Starting phenix.real_space_refine on Thu Jul 31 09:55:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.map" model { file = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2025/7kew_22841.cif" } resolution = 4.16 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= 0.007 sd= 0.072 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 63 5.16 5 C 8325 2.51 5 N 2235 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13173 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: I, H, C, B, J, L, D, F, N, Q, P, R Time building chain proxies: 6.76, per 1000 atoms: 0.51 Number of scatterers: 13173 At special positions: 0 Unit cell: (136.99, 151.41, 129.78, 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 63 16.00 O 2550 8.00 N 2235 7.00 C 8325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS D 609 " distance=2.08 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 G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.10 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 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 O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG B 401 " - " ASN B 228 " " NAG C 401 " - " ASN C 228 " " NAG M 1 " - " ASN B 257 " " NAG N 1 " - " ASN A 257 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.1% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 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 78 through 84 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 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 78 through 84 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'E' and resid 553 through 575 removed outlier: 3.511A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 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 78 through 84 Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'F' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing sheet with id=AA1, first strand: chain 'D' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 136 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 138 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 274 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER G 59 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 35 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE G 100E" --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU G 96 " --> pdb=" O PHE G 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 94 " --> pdb=" O SER G 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA6, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 601 through 602 removed outlier: 6.879A pdb=" N CYS D 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'E' and resid 543 through 549 removed outlier: 5.538A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 136 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 138 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 274 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER H 59 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE H 35 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE H 100E" --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU H 96 " --> pdb=" O PHE H 100E" (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 94 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AC4, first strand: chain 'F' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG C 136 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 138 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 274 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER I 59 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 35 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 