Starting phenix.real_space_refine on Fri Jan 17 01:24:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsu_44872/01_2025/9bsu_44872.cif" } resolution = 3.36 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= 0.015 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6482 2.51 5 N 1732 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10225 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2751 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Chain breaks: 2 Chain: "B" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2661 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain breaks: 3 Chain: "C" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2765 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 19, 'TRANS': 333} Chain breaks: 2 Chain: "E" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 927 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.51, per 1000 atoms: 0.64 Number of scatterers: 10225 At special positions: 0 Unit cell: (107.8, 116.6, 178.2, 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 43 16.00 O 1968 8.00 N 1732 7.00 C 6482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 556 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 609 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 609 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 511 " - pdb=" SG CYS C 556 " distance=2.03 Simple disulfide: pdb=" SG CYS C 601 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 6 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " BETA1-3 " BMA L 3 " - " BMA L 4 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG K 1 " - " ASN A 563 " " NAG L 1 " - " ASN B 563 " " NAG Y 1 " - " ASN C 563 " Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 22 sheets defined 17.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 removed outlier: 3.555A pdb=" N GLY A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.571A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 576 removed outlier: 3.535A pdb=" N ASN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 597 removed outlier: 3.513A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 removed outlier: 4.182A pdb=" N LYS B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.560A pdb=" N LEU B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 removed outlier: 4.424A pdb=" N ALA B 507 " --> pdb=" O ILE B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.646A pdb=" N TRP B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 565 removed outlier: 3.821A pdb=" N GLN B 560 " --> pdb=" O CYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 3.794A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 removed outlier: 3.680A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.676A pdb=" N GLY C 72 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 552 through 576 removed outlier: 3.742A pdb=" N THR C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLN C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA C 568 " --> pdb=" O GLU C 564 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 571 " --> pdb=" O GLN C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 597 removed outlier: 3.535A pdb=" N TRP C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.625A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.625A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 177 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 96 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.530A pdb=" N TRP A 518 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.496A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.496A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 45 Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.618A pdb=" N ALA B 177 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.381A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 15.960A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 236 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 516 through 519 Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.452A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'C' and resid 177 through 179 removed outlier: 7.141A pdb=" N VAL C 96 " --> pdb=" O THR C 581 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.450A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 14.431A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 518 through 520 Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.395A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER E 121 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 12 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.395A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER E 121 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 12 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E 