Starting phenix.real_space_refine on Wed Sep 17 17:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsu_44872/09_2025/9bsu_44872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsu_44872/09_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_44872/09_2025/9bsu_44872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsu_44872/09_2025/9bsu_44872.map" model { file = "/net/cci-nas-00/data/ceres_data/9bsu_44872/09_2025/9bsu_44872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsu_44872/09_2025/9bsu_44872.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.33, per 1000 atoms: 0.23 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: 0.99 Conformation dependent library (CDL) restraints added in 298.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.67 Time building geometry restraints manager: 1.21 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: 2.200 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG B 64 TYR 0.016 0.001 TYR A 162 PHE 0.029 0.001 PHE D 68 TRP 0.036 0.002 TRP C 275 HIS 0.004 0.001 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00388 (10464) covalent geometry : angle 0.78064 (14220) SS BOND : bond 0.00300 ( 16) SS BOND : angle 1.37600 ( 32) hydrogen bonds : bond 0.22898 ( 294) hydrogen bonds : angle 7.87776 ( 837) link_ALPHA1-3 : bond 0.04327 ( 2) link_ALPHA1-3 : angle 6.24617 ( 6) link_ALPHA1-6 : bond 0.03744 ( 4) link_ALPHA1-6 : angle 3.88987 ( 12) link_BETA1-3 : bond 0.04851 ( 1) link_BETA1-3 : angle 4.69523 ( 3) link_BETA1-4 : bond 0.04621 ( 6) link_BETA1-4 : angle 7.17201 ( 18) link_NAG-ASN : bond 0.02151 ( 3) link_NAG-ASN : angle 3.63473 ( 9) *********************** 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 : 0.407 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: 0.1262 time to fit residues: 19.5523 Evaluate side-chains 82 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 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** D 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.082366 restraints weight = 17767.746| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.83 r_work: 0.2880 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1253 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= 0.150 Angle : 0.699 10.794 14300 Z= 0.346 Chirality : 0.047 0.287 1608 Planarity : 0.005 0.052 1821 Dihedral : 14.066 111.946 1715 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.93 % Allowed : 5.70 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.22), residues: 1263 helix: 0.40 (0.39), residues: 179 sheet: -0.38 (0.29), residues: 312 loop : -1.21 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 67 TYR 0.027 0.002 TYR C 162 PHE 0.018 0.001 PHE B 234 TRP 0.023 0.001 TRP C 275 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00343 (10464) covalent geometry : angle 0.68428 (14220) SS BOND : bond 0.00307 ( 16) SS BOND : angle 1.09100 ( 32) hydrogen bonds : bond 0.04890 ( 294) hydrogen bonds : angle 5.27310 ( 837) link_ALPHA1-3 : bond 0.00216 ( 2) link_ALPHA1-3 : angle 3.32658 ( 6) link_ALPHA1-6 : bond 0.00923 ( 4) link_ALPHA1-6 : angle 1.60029 ( 12) link_BETA1-3 : bond 0.00770 ( 1) link_BETA1-3 : angle 1.94795 ( 3) link_BETA1-4 : bond 0.00605 ( 6) link_BETA1-4 : angle 2.97190 ( 18) link_NAG-ASN : bond 0.00848 ( 3) link_NAG-ASN : angle 1.71487 ( 9) *********************** 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 101 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8096 (m) cc_final: 0.7710 (p) REVERT: B 225 PHE cc_start: 0.8787 (t80) cc_final: 0.8515 (t80) REVERT: B 595 GLN cc_start: 0.7762 (tt0) cc_final: 0.7294 (tm-30) REVERT: C 193 PHE cc_start: 0.8109 (m-80) cc_final: 0.7851 (m-80) REVERT: D 79 MET cc_start: 0.8514 (tmm) cc_final: 0.8087 (tmm) REVERT: D 83 MET cc_start: 0.7572 (ppp) cc_final: 0.7005 (ppp) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1058 time to fit residues: 14.2659 Evaluate side-chains 89 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 39 HIS Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 214 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.134188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082632 restraints weight = 18654.279| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.86 r_work: 0.2913 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10496 Z= 0.161 Angle : 0.662 9.572 14300 Z= 0.330 Chirality : 0.046 0.297 1608 Planarity : 0.005 0.088 1821 Dihedral : 11.081 105.293 1715 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 1.12 % Allowed : 8.60 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.23), residues: 