100E through 103 removed outlier: 6.928A pdb=" N PHE I 100E" --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU I 96 " --> pdb=" O PHE I 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG I 94 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1302 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: 4.30 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2227 1.31 - 1.45: 4355 1.45 - 1.59: 6747 1.59 - 1.73: 66 1.73 - 1.87: 78 Bond restraints: 13473 Sorted by residual: bond pdb=" CB ILE C 33 " pdb=" CG1 ILE C 33 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" NE1 TRP I 103 " pdb=" CE2 TRP I 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.34e+01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" NE1 TRP G 103 " pdb=" CE2 TRP G 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.23e+01 ... (remaining 13468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 15954 2.60 - 5.21: 1932 5.21 - 7.81: 363 7.81 - 10.42: 35 10.42 - 13.02: 16 Bond angle restraints: 18300 Sorted by residual: angle pdb=" N GLU C 71 " pdb=" CA GLU C 71 " pdb=" C GLU C 71 " ideal model delta sigma weight residual 114.62 104.18 10.44 1.14e+00 7.69e-01 8.39e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 114.62 104.26 10.36 1.14e+00 7.69e-01 8.26e+01 angle pdb=" N GLU A 71 " pdb=" CA GLU A 71 " pdb=" C GLU A 71 " ideal model delta sigma weight residual 114.62 104.27 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" N ARG C 247 " pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 114.75 104.25 10.50 1.26e+00 6.30e-01 6.95e+01 angle pdb=" N ARG A 247 " pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.86e+01 ... (remaining 18295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 8030 21.41 - 42.81: 148 42.81 - 64.22: 45 64.22 - 85.63: 27 85.63 - 107.03: 12 Dihedral angle restraints: 8262 sinusoidal: 3555 harmonic: 4707 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.17 40.83 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.18 40.82 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1453 0.103 - 0.207: 482 0.207 - 0.310: 128 0.310 - 0.414: 30 0.414 - 0.517: 13 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 ... (remaining 2103 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 103 " -0.065 2.00e-02 2.50e+03 3.04e-02 2.31e+01 pdb=" CG TRP H 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 103 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 103 " -0.065 2.00e-02 2.50e+03 3.03e-02 2.29e+01 pdb=" CG TRP I 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP I 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 103 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 103 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 103 " -0.065 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CG TRP G 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP G 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 103 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP G 103 " -0.027 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 116 2.61 - 3.18: 11555 3.18 - 3.75: 20837 3.75 - 4.33: 30200 4.33 - 4.90: 46597 Nonbonded interactions: 109305 Sorted by model distance: nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS F 601 " pdb=" SG CYS F 608 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS E 601 " pdb=" SG CYS E 608 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS B 53 " pdb=" SG CYS E 609 " model vdw 2.081 3.760 ... (remaining 109300 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: 0.09 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.010 