Starting phenix.real_space_refine on Mon Jun 9 02:54:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsu_44872/06_2025/9bsu_44872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsu_44872/06_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_44872/06_2025/9bsu_44872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsu_44872/06_2025/9bsu_44872.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsu_44872/06_2025/9bsu_44872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsu_44872/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.35, per 1000 atoms: 0.72 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: 3.05 Conformation dependent library (CDL) restraints added in 1.3 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: 1.63 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: 3.46 Time building geometry restraints manager: 3.55 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: 2.120 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.170 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- 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 0.049 10496 Z= 0.221 Angle : 0.847 13.888 14300 Z= 0.422 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02151 ( 3) link_NAG-ASN : angle 3.63473 ( 9) link_ALPHA1-6 : bond 0.03744 ( 4) link_ALPHA1-6 : angle 3.88987 ( 12) link_BETA1-4 : bond 0.04621 ( 6) link_BETA1-4 : angle 7.17201 ( 18) link_ALPHA1-3 : bond 0.04327 ( 2) link_ALPHA1-3 : angle 6.24617 ( 6) hydrogen bonds : bond 0.22898 ( 294) hydrogen bonds : angle 7.87776 ( 837) SS BOND : bond 0.00300 ( 16) SS BOND : angle 1.37600 ( 32) link_BETA1-3 : bond 0.04851 ( 1) link_BETA1-3 : angle 4.69523 ( 3) covalent geometry : bond 0.00388 (10464) covalent geometry : angle 0.78064 (14220) *********************** 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 : 0.912 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: 0.2787 time to fit residues: 42.9905 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 : 1.255 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082397 restraints weight = 17847.168| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.82 r_work: 0.2879 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- 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 10496 Z= 0.151 Angle : 0.702 10.671 14300 Z= 0.348 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 3) link_NAG-ASN : angle 1.69119 ( 9) link_ALPHA1-6 : bond 0.00964 ( 4) link_ALPHA1-6 : angle 1.57988 ( 12) link_BETA1-4 : bond 0.00554 ( 6) link_BETA1-4 : angle 2.94325 ( 18) link_ALPHA1-3 : bond 0.00248 ( 2) link_ALPHA1-3 : angle 3.40695 ( 6) hydrogen bonds : bond 0.04714 ( 294) hydrogen bonds : angle 5.25656 ( 837) SS BOND : bond 0.00309 ( 16) SS BOND : angle 1.06682 ( 32) link_BETA1-3 : bond 0.00780 ( 1) link_BETA1-3 : angle 1.89619 ( 3) covalent geometry : bond 0.00344 (10464) covalent geometry : angle 0.68780 (14220) *********************** 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 : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8084 (m) cc_final: 0.7696 (p) REVERT: B 225 PHE cc_start: 0.8788 (t80) cc_final: 0.8519 (t80) REVERT: B 595 GLN cc_start: 0.7753 (tt0) cc_final: 0.7288 (tm-30) REVERT: C 193 PHE cc_start: 0.8109 (m-80) cc_final: 0.7854 (m-80) REVERT: D 79 MET cc_start: 0.8517 (tmm) cc_final: 0.8079 (tmm) REVERT: D 83 MET cc_start: 0.7521 (ppp) cc_final: 0.6932 (ppp) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2583 time to fit residues: 34.4035 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 : 1.128 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.132772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081236 restraints weight = 18748.231| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.85 