SER cc_start: 0.8344 (m) cc_final: 0.7562 (p) outliers start: 40 outliers final: 25 residues processed: 462 average time/residue: 0.8005 time to fit residues: 576.1006 Evaluate side-chains 445 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 418 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 353 LEU 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 78 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 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 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 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 205 optimal weight: 5.9990 chunk 331 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 347 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 760 ASN ** 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: 0.8126 moved from start: 0.8353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27321 Z= 0.176 Angle : 0.486 6.581 37101 Z= 0.252 Chirality : 0.040 0.228 4379 Planarity : 0.004 0.050 4746 Dihedral : 3.770 19.224 3732 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.05 % Allowed : 14.02 % Favored : 84.94 % 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 (0.15), residues: 3513 helix: 1.97 (0.12), residues: 1988 sheet: -0.39 (0.24), residues: 443 loop : -0.71 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.003 0.000 HIS E 52 PHE 0.017 0.001 PHE A 682 TYR 0.010 0.001 TYR A 554 ARG 0.009 0.000 ARG C 263 ********************** 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 458 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 428 time to evaluate : 2.999 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 108 GLN cc_start: 0.8347 (tt0) cc_final: 0.8079 (tt0) REVERT: A 112 GLN cc_start: 0.7702 (tp40) cc_final: 0.7403 (mm-40) REVERT: A 468 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7516 (ttp80) REVERT: A 470 PHE cc_start: 0.8606 (m-80) cc_final: 0.8335 (m-10) REVERT: A 498 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7592 (ptmm) REVERT: A 673 GLU cc_start: 0.6467 (mp0) cc_final: 0.6194 (mp0) REVERT: A 850 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8213 (mmmm) REVERT: A 980 LEU cc_start: 0.8564 (tp) cc_final: 0.8053 (mt) REVERT: B 248 LYS cc_start: 0.8566 (mttp) cc_final: 0.8266 (mtpp) REVERT: B 356 TYR cc_start: 0.8207 (t80) cc_final: 0.7857 (t80) REVERT: B 417 GLU cc_start: 0.7819 (tp30) cc_final: 0.7440 (tp30) REVERT: B 447 MET cc_start: 0.7925 (mmp) cc_final: 0.7711 (mmp) REVERT: B 554 TYR cc_start: 0.8310 (t80) cc_final: 0.7461 (t80) REVERT: B 558 ARG cc_start: 0.7490 (mtp-110) cc_final: 0.7265 (ttm170) REVERT: B 730 ASP cc_start: 0.7845 (m-30) cc_final: 0.7581 (m-30) REVERT: B 815 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8054 (ttt180) REVERT: C 20 MET cc_start: 0.8012 (mtt) cc_final: 0.7773 (mtt) REVERT: C 120 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7131 (tp40) REVERT: C 737 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7457 (mm-40) REVERT: C 781 MET cc_start: 0.8813 (mmp) cc_final: 0.8008 (mmp) REVERT: E 81 SER cc_start: 0.8374 (m) cc_final: 0.7634 (p) outliers start: 30 outliers final: 25 residues processed: 450 average time/residue: 0.8306 time to fit residues: 579.4831 Evaluate side-chains 446 residues out of total 2859 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 420 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 561 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 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 624 THR Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 74 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: 4.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 277 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 284 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.103833 restraints weight = 108211.665| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.61 r_work: 0.2909 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.8598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27321 Z= 0.236 Angle : 0.515 8.862 37101 Z= 0.269 Chirality : 0.040 0.208 4379 Planarity : 0.004 0.061 4746 Dihedral : 3.858 18.916 3732 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.29 % Allowed : 13.74 % Favored : 84.97 % 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: 1.23 (0.15), residues: 3513 helix: 1.91 (0.12), residues: 1988 sheet: -0.33 (0.24), residues: 448 loop : -0.72 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.003 0.001 HIS A 596 PHE 0.017 0.001 PHE A 682 TYR 0.015 0.001 TYR C 157 ARG 0.010 0.001 ARG B 620 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11829.46 seconds wall clock time: 204 minutes 39.42 seconds (12279.42 seconds total)