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.022 0.136 13510 Z= 1.150 Angle : 1.894 13.024 18398 Z= 1.237 Chirality : 0.117 0.517 2106 Planarity : 0.009 0.037 2310 Dihedral : 11.742 107.032 5211 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.16 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 7.41 % 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: 0.12 (0.21), residues: 1614 helix: -0.03 (0.30), residues: 210 sheet: -0.04 (0.25), residues: 438 loop : 0.31 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.013 TRP H 103 HIS 0.008 0.002 HIS C 238 PHE 0.031 0.007 PHE H 29 TYR 0.066 0.013 TYR D 534 ARG 0.007 0.001 ARG F 559 Details of bonding type rmsd link_NAG-ASN : bond 0.07894 ( 9) link_NAG-ASN : angle 1.59115 ( 27) link_ALPHA1-6 : bond 0.05519 ( 3) link_ALPHA1-6 : angle 3.13911 ( 9) link_BETA1-4 : bond 0.07290 ( 9) link_BETA1-4 : angle 5.30207 ( 27) link_ALPHA1-3 : bond 0.08348 ( 3) link_ALPHA1-3 : angle 3.75787 ( 9) hydrogen bonds : bond 0.17125 ( 461) hydrogen bonds : angle 7.86842 ( 1302) SS BOND : bond 0.02397 ( 13) SS BOND : angle 2.73270 ( 26) covalent geometry : bond 0.02171 (13473) covalent geometry : angle 1.88152 (18300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6660 (tp30) REVERT: A 230 THR cc_start: 0.7277 (m) cc_final: 0.6749 (m) REVERT: A 235 GLN cc_start: 0.9171 (tt0) cc_final: 0.8890 (tm-30) REVERT: G 48 MET cc_start: 0.8819 (mtp) cc_final: 0.8369 (mtp) REVERT: J 70 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8777 (mm-30) REVERT: J 97 THR cc_start: 0.7532 (t) cc_final: 0.6244 (p) REVERT: B 156 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6768 (tp30) REVERT: B 235 GLN cc_start: 0.9153 (tt0) cc_final: 0.8672 (tm-30) REVERT: H 48 MET cc_start: 0.8772 (mtp) cc_final: 0.8325 (mtp) REVERT: H 101 ASP cc_start: 0.7210 (m-30) cc_final: 0.6877 (m-30) REVERT: K 70 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8885 (mm-30) REVERT: K 97 THR cc_start: 0.7740 (t) cc_final: 0.6526 (p) REVERT: C 156 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6595 (tp30) REVERT: C 230 THR cc_start: 0.7141 (m) cc_final: 0.6461 (m) REVERT: C 235 GLN cc_start: 0.9246 (tt0) cc_final: 0.8941 (tm-30) REVERT: I 23 ARG cc_start: 0.9050 (ttt180) cc_final: 0.8843 (tpp80) REVERT: I 48 MET cc_start: 0.8804 (mtp) cc_final: 0.8357 (mtp) REVERT: I 68 THR cc_start: 0.8376 (m) cc_final: 0.8108 (p) REVERT: I 81 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7233 (mt-10) REVERT: I 101 ASP cc_start: 0.7397 (m-30) cc_final: 0.6888 (m-30) REVERT: L 70 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8859 (mm-30) REVERT: L 97 THR cc_start: 0.7493 (t) cc_final: 0.6182 (p) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.3208 time to fit residues: 221.9893 Evaluate side-chains 228 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN J 32 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS H 64 GLN K 32 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 602 HIS L 6 GLN L 32 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.132379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.098389 restraints weight = 33056.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.103410 restraints weight = 19258.