r_work: 0.2888 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10496 Z= 0.199 Angle : 0.691 9.843 14300 Z= 0.344 Chirality : 0.047 0.293 1608 Planarity : 0.005 0.060 1821 Dihedral : 11.083 103.232 1715 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 1.31 % Allowed : 8.88 % Favored : 89.81 % 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: 328 loop : -1.14 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 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 0.006 0.001 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 3) link_NAG-ASN : angle 1.79634 ( 9) link_ALPHA1-6 : bond 0.00857 ( 4) link_ALPHA1-6 : angle 2.11592 ( 12) link_BETA1-4 : bond 0.00347 ( 6) link_BETA1-4 : angle 2.79301 ( 18) link_ALPHA1-3 : bond 0.00472 ( 2) link_ALPHA1-3 : angle 3.25101 ( 6) hydrogen bonds : bond 0.04797 ( 294) hydrogen bonds : angle 4.97157 ( 837) SS BOND : bond 0.00370 ( 16) SS BOND : angle 1.20745 ( 32) link_BETA1-3 : bond 0.00373 ( 1) link_BETA1-3 : angle 1.71168 ( 3) covalent geometry : bond 0.00484 (10464) covalent geometry : angle 0.67561 (14220) *********************** 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 96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7743 (p) REVERT: B 595 GLN cc_start: 0.8063 (tt0) cc_final: 0.7560 (tm-30) REVERT: C 193 PHE cc_start: 0.8247 (m-80) cc_final: 0.8013 (m-80) REVERT: D 79 MET cc_start: 0.8501 (tmm) cc_final: 0.7920 (tmm) REVERT: D 83 MET cc_start: 0.7252 (ppp) cc_final: 0.6932 (ppp) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.2482 time to fit residues: 31.1672 Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 4 LEU 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: 0.7980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 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 = 0.133822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.082335 restraints weight = 18459.971| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.86 r_work: 0.2906 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10496 Z= 0.144 Angle : 0.649 10.860 14300 Z= 0.322 Chirality : 0.045 0.302 1608 Planarity : 0.005 0.118 1821 Dihedral : 9.843 94.395 1715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 1.21 % Allowed : 10.65 % Favored : 88.13 % 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: -0.89 (0.23), residues: 1263 helix: 0.98 (0.42), residues: 180 sheet: -0.48 (0.27), residues: 345 loop : -1.05 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 597 HIS 0.003 0.001 HIS B 549 PHE 0.027 0.001 PHE B 225 TYR 0.025 0.002 TYR C 162 ARG 0.006 0.000 ARG E 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 3) link_NAG-ASN : angle 1.66185 ( 9) link_ALPHA1-6 : bond 0.01056 ( 4) link_ALPHA1-6 : angle 1.98953 ( 12) link_BETA1-4 : bond 0.00390 ( 6) link_BETA1-4 : angle 2.54413 ( 18) link_ALPHA1-3 : bond 0.00625 ( 2) link_ALPHA1-3 : angle 3.23272 ( 6) hydrogen bonds : bond 0.04030 ( 294) hydrogen bonds : angle 4.66563 ( 837) SS BOND : bond 0.00316 ( 16) SS BOND : angle 0.97259 ( 32) link_BETA1-3 : bond 0.00399 ( 1) link_BETA1-3 : angle 1.76183 ( 3) covalent geometry : bond 0.00335 (10464) covalent geometry : angle 0.63500 (14220) *********************** 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 : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8183 (m) cc_final: 0.7809 (p) REVERT: B 595 GLN cc_start: 0.8085 (tt0) cc_final: 0.7591 (tm-30) REVERT: C 193 PHE cc_start: 0.8296 (m-80) cc_final: 0.8026 (m-80) REVERT: E 83 MET cc_start: 0.6814 (ppp) cc_final: 0.6575 (ppp) REVERT: E 110 ASP cc_start: 0.8636 (t0) cc_final: 0.8428 (t0) REVERT: D 79 MET cc_start: 0.8314 (tmm) cc_final: 0.7775 (tmm) REVERT: D 83 MET cc_start: 0.7173 (ppp) cc_final: 0.6903 (ppp) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.2306 time to fit residues: 30.5033 Evaluate side-chains 85 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 D residue 6 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.133081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081755 restraints weight = 18582.347| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.85 r_work: 0.2896 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.004 0.040 10496 Z= 0.159 Angle : 0.655 11.852 14300 Z= 0.323 Chirality : 0.045 0.297 1608 Planarity : 0.005 0.068 1821 Dihedral : 8.501 62.196 1715 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.40 % Allowed : 11.59 % Favored : 87.01 % 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: -0.83 (0.23), residues: 1263 helix: 1.29 (0.42), residues: 174 sheet: -0.45 (0.28), residues: 347 loop : -1.05 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 597 HIS 0.003 0.001 HIS B 139 PHE 0.026 0.002 PHE B 225 TYR 0.025 0.002 TYR C 162 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 3) link_NAG-ASN : angle 1.72829 ( 9) link_ALPHA1-6 : bond 0.01077 ( 4) link_ALPHA1-6 : angle 1.78323 ( 12) link_BETA1-4 : bond 0.00274 ( 6) link_BETA1-4 : angle 2.55942 ( 18) link_ALPHA1-3 : bond 0.00641 ( 2) link_ALPHA1-3 : angle 3.26956 ( 6) hydrogen bonds : bond 0.04029 ( 294) hydrogen bonds : angle 4.53810 ( 837) SS BOND : bond 0.00289 ( 16) SS BOND : angle 1.05879 ( 32) link_BETA1-3 : bond 0.00420 ( 1) link_BETA1-3 : angle 1.73220 ( 3) covalent geometry : bond 0.00377 (10464) covalent geometry : angle 0.64087 (14220) *********************** 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 97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7823 (p) REVERT: B 595 GLN cc_start: 0.8128 (tt0) cc_final: 0.7631 (tm-30) REVERT: C 193 PHE cc_start: 0.8347 (m-80) cc_final: 0.8092 (m-80) REVERT: E 73 ASP cc_start: 0.9028 (t0) cc_final: 0.8676 (p0) REVERT: E 83 MET cc_start: 0.6905 (ppp) cc_final: 0.6662 (ppp) REVERT: D 39 GLN cc_start: 0.8227 (tt0) cc_final: 0.7450 (tt0) REVERT: D 72 ARG cc_start: 0.7372 (ptt180) cc_final: 0.6935 (ptt180) REVERT: D 79 MET cc_start: 0.8270 (tmm) cc_final: 0.7959 (tmm) REVERT: D 83 MET cc_start: 0.7299 (ppp) cc_final: 0.7093 (ppp) REVERT: D 95 TYR cc_start: 0.8839 (m-80) cc_final: 0.8464 (m-80) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.2545 time to fit residues: 32.6507 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 : 1.262 ------------------------------------------------------------------------------- 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 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 D residue 58 THR 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: 0.9980 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.132503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081410 restraints weight = 18513.207| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.82 r_work: 0.2891 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10496 Z= 0.160 Angle : 0.631 8.074 14300 Z= 0.318 Chirality : 0.044 0.298 1608 Planarity : 0.004 0.067 1821 Dihedral : 7.645 58.502 1715 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % 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: 1.34 (0.42), residues: 174 sheet: -0.42 (0.28), residues: 347 loop : -1.04 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 597 HIS 0.003 0.001 HIS B 139 PHE 0.023 0.001 PHE B 225 TYR 0.024 0.001 TYR C 162 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 3) link_NAG-ASN : angle 1.76110 ( 9) link_ALPHA1-6 : bond 0.01019 ( 4) link_ALPHA1-6 : angle 1.44591 ( 12) link_BETA1-4 : bond 0.00355 ( 6) link_BETA1-4 : angle 2.17334 ( 18) link_ALPHA1-3 : bond 0.00660 ( 