Starting phenix.real_space_refine (version: dev) on Fri Feb 24 14:24:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b8p_12088/02_2023/7b8p_12088.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 678": "OD1" <-> "OD2" Residue "A TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ASP 189": "OD1" <-> "OD2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 678": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 723": "OD1" <-> "OD2" Residue "B PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "B TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 952": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 582": "OE1" <-> "OE2" Residue "C ASP 597": "OD1" <-> "OD2" Residue "C ASP 600": "OD1" <-> "OD2" Residue "C PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 678": "OD1" <-> "OD2" Residue "C TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 723": "OD1" <-> "OD2" Residue "C PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 836": "OE1" <-> "OE2" Residue "C TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 857": "OE1" <-> "OE2" Residue "C PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C GLU 952": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23202 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "B" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Time building chain proxies: 13.38, per 1000 atoms: 0.58 Number of scatterers: 23202 At special positions: 0 Unit cell: (119.7, 112.35, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4293 8.00 N 3774 7.00 C 15000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 10.07 Conformation dependent library (CDL) restraints added in 3.4 seconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 59.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.951A pdb=" N ARG A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.611A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 370 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.777A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.574A 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 512 through 534 removed outlier: 3.768A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.596A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU A 867 " --> pdb=" O GLN A 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 868 " --> pdb=" O MET A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.612A 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 70 removed outlier: 3.855A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.514A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 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 360 Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.327A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.777A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.574A 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 512 through 534 removed outlier: 3.767A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 841 Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1022 removed outlier: 4.122A pdb=" N VAL B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.612A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) 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 168 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 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.775A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 496 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.574A 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 512 through 534 removed outlier: 3.767A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP C 642 " --> pdb=" O LYS C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU C 867 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 4.611A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL C1014 " --> pdb=" O PHE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.832A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 605 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 572 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 8.353A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 8.349A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1563 hydrogen bonds defined for protein. 4545 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: 9.98 Time building geometry restraints manager: 10.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7320 1.34 - 1.46: 4193 1.46 - 1.58: 11836 1.58 - 1.70: 6 1.70 - 1.81: 264 Bond restraints: 23619 Sorted by residual: bond pdb=" CA LEU B 198 " pdb=" C LEU B 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.43e+01 bond pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 1.526 1.591 -0.066 1.36e-02 5.41e+03 2.34e+01 bond pdb=" CA VAL C 259 " pdb=" CB VAL C 259 " ideal model delta sigma weight residual 1.533 1.482 0.052 1.13e-02 7.83e+03 2.09e+01 bond pdb=" CA VAL A 259 " pdb=" CB VAL A 259 " ideal model delta sigma weight residual 1.533 1.482 0.051 1.13e-02 7.83e+03 2.07e+01 ... (remaining 23614 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.47: 514 104.47 - 111.87: 11710 111.87 - 119.27: 7886 119.27 - 126.67: 11668 126.67 - 134.08: 259 Bond angle restraints: 32037 Sorted by residual: angle pdb=" N LYS A 226 " pdb=" CA LYS A 226 " pdb=" C LYS A 226 " ideal model delta sigma weight residual 110.35 98.53 11.82 1.40e+00 5.10e-01 7.13e+01 angle pdb=" N LYS B 226 " pdb=" CA LYS B 226 " pdb=" C LYS B 226 " ideal model delta sigma weight residual 110.35 98.58 11.77 1.40e+00 5.10e-01 7.07e+01 angle pdb=" N LYS C 226 " pdb=" CA LYS C 226 " pdb=" C LYS C 226 " ideal model delta sigma weight residual 110.35 98.61 11.74 1.40e+00 5.10e-01 7.04e+01 angle pdb=" N LYS B 254 " pdb=" CA LYS B 254 " pdb=" C LYS B 254 " ideal model delta sigma weight residual 110.80 127.46 -16.66 2.13e+00 2.20e-01 6.12e+01 angle pdb=" N LYS C 254 " pdb=" CA LYS C 254 " pdb=" C LYS C 254 " ideal model delta sigma weight residual 110.80 127.45 -16.65 2.13e+00 2.20e-01 