99 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.521A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR D 32 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR D 52 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.521A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 99 " --> pdb=" O ALA D 33 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 837 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: 3.27 Time building geometry restraints manager: 3.07 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: 3302 1.34 - 1.46: 2502 1.46 - 1.58: 4608 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 10464 Sorted by residual: bond pdb=" N ILE A 544 " pdb=" CA ILE A 544 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.15e-02 7.56e+03 9.03e+00 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.58e+00 bond pdb=" N ILE A 260 " pdb=" CA ILE A 260 " ideal model delta sigma weight residual 1.460 1.494 -0.033 1.19e-02 7.06e+03 7.91e+00 bond pdb=" N ILE C 544 " pdb=" CA ILE C 544 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.12e+00 bond pdb=" N ILE A 281 " pdb=" CA ILE A 281 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.93e+00 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 13923 2.50 - 4.99: 270 4.99 - 7.49: 23 7.49 - 9.98: 2 9.98 - 12.48: 2 Bond angle restraints: 14220 Sorted by residual: angle pdb=" N PRO A 279 " pdb=" CA PRO A 279 " pdb=" C PRO A 279 " ideal model delta sigma weight residual 113.53 107.48 6.05 1.39e+00 5.18e-01 1.90e+01 angle pdb=" N PRO E 105 " pdb=" CA PRO E 105 " pdb=" C PRO E 105 " ideal model delta sigma weight residual 110.70 115.63 -4.93 1.22e+00 6.72e-01 1.63e+01 angle pdb=" CA ILE A 544 " pdb=" C ILE A 544 " pdb=" O ILE A 544 " ideal model delta sigma weight residual 121.75 117.32 4.43 1.18e+00 7.18e-01 1.41e+01 angle pdb=" N PRO D 105 " pdb=" CA PRO D 105 " pdb=" C PRO D 105 " ideal model delta sigma weight residual 110.70 115.16 -4.46 1.22e+00 6.72e-01 1.34e+01 angle pdb=" CA LEU B 51 " pdb=" CB LEU B 51 " pdb=" CG LEU B 51 " ideal model delta sigma weight residual 116.30 128.78 -12.48 3.50e+00 8.16e-02 1.27e+01 ... (remaining 14215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 5975 24.23 - 48.46: 314 48.46 - 72.70: 51 72.70 - 96.93: 31 96.93 - 121.16: 27 Dihedral angle restraints: 6398 sinusoidal: 2725 harmonic: 3673 Sorted by residual: dihedral pdb=" CB CYS A 601 " pdb=" SG CYS A 601 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 3.74 89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS C 601 " pdb=" SG CYS C 601 " pdb=" SG CYS C 608 " pdb=" CB CYS C 608 " ideal model delta sinusoidal sigma weight residual -86.00 -1.51 -84.49 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS C 53 " pdb=" SG CYS C 53 " pdb=" SG CYS C 609 " pdb=" CB CYS C 609 " ideal model delta sinusoidal sigma weight residual 93.00 148.13 -55.13 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 6395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1565 0.118 - 0.236: 33 0.236 - 0.355: 7 0.355 - 0.473: 0 0.473 - 0.591: 3 Chirality restraints: 1608 Sorted by residual: chirality pdb=" C1 BMA L 4 " pdb=" O3 BMA L 3 " pdb=" C2 BMA L 4 " pdb=" O5 BMA L 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-02 2.50e+03 8.73e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.63e+02 chirality pdb=" C1 MAN K 4 " pdb=" O3 BMA K 3 " pdb=" C2 MAN K 4 " pdb=" O5 MAN K 4 " both_signs ideal model delta sigma weight residual False 2.40 2.22 0.18 2.00e-02 2.50e+03 8.04e+01 ... (remaining 1605 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.070 2.00e-02 2.50e+03 5.78e-02 4.17e+01 pdb=" C7 NAG Y 2 " 0.018 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.052 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.093 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.056 2.00e-02 2.50e+03 4.63e-02 2.68e+01 pdb=" C7 NAG L 1 " -0.009 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " -0.043 2.00e-02 2.50e+03 3.53e-02 1.55e+01 pdb=" C7 NAG Y 1 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " 0.053 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.007 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 145 2.65 - 3.22: 9078 3.22 - 3.78: 14345 3.78 - 4.34: 19858 4.34 - 4.90: 33561 Nonbonded interactions: 76987 Sorted by model distance: nonbonded pdb=" O LYS C 276 " pdb=" OH TYR D 109 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU D 108 " pdb=" OH TYR D 111 " model vdw 2.175 3.040 nonbonded pdb=" OD1 ASP C 163 " pdb=" OH TYR C 543 " model vdw 2.181 3.040 nonbonded pdb=" O LYS A 276 " pdb=" OH TYR E 109 " model vdw 2.217 3.040 nonbonded pdb=" N GLU D 89 " pdb=" OE1 GLU D 89 " model vdw 2.243 3.120 ... (remaining 76982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 261 or resid 271 through 280 