2) link_ALPHA1-3 : angle 3.27475 ( 6) hydrogen bonds : bond 0.03990 ( 294) hydrogen bonds : angle 4.45634 ( 837) SS BOND : bond 0.00303 ( 16) SS BOND : angle 1.09082 ( 32) link_BETA1-3 : bond 0.00409 ( 1) link_BETA1-3 : angle 1.61198 ( 3) covalent geometry : bond 0.00382 (10464) covalent geometry : angle 0.61856 (14220) *********************** 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 91 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7893 (p) REVERT: B 595 GLN cc_start: 0.8117 (tt0) cc_final: 0.7624 (tm-30) REVERT: C 193 PHE cc_start: 0.8375 (m-80) cc_final: 0.8158 (m-80) REVERT: E 1 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: E 83 MET cc_start: 0.6889 (ppp) cc_final: 0.6628 (ppp) REVERT: D 39 GLN cc_start: 0.8215 (tt0) cc_final: 0.7491 (tt0) REVERT: D 79 MET cc_start: 0.8277 (tmm) cc_final: 0.7801 (tmm) REVERT: D 95 TYR cc_start: 0.8853 (m-80) cc_final: 0.8265 (m-80) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.2439 time to fit residues: 29.1657 Evaluate side-chains 88 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 57 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.131121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.079915 restraints weight = 18841.528| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.87 r_work: 0.2862 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10496 Z= 0.208 Angle : 0.665 8.111 14300 Z= 0.338 Chirality : 0.046 0.293 1608 Planarity : 0.005 0.065 1821 Dihedral : 7.522 59.339 1715 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 1.50 % Allowed : 12.43 % 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: -0.86 (0.23), residues: 1263 helix: 1.36 (0.42), residues: 171 sheet: -0.60 (0.27), residues: 357 loop : -1.02 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 597 HIS 0.004 0.001 HIS B 139 PHE 0.024 0.002 PHE B 225 TYR 0.025 0.002 TYR C 162 ARG 0.002 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 3) link_NAG-ASN : angle 1.84188 ( 9) link_ALPHA1-6 : bond 0.00744 ( 4) link_ALPHA1-6 : angle 1.41510 ( 12) link_BETA1-4 : bond 0.00213 ( 6) link_BETA1-4 : angle 2.14042 ( 18) link_ALPHA1-3 : bond 0.00613 ( 2) link_ALPHA1-3 : angle 3.34331 ( 6) hydrogen bonds : bond 0.04462 ( 294) hydrogen bonds : angle 4.55873 ( 837) SS BOND : bond 0.00372 ( 16) SS BOND : angle 1.24628 ( 32) link_BETA1-3 : bond 0.00384 ( 1) link_BETA1-3 : angle 1.58408 ( 3) covalent geometry : bond 0.00506 (10464) covalent geometry : angle 0.65264 (14220) *********************** 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 96 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7997 (p) REVERT: B 595 GLN cc_start: 0.8172 (tt0) cc_final: 0.7677 (tm-30) REVERT: E 83 MET cc_start: 0.6848 (ppp) cc_final: 0.6556 (ppp) REVERT: D 79 MET cc_start: 0.8187 (tmm) cc_final: 0.7788 (tmm) REVERT: D 95 TYR cc_start: 0.8747 (m-80) cc_final: 0.8277 (m-80) outliers start: 16 outliers final: 12 residues processed: 91 average time/residue: 0.2396 time to fit residues: 31.0464 Evaluate side-chains 86 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 D residue 58 THR 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: 3.9990 chunk 99 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 125 optimal weight: 0.3980 chunk 95 optimal weight: 0.7980 chunk 87 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 118 optimal weight: 0.7980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.134166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083244 restraints weight = 18535.861| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.82 r_work: 0.2925 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10496 Z= 0.116 Angle : 0.615 8.255 14300 Z= 0.312 Chirality : 0.043 0.298 1608 Planarity : 