6.11e+01 ... (remaining 32032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 12519 15.70 - 31.41: 1336 31.41 - 47.11: 353 47.11 - 62.81: 93 62.81 - 78.52: 24 Dihedral angle restraints: 14325 sinusoidal: 5553 harmonic: 8772 Sorted by residual: dihedral pdb=" CA TYR B 49 " pdb=" C TYR B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR C 49 " pdb=" C TYR C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 49 " pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 14322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3287 0.071 - 0.142: 457 0.142 - 0.212: 96 0.212 - 0.283: 9 0.283 - 0.354: 3 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL B 707 " pdb=" N VAL B 707 " pdb=" C VAL B 707 " pdb=" CB VAL B 707 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL C 707 " pdb=" N VAL C 707 " pdb=" C VAL C 707 " pdb=" CB VAL C 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL A 707 " pdb=" N VAL A 707 " pdb=" C VAL A 707 " pdb=" CB VAL A 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3849 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 35 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 36 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " 0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 35 " 0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.049 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 10123 2.92 - 3.41: 24347 3.41 - 3.91: 38792 3.91 - 4.40: 45193 4.40 - 4.90: 75260 Nonbonded interactions: 193715 Sorted by model distance: nonbonded pdb=" O GLU A 225 " pdb=" C LYS A 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU B 225 " pdb=" C LYS B 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU C 225 " pdb=" C LYS C 226 " model vdw 2.425 3.270 nonbonded pdb=" NZ LYS C 931 " pdb=" OD1 ASN C 932 " model vdw 2.466 2.520 nonbonded pdb=" NZ LYS B 931 " pdb=" OD1 ASN B 932 " model vdw 2.466 2.520 ... (remaining 193710 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15000 2.51 5 N 3774 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.850 Check model and map are aligned: 0.110 Process input model: 62.970 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.210 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.168 23619 Z= 0.371 Angle : 0.972 16.664 32037 Z= 0.648 Chirality : 0.053 0.354 3852 Planarity : 0.006 0.091 4032 Dihedral : 14.537 78.516 8649 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 3033 helix: -1.03 (0.11), residues: 1701 sheet: -2.78 (0.20), residues: 516 loop : -2.59 (0.19), residues: 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 559 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 570 average time/residue: 0.3553 time to fit residues: 313.9182 Evaluate side-chains 357 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 2.535 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5749 time to fit residues: 4.2126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 574 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 415 ASN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN C 239 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 574 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 23619 Z= 0.254 Angle : 0.591 8.406 32037 Z= 0.304 Chirality : 0.042 0.225 3852 Planarity : 0.004 0.057 4032 Dihedral : 4.013 19.781 3183 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3033 helix: 0.54 (0.12), residues: 1710 sheet: -2.71 (0.21), residues: 486 loop : -1.58 (0.22), residues: 837 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 376 time to evaluate : 2.557 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 39 residues processed: 429 average time/residue: 0.3073 time to fit residues: 217.6724 Evaluate side-chains 364 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 325 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2119 time to fit residues: 19.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 273 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 574 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 23619 Z= 0.195 Angle : 0.537 7.535 32037 Z= 0.274 Chirality : 0.040 0.146 3852 Planarity : 0.004 0.055 4032 Dihedral : 3.846 16.800 3183 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.10 (0.16), residues: 3033 helix: 1.14 (0.13), residues: 1716 sheet: -1.97 (0.23), residues: 468 loop : -1.28 (0.22), residues: 849 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 2.664 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 397 average time/residue: 0.3124 time to fit residues: 204.4719 Evaluate side-chains 347 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 326 time to evaluate : 2.978 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2398 time to fit residues: 13.4501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 143 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 185 optimal weight: 0.3980 chunk 276 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23619 Z= 0.166 Angle : 0.517 8.279 32037 Z= 0.262 Chirality : 0.040 0.167 3852 Planarity : 0.004 0.054 4032 Dihedral : 3.768 16.441 3183 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.35 (0.16), residues: 3033 helix: 1.48 (0.13), residues: 1707 sheet: -1.73 (0.22), residues: 483 loop : -1.02 (0.23), residues: 843 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 372 time to evaluate : 3.435 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 395 average time/residue: 0.3459 time to fit residues: 221.1432 Evaluate side-chains 347 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 335 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2124 time to fit residues: 8.7754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 0.0370 chunk 120 optimal weight: 0.0050 chunk 249 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 262 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 273 GLN ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 23619 Z= 0.157 Angle : 0.514 9.165 32037 Z= 0.260 Chirality : 