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.107691 restraints weight = 10165.677| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13510 Z= 0.190 Angle : 0.828 9.404 18398 Z= 0.441 Chirality : 0.050 0.248 2106 Planarity : 0.006 0.051 2310 Dihedral : 10.513 86.831 2268 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.33 (0.21), residues: 1614 helix: 0.54 (0.34), residues: 234 sheet: 0.10 (0.25), residues: 432 loop : -0.52 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 275 HIS 0.007 0.001 HIS B 238 PHE 0.045 0.003 PHE G 29 TYR 0.033 0.003 TYR D 534 ARG 0.008 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00795 ( 9) link_NAG-ASN : angle 3.11179 ( 27) link_ALPHA1-6 : bond 0.00828 ( 3) link_ALPHA1-6 : angle 1.97145 ( 9) link_BETA1-4 : bond 0.01074 ( 9) link_BETA1-4 : angle 3.13541 ( 27) link_ALPHA1-3 : bond 0.01621 ( 3) link_ALPHA1-3 : angle 1.66950 ( 9) hydrogen bonds : bond 0.05292 ( 461) hydrogen bonds : angle 6.47982 ( 1302) SS BOND : bond 0.00789 ( 13) SS BOND : angle 1.91395 ( 26) covalent geometry : bond 0.00431 (13473) covalent geometry : angle 0.80780 (18300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8400 (mttp) REVERT: A 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8696 (tm-30) REVERT: G 20 VAL cc_start: 0.8693 (t) cc_final: 0.8475 (t) REVERT: G 23 ARG cc_start: 0.8969 (ttt180) cc_final: 0.8543 (ttm-80) REVERT: G 37 VAL cc_start: 0.8324 (m) cc_final: 0.8057 (m) REVERT: G 46 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7282 (mm-30) REVERT: G 48 MET cc_start: 0.8563 (mtp) cc_final: 0.8021 (mtp) REVERT: G 52 MET cc_start: 0.7744 (mmm) cc_final: 0.7500 (mmm) REVERT: G 53 ILE cc_start: 0.7964 (tt) cc_final: 0.7677 (mm) REVERT: G 90 TYR cc_start: 0.8199 (m-80) cc_final: 0.7896 (m-80) REVERT: J 70 GLU cc_start: 0.9345 (mt-10) cc_final: 0.9074 (mm-30) REVERT: J 97 THR cc_start: 0.5771 (t) cc_final: 0.4816 (p) REVERT: B 120 GLU cc_start: 0.7216 (pp20) cc_final: 0.6969 (pp20) REVERT: B 130 ARG cc_start: 0.6775 (ptt-90) cc_final: 0.6376 (ptt90) REVERT: B 156 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6918 (tp30) REVERT: B 235 GLN cc_start: 0.9192 (tt0) cc_final: 0.8558 (tm-30) REVERT: H 20 VAL cc_start: 0.8608 (t) cc_final: 0.8258 (p) REVERT: H 46 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7094 (mm-30) REVERT: H 48 MET cc_start: 0.8498 (mtp) cc_final: 0.8224 (mtp) REVERT: K 33 LEU cc_start: 0.8752 (mt) cc_final: 0.8492 (mp) REVERT: K 71 PHE cc_start: 0.7784 (m-80) cc_final: 0.7095 (m-10) REVERT: K 90 GLN cc_start: 0.7107 (tt0) cc_final: 0.6784 (tt0) REVERT: K 97 THR cc_start: 0.6236 (t) cc_final: 0.5341 (p) REVERT: C 124 GLU cc_start: 0.8529 (tp30) cc_final: 0.8181 (tp30) REVERT: C 235 GLN cc_start: 0.9204 (tt0) cc_final: 0.8761 (tm-30) REVERT: I 20 VAL cc_start: 0.8641 (t) cc_final: 0.8318 (t) REVERT: I 32 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8800 (tptp) REVERT: I 46 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7167 (mm-30) REVERT: I 48 MET cc_start: 0.8591 (mtp) cc_final: 0.8181 (mtp) REVERT: I 53 ILE cc_start: 0.7984 (tt) cc_final: 0.7764 (mm) REVERT: L 23 CYS cc_start: 0.7449 (m) cc_final: 0.7111 (m) REVERT: L 103 LYS cc_start: 0.8077 (tttt) cc_final: 0.7856 (tttm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3059 time to fit residues: 141.0715 Evaluate side-chains 221 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.119842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088533 restraints weight = 34823.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.091120 restraints weight = 15962.