0.005 0.067 1821 Dihedral : 7.060 58.771 1715 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 1.03 % Allowed : 12.43 % 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: -0.74 (0.23), residues: 1263 helix: 1.19 (0.42), residues: 183 sheet: -0.49 (0.28), residues: 353 loop : -0.91 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 597 HIS 0.002 0.000 HIS B 549 PHE 0.024 0.001 PHE B 234 TYR 0.025 0.001 TYR C 162 ARG 0.008 0.000 ARG D 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 3) link_NAG-ASN : angle 1.44293 ( 9) link_ALPHA1-6 : bond 0.00969 ( 4) link_ALPHA1-6 : angle 1.38735 ( 12) link_BETA1-4 : bond 0.00411 ( 6) link_BETA1-4 : angle 1.91455 ( 18) link_ALPHA1-3 : bond 0.00682 ( 2) link_ALPHA1-3 : angle 3.11951 ( 6) hydrogen bonds : bond 0.03556 ( 294) hydrogen bonds : angle 4.23858 ( 837) SS BOND : bond 0.00261 ( 16) SS BOND : angle 0.79015 ( 32) link_BETA1-3 : bond 0.00556 ( 1) link_BETA1-3 : angle 1.32870 ( 3) covalent geometry : bond 0.00260 (10464) covalent geometry : angle 0.60541 (14220) *********************** 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 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7986 (p) REVERT: B 595 GLN cc_start: 0.7956 (tt0) cc_final: 0.7476 (tm-30) REVERT: E 83 MET cc_start: 0.6865 (ppp) cc_final: 0.6582 (ppp) REVERT: D 79 MET cc_start: 0.8041 (tmm) cc_final: 0.7774 (tmm) REVERT: D 95 TYR cc_start: 0.8651 (m-80) cc_final: 0.8382 (m-80) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.2700 time to fit residues: 33.1646 Evaluate side-chains 83 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.079275 restraints weight = 18675.525| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.78 r_work: 0.2854 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10496 Z= 0.247 Angle : 0.699 8.742 14300 Z= 0.354 Chirality : 0.047 0.286 1608 Planarity : 0.005 0.072 1821 Dihedral : 7.151 58.032 1715 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.49 % Favored : 93.35 % Rotamer: Outliers : 1.31 % Allowed : 12.80 % Favored : 85.89 % 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: -0.84 (0.23), residues: 1263 helix: 1.35 (0.43), residues: 171 sheet: -0.62 (0.27), residues: 367 loop : -0.97 (0.22), residues: 725 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 0.023 0.002 PHE B 225 TYR 0.025 0.002 TYR C 162 ARG 0.004 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 3) link_NAG-ASN : angle 1.93660 ( 9) link_ALPHA1-6 : bond 0.00710 ( 4) link_ALPHA1-6 : angle 1.51299 ( 12) link_BETA1-4 : bond 0.00270 ( 6) link_BETA1-4 : angle 2.14843 ( 18) link_ALPHA1-3 : bond 0.00569 ( 2) link_ALPHA1-3 : angle 3.41289 ( 6) hydrogen bonds : bond 0.04739 ( 294) hydrogen bonds : angle 4.56212 ( 837) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.38912 ( 32) link_BETA1-3 : bond 0.00192 ( 1) link_BETA1-3 : angle 1.72604 ( 3) covalent geometry : bond 0.00602 (10464) covalent geometry : angle 0.68629 (14220) *********************** 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 94 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 600 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8073 (p) REVERT: B 595 GLN cc_start: 0.8248 (tt0) cc_final: 0.7735 (tm-30) REVERT: C 162 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: C 595 GLN cc_start: 0.9066 (tt0) cc_final: 0.8734 (tm-30) REVERT: E 83 MET cc_start: 0.6868 (ppp) cc_final: 0.6581 (ppp) REVERT: D 32 TYR cc_start: 0.7690 (t80) cc_final: 0.7478 (t80) REVERT: D 79 MET cc_start: 0.7929 (tmm) cc_final: 0.7639 (tmm) REVERT: D 95 TYR cc_start: 0.8762 (m-80) cc_final: 0.8289 (m-80) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.2527 time to fit residues: 31.0098 Evaluate side-chains 90 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 