0.040 0.187 3852 Planarity : 0.004 0.052 4032 Dihedral : 3.714 17.426 3183 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.63 (0.16), residues: 3033 helix: 1.66 (0.13), residues: 1704 sheet: -1.44 (0.22), residues: 513 loop : -0.87 (0.24), residues: 816 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 360 time to evaluate : 2.753 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 378 average time/residue: 0.3178 time to fit residues: 197.1334 Evaluate side-chains 342 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 2.739 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2154 time to fit residues: 10.8999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 171 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23619 Z= 0.172 Angle : 0.519 8.907 32037 Z= 0.262 Chirality : 0.040 0.186 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.703 16.269 3183 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.83 (0.16), residues: 3033 helix: 1.80 (0.13), residues: 1698 sheet: -1.34 (0.22), residues: 513 loop : -0.69 (0.24), residues: 822 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 346 time to evaluate : 2.813 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 356 average time/residue: 0.3264 time to fit residues: 189.0088 Evaluate side-chains 322 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 315 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2190 time to fit residues: 6.6218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 246 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 292 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 23619 Z= 0.200 Angle : 0.532 9.353 32037 Z= 0.266 Chirality : 0.041 0.185 3852 Planarity : 0.004 0.050 4032 Dihedral : 3.725 16.585 3183 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.91 (0.16), residues: 3033 helix: 1.84 (0.13), residues: 1695 sheet: -1.35 (0.22), residues: 534 loop : -0.54 (0.25), residues: 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 334 time to evaluate : 2.881 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 353 average time/residue: 0.3252 time to fit residues: 188.0109 Evaluate side-chains 332 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 313 time to evaluate : 2.698 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2076 time to fit residues: 11.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 0.7980 chunk 116 optimal weight: 0.0060 chunk 174 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 23619 Z= 0.165 Angle : 0.531 9.968 32037 Z= 0.265 Chirality : 0.040 0.241 3852 Planarity : 0.004 0.050 4032 Dihedral : 3.705 18.331 3183 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.03 (0.16), residues: 3033 helix: 1.92 (0.13), residues: 1695 sheet: -1.27 (0.22), residues: 534 loop : -0.46 (0.25), residues: 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 336 time to evaluate : 2.826 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 342 average time/residue: 0.3340 time to fit residues: 186.3449 Evaluate side-chains 318 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 315 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2154 time to fit residues: 4.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 0.0970 chunk 279 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 163 optimal weight: 0.0770 chunk 118 optimal weight: 0.0570 chunk 213 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 245 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 273 GLN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 23619 Z= 0.147 Angle : 0.531 10.481 32037 Z= 0.265 Chirality : 0.040 0.178 3852 Planarity : 0.004 0.050 4032 Dihedral : 3.665 21.073 3183 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.17 (0.16), residues: 3033 helix: 1.97 (0.13), residues: 1698 sheet: -1.05 (0.22), residues: 510 loop : -0.43 (0.24), residues: 825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 357 time to evaluate : 2.706 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 360 average time/residue: 0.3226 time to fit residues: 188.5715 Evaluate side-chains 337 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 2.919 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2285 time to fit residues: 6.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 301 optimal weight: 0.0370 chunk 277 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 23619 Z= 0.176 Angle : 0.556 10.263 32037 Z= 0.274 Chirality : 0.041 0.173 3852 Planarity : 0.004 0.049 4032 Dihedral : 3.704 22.040 3183 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.17 (0.16), residues: 3033 helix: 1.97 (0.13), residues: 1695 sheet: -1.08 (0.22), residues: 531 loop : -0.36 (0.25), residues: 807 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 332 time to evaluate : 2.838 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 337 average time/residue: 0.3316 time to fit residues: 181.9582 Evaluate side-chains 326 residues out of total 2550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2142 time to fit residues: 5.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 240 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 247 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106362 restraints weight = 32510.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108944 restraints weight = 19524.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110691 restraints weight = 13764.304| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 23619 Z= 0.175 Angle : 0.549 10.003 32037 Z= 0.272 Chirality : 0.041 0.196 3852 Planarity : 0.004 0.049 4032 Dihedral : 3.685 22.352 3183 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.16), residues: 3033 helix: 2.03 (0.13), residues: 1686 sheet: -1.02 (0.22), residues: 531 loop : -0.35 (0.24), residues: 816 =============================================================================== Job complete usr+sys time: 4349.48 seconds wall clock time: 80 minutes 8.83 seconds (4808.83 seconds total)