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.091853 restraints weight = 11033.080| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 13510 Z= 0.353 Angle : 0.971 9.555 18398 Z= 0.500 Chirality : 0.054 0.271 2106 Planarity : 0.007 0.079 2310 Dihedral : 9.935 76.519 2268 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.36 % Allowed : 4.78 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -1.05 (0.20), residues: 1614 helix: 0.12 (0.35), residues: 231 sheet: -0.51 (0.22), residues: 507 loop : -0.99 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP B 275 HIS 0.009 0.003 HIS G 100C PHE 0.041 0.004 PHE E 592 TYR 0.034 0.004 TYR E 534 ARG 0.011 0.001 ARG J 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00761 ( 9) link_NAG-ASN : angle 2.32901 ( 27) link_ALPHA1-6 : bond 0.00496 ( 3) link_ALPHA1-6 : angle 3.17266 ( 9) link_BETA1-4 : bond 0.00542 ( 9) link_BETA1-4 : angle 2.67738 ( 27) link_ALPHA1-3 : bond 0.01059 ( 3) link_ALPHA1-3 : angle 2.62594 ( 9) hydrogen bonds : bond 0.05724 ( 461) hydrogen bonds : angle 6.90071 ( 1302) SS BOND : bond 0.00707 ( 13) SS BOND : angle 2.24802 ( 26) covalent geometry : bond 0.00813 (13473) covalent geometry : angle 0.95594 (18300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7639 (p) cc_final: 0.6885 (t) REVERT: A 229 MET cc_start: 0.8502 (pmm) cc_final: 0.8215 (pmm) REVERT: A 230 THR cc_start: 0.7048 (m) cc_final: 0.6781 (m) REVERT: A 235 GLN cc_start: 0.9128 (tt0) cc_final: 0.8492 (tm-30) REVERT: G 32 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8707 (tptt) REVERT: G 48 MET cc_start: 0.8988 (mtp) cc_final: 0.8620 (mtp) REVERT: G 96 GLU cc_start: 0.7514 (tt0) cc_final: 0.7177 (tp30) REVERT: J 70 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9215 (mm-30) REVERT: J 71 PHE cc_start: 0.8448 (m-10) cc_final: 0.7518 (m-10) REVERT: D 564 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 77 THR cc_start: 0.7447 (p) cc_final: 0.6933 (t) REVERT: B 229 MET cc_start: 0.8603 (pmm) cc_final: 0.8319 (pmm) REVERT: B 230 THR cc_start: 0.6758 (m) cc_final: 0.6482 (m) REVERT: B 235 GLN cc_start: 0.9137 (tt0) cc_final: 0.8643 (tm-30) REVERT: H 48 MET cc_start: 0.8290 (mtp) cc_final: 0.7776 (mtp) REVERT: H 90 TYR cc_start: 0.8422 (m-10) cc_final: 0.8070 (m-80) REVERT: H 100 TRP cc_start: 0.6089 (p90) cc_final: 0.5817 (p90) REVERT: K 35 TRP cc_start: 0.6269 (m-90) cc_final: 0.5687 (m-90) REVERT: K 48 ILE cc_start: 0.7376 (mm) cc_final: 0.6130 (mm) REVERT: K 90 GLN cc_start: 0.7404 (tt0) cc_final: 0.6783 (tt0) REVERT: K 97 THR cc_start: 0.7137 (t) cc_final: 0.6261 (p) REVERT: K 103 LYS cc_start: 0.7929 (tttp) cc_final: 0.7721 (tttm) REVERT: E 588 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8915 (mmmm) REVERT: E 592 PHE cc_start: 0.8203 (t80) cc_final: 0.7978 (t80) REVERT: C 48 ILE cc_start: 0.4134 (mp) cc_final: 0.3917 (mm) REVERT: C 229 MET cc_start: 0.8569 (pmm) cc_final: 0.8275 (pmm) REVERT: C 230 THR cc_start: 0.6694 (m) cc_final: 0.6384 (m) REVERT: C 235 GLN cc_start: 0.9257 (tt0) cc_final: 0.8503 (tm-30) REVERT: I 46 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7634 (mm-30) REVERT: I 48 MET cc_start: 0.9047 (mtp) cc_final: 0.8734 (mtp) REVERT: I 64 GLN cc_start: 0.8326 (mt0) cc_final: 0.7993 (tp40) REVERT: I 97 ILE cc_start: 0.8406 (tp) cc_final: 0.8195 (tp) REVERT: L 33 LEU cc_start: 0.8818 (tp) cc_final: 0.8575 (tp) REVERT: L 58 ILE cc_start: 0.7524 (tt) cc_final: 0.6362 (tt) REVERT: L 70 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8755 (mm-30) REVERT: L 88 CYS cc_start: 0.8152 (m) cc_final: 0.7184 (p) REVERT: L 90 GLN cc_start: 0.7133 (tt0) cc_final: 0.6588 (tt0) REVERT: L 97 THR cc_start: 0.7257 (p) cc_final: 0.6413 (p) REVERT: F 545 GLU cc_start: 0.7574 (pm20) cc_final: 0.7254 (mt-10) REVERT: F 564 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8546 (tm-30) outliers start: 5 outliers final: 3 residues processed: 306 average time/residue: 0.3132 time to fit residues: 132.3695 Evaluate side-chains 217 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 114 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 146 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 151 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 263 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS F 602 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.123218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.091984 restraints weight = 34755.