162 TYR 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 55 VAL Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081491 restraints weight = 18451.016| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.81 r_work: 0.2896 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10496 Z= 0.137 Angle : 0.631 9.246 14300 Z= 0.319 Chirality : 0.044 0.287 1608 Planarity : 0.005 0.071 1821 Dihedral : 6.813 57.912 1715 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 1.03 % Allowed : 13.08 % Favored : 85.89 % 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: -0.71 (0.23), residues: 1263 helix: 1.54 (0.43), residues: 171 sheet: -0.55 (0.27), residues: 366 loop : -0.90 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 597 HIS 0.003 0.001 HIS B 139 PHE 0.024 0.001 PHE B 234 TYR 0.025 0.001 TYR C 162 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 3) link_NAG-ASN : angle 1.58515 ( 9) link_ALPHA1-6 : bond 0.00833 ( 4) link_ALPHA1-6 : angle 1.38494 ( 12) link_BETA1-4 : bond 0.00361 ( 6) link_BETA1-4 : angle 1.94446 ( 18) link_ALPHA1-3 : bond 0.00713 ( 2) link_ALPHA1-3 : angle 3.17134 ( 6) hydrogen bonds : bond 0.03845 ( 294) hydrogen bonds : angle 4.29164 ( 837) SS BOND : bond 0.00290 ( 16) SS BOND : angle 0.95874 ( 32) link_BETA1-3 : bond 0.00426 ( 1) link_BETA1-3 : angle 1.39066 ( 3) covalent geometry : bond 0.00325 (10464) covalent geometry : angle 0.62127 (14220) ********************** 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 91 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8028 (p) REVERT: B 595 GLN cc_start: 0.8106 (tt0) cc_final: 0.7620 (tm-30) REVERT: C 595 GLN cc_start: 0.8989 (tt0) cc_final: 0.8682 (tm-30) REVERT: E 83 MET cc_start: 0.6842 (ppp) cc_final: 0.6565 (ppp) REVERT: D 32 TYR cc_start: 0.7573 (t80) cc_final: 0.7356 (t80) REVERT: D 79 MET cc_start: 0.8028 (tmm) cc_final: 0.7821 (tmm) REVERT: D 95 TYR cc_start: 0.8739 (m-80) cc_final: 0.8284 (m-80) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.2765 time to fit residues: 32.4395 Evaluate side-chains 87 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 214 TYR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain D residue 100 LEU 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: 0.0970 chunk 77 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082616 restraints weight = 18448.856| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.82 r_work: 0.2919 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10496 Z= 0.120 Angle : 0.617 9.275 14300 Z= 0.311 Chirality : 0.044 0.275 1608 Planarity : 0.005 0.073 1821 Dihedral : 6.527 57.809 1715 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.12 % Allowed : 13.18 % Favored : 85.70 % 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: -0.63 (0.23), residues: 1263 helix: 1.64 (0.43), residues: 171 sheet: -0.44 (0.28), residues: 351 loop : -0.89 (0.22), residues: 741 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 0.026 0.001 PHE B 234 TYR 0.024 0.001 TYR C 162 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 3) link_NAG-ASN : angle 1.49880 ( 9) link_ALPHA1-6 : bond 0.00854 ( 4) link_ALPHA1-6 : angle 1.41521 ( 12) link_BETA1-4 : bond 0.00388 ( 6) link_BETA1-4 : angle 1.92831 ( 18) link_ALPHA1-3 : bond 0.00627 ( 2) link_ALPHA1-3 : angle 3.09786 ( 6) hydrogen bonds : bond 0.03475 ( 294) hydrogen bonds : angle 4.13805 ( 837) SS BOND : bond 0.00257 ( 16) SS BOND : angle 0.88971 ( 32) link_BETA1-3 : bond 0.00413 ( 1) link_BETA1-3 : angle 1.43163 ( 3) covalent geometry : bond 0.00275 (10464) covalent geometry : angle 0.60741 (14220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5374.59 seconds wall clock time: 93 minutes 47.93 seconds (5627.93 seconds total)