or resid 503 throu \ gh 613)) selection = chain 'B' selection = (chain 'C' and (resid 32 through 261 or resid 271 through 280 or resid 503 throu \ gh 613)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'K' and (resid 1 through 3 or resid 5)) selection = (chain 'L' and (resid 1 through 3 or resid 5)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.380 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 0.042 10464 Z= 0.253 Angle : 0.781 12.481 14220 Z= 0.408 Chirality : 0.056 0.591 1608 Planarity : 0.005 0.058 1821 Dihedral : 17.458 121.159 4012 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.02 % Favored : 93.75 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.21), residues: 1263 helix: -1.61 (0.32), residues: 185 sheet: -0.49 (0.28), residues: 299 loop : -1.31 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 275 HIS 0.004 0.001 HIS B 516 PHE 0.029 0.001 PHE D 68 TYR 0.016 0.001 TYR A 162 ARG 0.007 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 6 GLU cc_start: 0.7304 (pm20) cc_final: 0.7060 (pm20) REVERT: D 83 MET cc_start: 0.6033 (ppp) cc_final: 0.5778 (ppp) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.2685 time to fit residues: 42.0458 Evaluate side-chains 83 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 115 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.133666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.082350 restraints weight = 17847.168| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.83 r_work: 0.2878 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10464 Z= 0.225 Angle : 0.688 10.671 14220 Z= 0.345 Chirality : 0.047 0.279 1608 Planarity : 0.005 0.053 1821 Dihedral : 14.013 111.872 1715 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.65 % Allowed : 6.07 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.22), residues: 1263 helix: 0.35 (0.39), residues: 179 sheet: -0.37 (0.29), residues: 312 loop : -1.21 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 275 HIS 0.003 0.001 HIS B 549 PHE 0.018 0.001 PHE B 234 TYR 0.027 0.002 TYR C 162 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8081 (m) cc_final: 0.7692 (p) REVERT: B 225 PHE cc_start: 0.8789 (t80) cc_final: 0.8520 (t80) REVERT: B 595 GLN cc_start: 0.7755 (tt0) cc_final: 0.7290 (tm-30) REVERT: C 193 PHE cc_start: 0.8109 (m-80) cc_final: 0.7854 (m-80) REVERT: D 79 MET cc_start: 0.8518 (tmm) cc_final: 0.8080 (tmm) REVERT: D 83 MET cc_start: 0.7525 (ppp) cc_final: 0.6935 (ppp) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2466 time to fit residues: 32.8609 Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 184 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081428 restraints weight = 18741.349| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.84 r_work: 0.2890 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10464 Z= 0.310 Angle : 0.670 9.881 14220 Z= 0.338 Chirality : 0.047 0.291 1608 Planarity : 0.005 0.061 1821 Dihedral : 11.099 103.582 1715 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 1.21 % Allowed : 8.88 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.23), residues: 1263 helix: 0.83 (0.42), residues: 180 sheet: -0.44 (0.28), residues: 330 loop : -1.14 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 275 HIS 0.005 0.001 HIS B 139 PHE 0.019 0.002 PHE B 234 TYR 0.025 0.002 TYR C 162 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7733 (p) REVERT: B 595 GLN cc_start: 0.8053 (tt0) cc_final: 0.7551 (tm-30) REVERT: C 193 PHE cc_start: 0.8278 (m-80) cc_final: 0.8016 (m-80) REVERT: D 79 MET cc_start: 0.8497 (tmm) cc_final: 0.7916 (tmm) REVERT: D 83 MET cc_start: 0.7254 (ppp) cc_final: 0.6934 (ppp) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.2628 time to fit residues: 32.8799 Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 84 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082480 restraints weight = 18393.854| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.82 r_work: 0.2910 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10464 Z= 0.218 Angle : 0.632 10.827 14220 Z= 0.317 Chirality : 0.045 0.303 1608 Planarity : 0.005 0.066 1821 Dihedral : 9.850 94.589 1715 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 1.21 % Allowed : 10.56 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.23), residues: 1263 helix: 1.00 (0.42), residues: 180 sheet: -0.33 (0.28), residues: 329 loop : -1.09 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 597 HIS 0.003 0.001 HIS B 549 PHE 0.027 0.001 PHE B 225 TYR 0.025 0.001 TYR C 162 ARG 0.004 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8155 (m) cc_final: 0.7776 (p) REVERT: B 595 GLN cc_start: 0.8012 (tt0) cc_final: 0.7509 (tm-30) REVERT: C 193 PHE cc_start: 0.8285 (m-80) cc_final: 0.8015 (m-80) REVERT: E 83 