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.093554 restraints weight = 18570.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.095168 restraints weight = 11856.561| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13510 Z= 0.153 Angle : 0.729 8.802 18398 Z= 0.380 Chirality : 0.049 0.268 2106 Planarity : 0.005 0.045 2310 Dihedral : 8.861 69.086 2268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.94 (0.20), residues: 1614 helix: 0.57 (0.36), residues: 234 sheet: -0.45 (0.23), residues: 486 loop : -1.03 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 103 HIS 0.006 0.002 HIS B 154 PHE 0.016 0.002 PHE L 83 TYR 0.037 0.002 TYR D 534 ARG 0.012 0.001 ARG I 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 9) link_NAG-ASN : angle 2.04997 ( 27) link_ALPHA1-6 : bond 0.00916 ( 3) link_ALPHA1-6 : angle 2.38461 ( 9) link_BETA1-4 : bond 0.00299 ( 9) link_BETA1-4 : angle 2.33881 ( 27) link_ALPHA1-3 : bond 0.00952 ( 3) link_ALPHA1-3 : angle 1.43903 ( 9) hydrogen bonds : bond 0.04281 ( 461) hydrogen bonds : angle 6.05529 ( 1302) SS BOND : bond 0.00589 ( 13) SS BOND : angle 2.28786 ( 26) covalent geometry : bond 0.00350 (13473) covalent geometry : angle 0.71365 (18300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7582 (p) cc_final: 0.6792 (t) REVERT: A 148 PRO cc_start: 0.8296 (Cg_exo) cc_final: 0.7921 (Cg_endo) REVERT: A 167 SER cc_start: 0.8437 (m) cc_final: 0.8151 (p) REVERT: A 229 MET cc_start: 0.8458 (pmm) cc_final: 0.8238 (pmm) REVERT: A 235 GLN cc_start: 0.9094 (tt0) cc_final: 0.8380 (tm-30) REVERT: G 19 LYS cc_start: 0.8933 (tptt) cc_final: 0.8418 (tptp) REVERT: G 48 MET cc_start: 0.8939 (mtp) cc_final: 0.8346 (mtp) REVERT: G 80 MET cc_start: 0.8670 (ptp) cc_final: 0.8408 (ptm) REVERT: J 70 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9049 (mm-30) REVERT: J 75 ILE cc_start: 0.9491 (mt) cc_final: 0.9171 (tt) REVERT: B 77 THR cc_start: 0.7609 (p) cc_final: 0.7049 (t) REVERT: B 130 ARG cc_start: 0.7484 (ptt-90) cc_final: 0.6654 (ptt-90) REVERT: B 229 MET cc_start: 0.8488 (pmm) cc_final: 0.8242 (pmm) REVERT: B 230 THR cc_start: 0.6800 (m) cc_final: 0.6574 (m) REVERT: B 235 GLN cc_start: 0.9136 (tt0) cc_final: 0.8368 (tm-30) REVERT: H 19 LYS cc_start: 0.8918 (tptt) cc_final: 0.8367 (tptp) REVERT: H 20 VAL cc_start: 0.8672 (t) cc_final: 0.8169 (t) REVERT: H 48 MET cc_start: 0.8375 (mtp) cc_final: 0.7775 (mtp) REVERT: H 52 MET cc_start: 0.8590 (mpp) cc_final: 0.8341 (mmt) REVERT: H 90 TYR cc_start: 0.8398 (m-10) cc_final: 0.8008 (m-80) REVERT: K 27 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7122 (tm-30) REVERT: K 71 PHE cc_start: 0.8224 (m-80) cc_final: 0.7755 (m-10) REVERT: K 90 GLN cc_start: 0.7477 (tt0) cc_final: 0.6859 (tt0) REVERT: K 97 THR cc_start: 0.7080 (t) cc_final: 0.6344 (p) REVERT: E 596 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7378 (tpp80) REVERT: C 229 MET cc_start: 0.8562 (pmm) cc_final: 0.8267 (pmm) REVERT: C 230 THR cc_start: 0.6475 (m) cc_final: 0.6244 (m) REVERT: C 235 GLN cc_start: 0.9205 (tt0) cc_final: 0.8458 (tm-30) REVERT: I 23 ARG cc_start: 0.8837 (tpt170) cc_final: 0.8436 (tpp-160) REVERT: I 46 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7591 (mm-30) REVERT: I 48 MET cc_start: 0.9003 (mtp) cc_final: 0.8627 (mtp) REVERT: I 64 GLN cc_start: 0.8322 (mt0) cc_final: 0.8077 (tp40) REVERT: I 81 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7591 (tp30) REVERT: L 4 MET cc_start: 0.3729 (tpt) cc_final: 0.3126 (tpp) REVERT: L 27 GLN cc_start: 0.7426 (tm-30) cc_final: 0.7080 (tm-30) REVERT: L 33 LEU cc_start: 0.8908 (tp) cc_final: 0.8625 (tp) REVERT: L 71 PHE cc_start: 0.8484 (m-10) cc_final: 0.7957 (m-10) REVERT: L 73 LEU cc_start: 0.8866 (tp) cc_final: 0.8646 (tp) REVERT: L 88 CYS cc_start: 0.8099 (m) cc_final: 0.7466 (p) REVERT: L 90 GLN cc_start: 0.7111 (tt0) cc_final: 0.6633 (tt0) REVERT: L 97 THR cc_start: 0.7207 (p) cc_final: 0.6632 (p) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.3370 time to fit residues: 138.0449 Evaluate side-chains 199 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 263 ASN G 64 GLN J 32 ASN B 235 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.120402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087411 restraints weight = 35605.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.090978 restraints weight = 17812.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.092159 restraints weight = 10512.614| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13510 Z= 0.173 Angle : 0.719 8.408 18398 Z= 0.369 Chirality : 0.048 0.235 2106 Planarity : 0.005 0.046 2310 Dihedral : 8.235 62.721 2268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.07 % Allowed : 1.36 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.20), residues: 1614 helix: 1.19 (0.37), residues: 216 sheet: -0.40 (0.23), residues: 498 loop : -1.28 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.007 0.001 HIS G 100C PHE 0.019 0.002 PHE D 592 TYR 0.030 0.002 TYR I 33 ARG 0.009 0.001 ARG I 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 1.90845 ( 27) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 2.59114 ( 9) link_BETA1-4 : bond 0.00419 ( 9) link_BETA1-4 : angle 2.39457 ( 27) link_ALPHA1-3 : bond 0.00840 ( 3) link_ALPHA1-3 : angle 1.59299 ( 9) hydrogen bonds : bond 0.04160 ( 461) hydrogen bonds : angle 5.89035 ( 1302) SS BOND : bond 0.00577 ( 13) SS BOND : angle 1.96750 ( 26) covalent geometry : bond 0.00396 (13473) covalent geometry : angle 0.70368 (18300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7866 (p) cc_final: 0.7106 (t) REVERT: A 167 SER cc_start: 0.8496 (m) cc_final: 0.8205 (p) REVERT: A 229 MET cc_start: 0.8478 (pmm) cc_final: 0.8271 (pmm) REVERT: A 230 THR cc_start: 0.6960 (m) cc_final: 0.6696 (m) REVERT: A 235 GLN cc_start: 0.9069 (tt0) cc_final: 0.8401 (tm-30) REVERT: G 19 LYS cc_start: 0.8875 (tptt) cc_final: 0.8285 (tptp) REVERT: G 48 MET cc_start: 0.9041 (mtp) cc_final: 0.8636 (mtp) REVERT: G 53 ILE cc_start: 0.8178 (tt) cc_final: 0.7893 (pt) REVERT: G 64 GLN cc_start: 0.8191 (mm110) cc_final: 0.7907 (mm-40) REVERT: G 80 MET cc_start: 0.8749 (ptp) cc_final: 0.8365 (ptm) REVERT: J 70 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9111 (mm-30) REVERT: B 77 THR cc_start: 0.7579 (p) cc_final: 0.7004 (t) REVERT: B 130 ARG cc_start: 0.7656 (ptt-90) cc_final: 0.6739 (ptt-90) REVERT: B 229 MET cc_start: 0.8512 (pmm) cc_final: 0.8270 (pmm) REVERT: B 230 THR cc_start: 0.6775 (m) cc_final: 0.6513 (m) REVERT: B 235 GLN cc_start: 0.9101 (tt0) cc_final: 0.8312 (tm-30) REVERT: H 19 LYS cc_start: 0.8903 (tptt) cc_final: 0.8310 (tptp) REVERT: H 20 VAL cc_start: 0.8749 (t) cc_final: 0.8347 (t) REVERT: H 48 MET cc_start: 0.8534 (mtp) cc_final: 0.7958 (mtp) REVERT: H 52 MET cc_start: 0.8780 (mpp) cc_final: 0.8236 (mmt) REVERT: H 80 MET cc_start: 0.8302 (mtp) cc_final: 0.8091 (mtp) REVERT: H 90 TYR