1263 helix: 0.86 (0.42), residues: 180 sheet: -0.46 (0.28), residues: 326 loop : -1.09 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 38 TYR 0.024 0.002 TYR C 162 PHE 0.019 0.001 PHE B 234 TRP 0.024 0.002 TRP C 275 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00382 (10464) covalent geometry : angle 0.64723 (14220) SS BOND : bond 0.00341 ( 16) SS BOND : angle 1.07695 ( 32) hydrogen bonds : bond 0.04417 ( 294) hydrogen bonds : angle 4.83920 ( 837) link_ALPHA1-3 : bond 0.00582 ( 2) link_ALPHA1-3 : angle 3.22890 ( 6) link_ALPHA1-6 : bond 0.00969 ( 4) link_ALPHA1-6 : angle 2.12784 ( 12) link_BETA1-3 : bond 0.00634 ( 1) link_BETA1-3 : angle 1.64076 ( 3) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 2.70039 ( 18) link_NAG-ASN : bond 0.00442 ( 3) link_NAG-ASN : angle 1.66237 ( 9) *********************** 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: 12 poor density : 83 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7692 (p) REVERT: B 595 GLN cc_start: 0.7983 (tt0) cc_final: 0.7489 (tm-30) REVERT: C 193 PHE cc_start: 0.8217 (m-80) cc_final: 0.7948 (m-80) REVERT: D 79 MET cc_start: 0.8456 (tmm) cc_final: 0.7898 (tmm) REVERT: D 83 MET cc_start: 0.7216 (ppp) cc_final: 0.6924 (ppp) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 0.1215 time to fit residues: 14.9353 Evaluate side-chains 87 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 214 TYR Chi-restraints excluded: chain E residue 4 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.132605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081181 restraints weight = 18671.829| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.86 r_work: 0.2887 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1980 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= 0.185 Angle : 0.667 11.506 14300 Z= 0.332 Chirality : 0.046 0.299 1608 Planarity : 0.005 0.065 1821 Dihedral : 9.461 86.600 1715 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 1.03 % Allowed : 11.50 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.23), residues: 1263 helix: 0.98 (0.42), residues: 180 sheet: -0.38 (0.28), residues: 332 loop : -1.14 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 72 TYR 0.025 0.002 TYR C 162 PHE 0.031 0.002 PHE B 225 TRP 0.022 0.002 TRP C 275 HIS 0.004 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00447 (10464) covalent geometry : angle 0.65195 (14220) SS BOND : bond 0.00339 ( 16) SS BOND : angle 1.11476 ( 32) hydrogen bonds : bond 0.04321 ( 294) hydrogen bonds : angle 4.70796 ( 837) link_ALPHA1-3 : bond 0.00509 ( 2) link_ALPHA1-3 : angle 3.28129 ( 6) link_ALPHA1-6 : bond 0.01091 ( 4) link_ALPHA1-6 : angle 1.99272 ( 12) link_BETA1-3 : bond 0.00237 ( 1) link_BETA1-3 : angle 1.89768 ( 3) link_BETA1-4 : bond 0.00345 ( 6) link_BETA1-4 : angle 2.59107 ( 18) link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 1.79702 ( 9) *********************** 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 94 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8197 (m) cc_final: 0.7821 (p) REVERT: B 595 GLN cc_start: 0.8151 (tt0) cc_final: 0.7644 (tm-30) REVERT: C 193 PHE cc_start: 0.8342 (m-80) cc_final: 0.8114 (m-80) REVERT: E 83 MET cc_start: 0.8018 (ppp) cc_final: 0.7360 (ppp) REVERT: D 79 MET cc_start: 0.8307 (tmm) cc_final: 0.7721 (tmm) REVERT: D 83 MET cc_start: 0.7117 (ppp) cc_final: 0.6878 (ppp) outliers start: 11 outliers final: 6 residues processed: 91 average time/residue: 0.1090 time to fit residues: 14.1791 Evaluate side-chains 84 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.0000 overall best weight: 0.5402 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.133990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082865 restraints weight = 18477.988| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.83 r_work: 0.2920 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2183 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= 0.129 Angle : 0.632 10.981 14300 Z= 0.313 Chirality : 0.044 0.300 1608 Planarity : 0.005 0.116 1821 Dihedral : 8.155 58.815 1715 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 1.12 % Allowed : 12.15 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.23), residues: 1263 helix: 1.30 (0.42), residues: 174 sheet: -0.49 (0.28), residues: 343 loop : -1.01 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.024 0.001 TYR C 162 PHE 0.018 0.001 PHE B 225 TRP 0.028 0.001 TRP A 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00294 (10464) covalent geometry : angle 0.61851 (14220) SS BOND : bond 0.00307 ( 16) SS BOND : angle 0.86394 ( 32) hydrogen bonds : bond 0.03706 ( 294) hydrogen bonds : angle 4.43978 ( 837) link_ALPHA1-3 : bond 0.00733 ( 2) link_ALPHA1-3 : angle 3.21689 ( 6) link_ALPHA1-6 : bond 0.01093 ( 4) link_ALPHA1-6 : angle 1.62299 ( 12) link_BETA1-3 : bond 0.00501 ( 1) link_BETA1-3 : angle 1.57186 ( 3) link_BETA1-4 : bond 0.00335 ( 6) link_BETA1-4 : angle 2.54225 ( 18) link_NAG-ASN : bond 0.00301 ( 3) link_NAG-ASN : angle 1.56628 ( 9) *********************** 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: 12 poor density : 85 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 600 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7796 (p) REVERT: B 595 GLN cc_start: 0.8000 (tt0) cc_final: 0.7524 (tm-30) REVERT: C 193 PHE cc_start: 0.8356 (m-80) cc_final: 0.8058 (m-80) REVERT: E 83 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8104 (ppp) REVERT: D 72 ARG cc_start: 0.7397 (ptt180) cc_final: 0.6966 (ptt180) REVERT: D 79 MET cc_start: 0.8237 (tmm) cc_final: 0.7803 (tmm) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.1124 time to fit residues: 14.4151 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 : 0.352 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.132824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081648 restraints weight = 18687.780| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.86 r_work: 0.2898 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10496 Z= 0.155 Angle : 0.634 8.190 14300 Z= 0.318 Chirality : 0.044 0.298 1608 Planarity : 0.005 0.080 1821 Dihedral : 7.572 58.522 1715 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1263 helix: 1.37 (0.42), residues: 174 sheet: -0.59 (0.27), residues: 368 loop : -1.01 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.024 0.001 TYR C 162 PHE 0.026 0.001 PHE B 225 TRP 0.034 0.002 TRP A 597 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00369 (10464) covalent geometry : angle 0.62217 (14220) SS BOND : bond 0.00351 ( 16) SS BOND : angle 1.08692 ( 32) hydrogen bonds : bond 0.03918 ( 294) hydrogen bonds : angle 4.46112 ( 837) link_ALPHA1-3 : bond 0.00662 ( 2) link_ALPHA1-3 : angle 3.29091 ( 6) link_ALPHA1-6 : bond 0.01026 ( 4) link_ALPHA1-6 : angle 1.40754 ( 12) link_BETA1-3 : bond 0.00401 ( 1) link_BETA1-3 : angle 1.54825 ( 3) link_BETA1-4 : bond 0.00507 ( 6) link_BETA1-4 : angle 2.06125 ( 18) link_NAG-ASN : bond 0.00308 ( 3) link_NAG-ASN : angle 1.75697 ( 9) *********************** 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 94 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 600 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 595 GLN cc_start: 0.8089 (tt0) cc_final: 0.7595 (tm-30) REVERT: B 597 TRP cc_start: 0.7801 (m-90) cc_final: 0.7358 (m-90) REVERT: C 193 PHE cc_start: 0.8413 (m-80) cc_final: 0.8178 (m-80) REVERT: E 83 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8030 (ppp) REVERT: D 79 MET cc_start: 0.8249 (tmm) cc_final: 0.7812 (tmm) outliers start: 14 outliers final: 9 residues processed: 88 average time/residue: 0.1242 time to fit residues: 15.1342 Evaluate side-chains 89 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 4 LEU Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.132992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081991 restraints weight = 18552.200| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.83 r_work: 0.2905 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2451 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= 0.143 Angle : 0.617 8.047 14300 Z= 0.313 Chirality : 0.044 0.297 1608 Planarity : 0.004 0.066 1821 Dihedral : 7.307 59.433 1715 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 1.50 % Allowed : 12.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.23), residues: 1263 helix: 1.51 (0.43), residues: 171 sheet: -0.53 (0.27), residues: 368 loop : -1.00 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.024 0.001 TYR C 162 PHE 0.023 0.001 PHE B 225 TRP 0.036 0.002 TRP A 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00337 (10464) covalent geometry : angle 0.60635 (14220) SS BOND : bond 0.00272 ( 16) SS BOND : angle 1.01114 ( 32) hydrogen bonds : bond 0.03781 ( 294) hydrogen bonds : angle 4.38858 ( 837) link_ALPHA1-3 : bond 0.00678 ( 2) link_ALPHA1-3 : angle 3.23047 ( 6) link_ALPHA1-6 : bond 0.00920 ( 4) link_ALPHA1-6 : angle 1.41498 ( 12) link_BETA1-3 : bond 0.00431 ( 1) link_BETA1-3 : angle 1.47938 ( 3) link_BETA1-4 : bond 0.00281 ( 6) link_BETA1-4 : angle 2.02743 ( 