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8023 (ppp) REVERT: E 110 ASP cc_start: 0.8640 (t0) cc_final: 0.8407 (t0) REVERT: D 38 ARG cc_start: 0.7627 (ttp-170) cc_final: 0.7407 (ttp-170) REVERT: D 39 GLN cc_start: 0.8296 (tt0) cc_final: 0.7751 (tt0) REVERT: D 79 MET cc_start: 0.8315 (tmm) cc_final: 0.7775 (tmm) REVERT: D 83 MET cc_start: 0.7149 (ppp) cc_final: 0.6865 (ppp) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.2372 time to fit residues: 31.0384 Evaluate side-chains 86 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.133664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082383 restraints weight = 18536.990| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.83 r_work: 0.2909 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10464 Z= 0.216 Angle : 0.627 12.008 14220 Z= 0.313 Chirality : 0.044 0.299 1608 Planarity : 0.005 0.070 1821 Dihedral : 8.688 70.723 1715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.31 % Allowed : 12.15 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.23), residues: 1263 helix: 1.30 (0.42), residues: 174 sheet: -0.41 (0.28), residues: 347 loop : -1.03 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 597 HIS 0.003 0.001 HIS B 549 PHE 0.024 0.001 PHE B 225 TYR 0.024 0.001 TYR C 162 ARG 0.003 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 600 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7789 (p) REVERT: B 595 GLN cc_start: 0.8096 (tt0) cc_final: 0.7600 (tm-30) REVERT: C 193 PHE cc_start: 0.8312 (m-80) cc_final: 0.8077 (m-80) REVERT: E 83 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7980 (ppp) REVERT: D 38 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7470 (ttp-170) REVERT: D 39 GLN cc_start: 0.8169 (tt0) cc_final: 0.7322 (tt0) REVERT: D 72 ARG cc_start: 0.7383 (ptt180) cc_final: 0.6919 (ptt180) REVERT: D 79 MET cc_start: 0.8274 (tmm) cc_final: 0.7725 (tmm) REVERT: D 83 MET cc_start: 0.7285 (ppp) cc_final: 0.7065 (ppp) REVERT: D 95 TYR cc_start: 0.8836 (m-80) cc_final: 0.8474 (m-80) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.2471 time to fit residues: 30.1975 Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 41 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: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081798 restraints weight = 18360.945| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.82 r_work: 0.2883 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10464 Z= 0.284 Angle : 0.629 8.289 14220 Z= 0.320 Chirality : 0.045 0.297 1608 Planarity : 0.005 0.067 1821 Dihedral : 7.739 58.446 1715 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 1.40 % Allowed : 12.34 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.23), residues: 1263 helix: 1.33 (0.42), residues: 174 sheet: -0.43 (0.28), residues: 347 loop : -1.05 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 597 HIS 0.004 0.001 HIS B 139 PHE 0.023 0.002 PHE B 225 TYR 0.024 0.002 TYR C 162 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7842 (p) REVERT: B 595 GLN cc_start: 0.8159 (tt0) cc_final: 0.7668 (tm-30) REVERT: B 597 TRP cc_start: 0.7744 (m-90) cc_final: 0.7243 (m-90) REVERT: E 83 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7994 (ppp) REVERT: D 79 MET cc_start: 0.8301 (tmm) cc_final: 0.7744 (tmm) REVERT: D 95 TYR cc_start: 0.8859 (m-80) cc_final: 0.8503 (m-80) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.2574 time to fit residues: 31.6594 Evaluate side-chains 89 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 83 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 116 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081855 restraints weight = 18743.175| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.85 r_work: 0.2902 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10464 Z= 0.219 Angle : 0.607 8.172 14220 Z= 0.311 Chirality : 0.044 0.299 1608 Planarity : 0.004 0.066 1821 Dihedral : 7.392 59.568 1715 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.40 % Allowed : 12.52 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.23), residues: 1263 helix: 1.50 (0.43), residues: 171 sheet: -0.52 (0.27), residues: 357 loop : -0.94 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 597 HIS 0.003 0.001 HIS B 549 PHE 0.022 0.001 PHE B 225 TYR 0.024 0.001 TYR C 162 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 600 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7894 (p) REVERT: B 595 GLN cc_start: 0.8077 (tt0) cc_final: 0.7597 (tm-30) REVERT: E 83 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7977 (ppp) REVERT: D 79 MET cc_start: 0.8120 (tmm) cc_final: 0.7728 (tmm) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.2450 time to fit residues: 31.1051 Evaluate side-chains 91 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain D residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 0.2980 chunk 99 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082515 restraints weight = 18236.014| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.81 r_work: 0.2921 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10464 Z= 0.183 Angle : 0.598 8.223 14220 Z= 0.306 Chirality : 0.043 0.295 1608 Planarity : 0.005 0.074 1821 Dihedral : 7.075 58.728 1715 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 1.59 % Allowed : 12.34 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.23), residues: 1263 helix: 1.61 (0.43), residues: 170 sheet: -0.46 (0.28), residues: 356 loop : -0.92 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 597 HIS 0.003 0.001 HIS B 549 PHE 0.018 0.001 PHE B 225 TYR 0.027 0.001 TYR D 80 ARG 0.007 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 600 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7885 (p) REVERT: B 595 GLN cc_start: 0.7949 (tt0) cc_final: 0.7477 (tm-30) REVERT: E 83 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7918 (ppp) REVERT: D 79 MET cc_start: 0.8145 (tmm) cc_final: 0.7808 (tmm) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.2408 time to fit residues: 31.2011 Evaluate side-chains 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain D residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 7 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079560 restraints weight = 18566.005| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.85 r_work: 0.2843 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10464 Z= 0.427 Angle : 0.698 8.641 14220 Z= 0.359 Chirality : 0.047 0.290 1608 Planarity : 0.005 0.074 1821 Dihedral : 7.210 58.190 1715 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 1.59 % Allowed : 12.34 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.23), residues: 1263 helix: 1.32 (0.42), residues: 171 sheet: -0.74 (0.26), residues: 390 loop : -0.99 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 597 HIS 0.005 0.001 HIS B 139 PHE 0.025 0.002 PHE B 225 TYR 0.024 0.002 TYR C 162 ARG 0.009 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 600 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7999 (p) REVERT: B 595 GLN cc_start: 0.8276 (tt0) cc_final: 0.7746 (tm-30) REVERT: E 83 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7880 (ppp) REVERT: D 32 TYR cc_start: 0.7836 (t80) cc_final: 0.7606 (t80) REVERT: D 79 MET cc_start: 0.8008 (tmm) cc_final: 0.7578 (tmm) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.2403 time to fit residues: 29.6993 Evaluate side-chains 91 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 81 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081871 restraints weight = 18327.225| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.83 r_work: 0.2881 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10464 Z= 0.219 Angle : 0.634 8.988 14220 Z= 0.326 Chirality : 0.044 0.287 1608 Planarity : 0.005 0.078 1821 Dihedral : 6.943 58.056 1715 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 1.31 % Allowed : 12.71 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.23), residues: 1263 helix: 1.50 (0.43), residues: 171 sheet: -0.62 (0.26), residues: 388 loop : -0.90 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 597 HIS 0.003 0.001 HIS B 549 PHE 0.019 0.001 PHE B 225 TYR 0.025 0.001 TYR C 162 ARG 0.009 0.000 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 600 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7983 (p) REVERT: B 595 GLN cc_start: 0.8138 (tt0) cc_final: 0.7644 (tm-30) REVERT: E 83 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7905 (ppp) REVERT: D 79 MET cc_start: 0.7912 (tmm) cc_final: 0.7581 (tmm) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.2471 time to fit residues: 30.6175 Evaluate side-chains 89 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN D 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079672 restraints weight = 18596.991| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.79 r_work: 0.2862 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10464 Z= 0.352 Angle : 0.672 8.922 14220 Z= 0.346 Chirality : 0.046 0.284 1608 Planarity : 0.005 0.082 1821 Dihedral : 6.954 57.827 1715 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.33 % Favored : 93.51 % Rotamer: Outliers : 1.31 % Allowed : 12.52 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.23), residues: 1263 helix: 1.22 (0.42), residues: 177 sheet: -0.70 (0.26), residues: 388 loop : -0.93 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 597 HIS 0.004 0.001 HIS B 549 PHE 0.021 0.002 PHE B 225 TYR 0.024 0.002 TYR C 162 ARG 0.008 0.000 ARG E 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4959.67 seconds wall clock time: 88 minutes 48.94 seconds (5328.94 seconds total)