18) link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 1.63593 ( 9) *********************** 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 93 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8118 (tm-30) REVERT: A 600 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7882 (p) REVERT: B 595 GLN cc_start: 0.8090 (tt0) cc_final: 0.7606 (tm-30) REVERT: E 83 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7970 (ppp) REVERT: D 79 MET cc_start: 0.8101 (tmm) cc_final: 0.7746 (tmm) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 0.1137 time to fit residues: 13.9441 Evaluate side-chains 85 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.8422 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.132530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081612 restraints weight = 18394.961| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.81 r_work: 0.2898 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10496 Z= 0.154 Angle : 0.623 8.417 14300 Z= 0.316 Chirality : 0.044 0.292 1608 Planarity : 0.005 0.075 1821 Dihedral : 7.058 58.324 1715 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.23), residues: 1263 helix: 1.56 (0.43), residues: 170 sheet: -0.49 (0.27), residues: 368 loop : -1.00 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 53 TYR 0.025 0.001 TYR D 80 PHE 0.021 0.001 PHE B 225 TRP 0.049 0.002 TRP B 597 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00367 (10464) covalent geometry : angle 0.61165 (14220) SS BOND : bond 0.00303 ( 16) SS BOND : angle 1.11425 ( 32) hydrogen bonds : bond 0.03905 ( 294) hydrogen bonds : angle 4.37427 ( 837) link_ALPHA1-3 : bond 0.00635 ( 2) link_ALPHA1-3 : angle 3.23238 ( 6) link_ALPHA1-6 : bond 0.00789 ( 4) link_ALPHA1-6 : angle 1.40970 ( 12) link_BETA1-3 : bond 0.00388 ( 1) link_BETA1-3 : angle 1.48376 ( 3) link_BETA1-4 : bond 0.00309 ( 6) link_BETA1-4 : angle 1.98578 ( 18) link_NAG-ASN : bond 0.00275 ( 3) link_NAG-ASN : angle 1.68671 ( 9) *********************** 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 98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 600 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7890 (p) REVERT: B 595 GLN cc_start: 0.8022 (tt0) cc_final: 0.7528 (tm-30) REVERT: E 83 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7932 (ppp) REVERT: D 79 MET cc_start: 0.8112 (tmm) cc_final: 0.7717 (tmm) REVERT: D 95 TYR cc_start: 0.8667 (m-80) cc_final: 0.8289 (m-80) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.1206 time to fit residues: 15.1791 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 : 0.418 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 61 optimal weight: 0.4980 chunk 90 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 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 = 0.133071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082548 restraints weight = 18308.084| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.87 r_work: 0.2903 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2658 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= 0.136 Angle : 0.615 8.759 14300 Z= 0.313 Chirality : 0.044 0.289 1608 Planarity : 0.005 0.070 1821 Dihedral : 6.820 58.205 1715 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.38 % Rotamer: Outliers : 1.40 % Allowed : 12.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.23), residues: 1263 helix: 1.47 (0.42), residues: 177 sheet: -0.47 (0.27), residues: 374 loop : -0.94 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.024 0.001 TYR C 162 PHE 0.020 0.001 PHE B 225 TRP 0.039 0.002 TRP B 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00320 (10464) covalent geometry : angle 0.60478 (14220) SS BOND : bond 0.00268 ( 16) SS BOND : angle 0.89580 ( 32) hydrogen bonds : bond 0.03640 ( 294) hydrogen bonds : angle 4.23351 ( 837) link_ALPHA1-3 : bond 0.00643 ( 2) link_ALPHA1-3 : angle 3.16273 ( 6) link_ALPHA1-6 : bond 0.00856 ( 4) link_ALPHA1-6 : angle 1.40989 ( 12) link_BETA1-3 : bond 0.00418 ( 1) link_BETA1-3 : angle 1.43359 ( 3) link_BETA1-4 : bond 0.00315 ( 6) link_BETA1-4 : angle 1.94159 ( 18) link_NAG-ASN : bond 0.00298 ( 3) link_NAG-ASN : angle 1.58568 ( 9) *********************** 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 98 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8125 (tm-30) REVERT: A 600 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 595 GLN cc_start: 0.8096 (tt0) cc_final: 0.7593 (tm-30) REVERT: E 83 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7996 (ppp) REVERT: D 32 TYR cc_start: 0.7727 (t80) cc_final: 0.7494 (t80) REVERT: D 79 MET cc_start: 0.7909 (tmm) cc_final: 0.7681 (tmm) REVERT: D 95 TYR cc_start: 0.8688 (m-80) cc_final: 0.8378 (m-80) outliers start: 15 outliers final: 12 residues processed: 91 average time/residue: 0.1193 time to fit residues: 15.2302 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 : 0.338 ------------------------------------------------------------------------------- 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 1 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 30 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.133262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083129 restraints weight = 18063.289| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.80 r_work: 0.2911 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10496 Z= 0.127 Angle : 0.620 9.299 14300 Z= 0.313 Chirality : 0.044 0.284 1608 Planarity : 0.005 0.073 1821 Dihedral : 6.641 58.062 1715 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.62 % Favored : 94.22 % Rotamer: Outliers : 1.40 % Allowed : 12.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.23), residues: 1263 helix: 0.91 (0.40), residues: 195 sheet: -0.43 (0.28), residues: 358 loop : -0.98 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 596 TYR 0.024 0.001 TYR C 162 PHE 0.019 0.001 PHE B 225 TRP 0.044 0.002 TRP A 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00298 (10464) covalent geometry : angle 0.60963 (14220) SS BOND : bond 0.00269 ( 16) SS BOND : angle 0.95508 ( 32) hydrogen bonds : bond 0.03516 ( 294) hydrogen bonds : angle 4.13197 ( 837) link_ALPHA1-3 : bond 0.00649 ( 2) link_ALPHA1-3 : angle 3.13804 ( 6) link_ALPHA1-6 : bond 0.00851 ( 4) link_ALPHA1-6 : angle 1.41458 ( 12) link_BETA1-3 : bond 0.00400 ( 1) link_BETA1-3 : angle 1.43754 ( 3) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 1.92203 ( 18) link_NAG-ASN : bond 0.00289 ( 3) link_NAG-ASN : angle 1.55263 ( 9) ********************** 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 97 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 280 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 600 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 595 GLN cc_start: 0.8056 (tt0) cc_final: 0.7565 (tm-30) REVERT: E 83 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7867 (ppp) REVERT: D 32 TYR cc_start: 0.7685 (t80) cc_final: 0.7460 (t80) REVERT: D 79 MET cc_start: 0.7914 (tmm) cc_final: 0.7685 (tmm) REVERT: D 95 TYR cc_start: 0.8635 (m-80) cc_final: 0.8324 (m-80) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.1169 time to fit residues: 14.8802 Evaluate side-chains 92 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 600 THR Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 244 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 4 LEU Chi-restraints excluded: chain E residue 83 MET 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 73 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 83 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 1 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 = 0.3882 r_free = 0.3882 target = 0.133273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083148 restraints weight = 18330.020| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.83 r_work: 0.2912 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 10496 Z= 0.185 Angle : 0.906 59.198 14300 Z= 0.511 Chirality : 0.047 0.701 1608 Planarity : 0.005 0.074 1821 Dihedral : 6.639 58.178 1715 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 1.21 % Allowed : 12.90 % Favored : 85.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.23), residues: 1263 helix: 0.91 (0.40), residues: 195 sheet: -0.41 (0.27), residues: 363 loop : -0.94 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.035 0.001 TYR E 111 PHE 0.018 0.001 PHE B 225 TRP 0.039 0.002 TRP A 597 HIS 0.003 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00405 (10464) covalent geometry : angle 0.89993 (14220) SS BOND : bond 0.00278 ( 16) SS BOND : angle 0.94072 ( 32) hydrogen bonds : bond 0.03516 ( 294) hydrogen bonds : angle 4.13213 ( 837) link_ALPHA1-3 : bond 0.00906 ( 2) link_ALPHA1-3 : angle 3.23916 ( 6) link_ALPHA1-6 : bond 0.01279 ( 4) link_ALPHA1-6 : angle 1.55020 ( 12) link_BETA1-3 : bond 0.00407 ( 1) link_BETA1-3 : angle 1.44123 ( 3) link_BETA1-4 : bond 0.00356 ( 6) link_BETA1-4 : angle 1.93146 ( 18) link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 1.55266 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2503.52 seconds wall clock time: 43 minutes 43.73 seconds (2623.73 seconds total)