cc_start: 0.8422 (m-10) cc_final: 0.8032 (m-80) REVERT: K 71 PHE cc_start: 0.8641 (m-80) cc_final: 0.7615 (m-10) REVERT: K 90 GLN cc_start: 0.7770 (tt0) cc_final: 0.6938 (tt0) REVERT: K 97 THR cc_start: 0.7262 (t) cc_final: 0.5938 (p) REVERT: C 77 THR cc_start: 0.7584 (p) cc_final: 0.6880 (t) REVERT: C 229 MET cc_start: 0.8563 (pmm) cc_final: 0.8319 (pmm) REVERT: C 230 THR cc_start: 0.6812 (m) cc_final: 0.6520 (m) REVERT: C 235 GLN cc_start: 0.9181 (tt0) cc_final: 0.8406 (tm-30) REVERT: I 23 ARG cc_start: 0.8775 (tpt170) cc_final: 0.8441 (tpp-160) REVERT: I 46 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7537 (mm-30) REVERT: I 48 MET cc_start: 0.9074 (mtp) cc_final: 0.8720 (mtp) REVERT: I 52 MET cc_start: 0.8148 (mpp) cc_final: 0.7291 (mpp) REVERT: I 56 LEU cc_start: 0.8113 (mt) cc_final: 0.7840 (mp) REVERT: I 64 GLN cc_start: 0.8396 (mt0) cc_final: 0.8150 (tp40) REVERT: I 81 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7322 (tp30) REVERT: L 4 MET cc_start: 0.4230 (tpt) cc_final: 0.3270 (tpp) REVERT: L 27 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7360 (tm-30) REVERT: L 71 PHE cc_start: 0.8194 (m-10) cc_final: 0.7933 (m-10) REVERT: L 88 CYS cc_start: 0.8237 (m) cc_final: 0.7561 (p) REVERT: L 90 GLN cc_start: 0.7255 (tt0) cc_final: 0.6509 (tt0) REVERT: L 97 THR cc_start: 0.7301 (p) cc_final: 0.6151 (p) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.2764 time to fit residues: 109.6744 Evaluate side-chains 206 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.120679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.085255 restraints weight = 37121.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.088926 restraints weight = 19275.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.091402 restraints weight = 12443.687| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13510 Z= 0.167 Angle : 0.711 8.135 18398 Z= 0.366 Chirality : 0.048 0.241 2106 Planarity : 0.006 0.119 2310 Dihedral : 7.891 57.668 2268 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1614 helix: 1.66 (0.38), residues: 198 sheet: -0.41 (0.23), residues: 501 loop : -1.25 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 275 HIS 0.008 0.001 HIS G 100C PHE 0.018 0.002 PHE H 100E TYR 0.024 0.002 TYR H 33 ARG 0.007 0.001 ARG C 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.78491 ( 27) link_ALPHA1-6 : bond 0.00815 ( 3) link_ALPHA1-6 : angle 2.64126 ( 9) link_BETA1-4 : bond 0.00324 ( 9) link_BETA1-4 : angle 2.32101 ( 27) link_ALPHA1-3 : bond 0.00866 ( 3) link_ALPHA1-3 : angle 1.38744 ( 9) hydrogen bonds : bond 0.04022 ( 461) hydrogen bonds : angle 5.85722 ( 1302) SS BOND : bond 0.00447 ( 13) SS BOND : angle 1.84675 ( 26) covalent geometry : bond 0.00378 (13473) covalent geometry : angle 0.69707 (18300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7882 (p) cc_final: 0.7305 (t) REVERT: A 167 SER cc_start: 0.8448 (m) cc_final: 0.8192 (p) REVERT: A 230 THR cc_start: 0.7174 (m) cc_final: 0.6901 (m) REVERT: A 235 GLN cc_start: 0.9107 (tt0) cc_final: 0.8405 (tm-30) REVERT: G 19 LYS cc_start: 0.8862 (tptt) cc_final: 0.8270 (tptp) REVERT: G 20 VAL cc_start: 0.8446 (t) cc_final: 0.8206 (t) REVERT: G 46 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7103 (mm-30) REVERT: G 48 MET cc_start: 0.9090 (mtp) cc_final: 0.8711 (mtp) REVERT: G 52 MET cc_start: 0.8394 (mmp) cc_final: 0.8175 (mmm) REVERT: G 80 MET cc_start: 0.8788 (ptp) cc_final: 0.8305 (ptm) REVERT: G 94 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6913 (mtp180) REVERT: J 70 GLU cc_start: 0.9362 (mt-10) cc_final: 0.9099 (mm-30) REVERT: B 77 THR cc_start: 0.7720 (p) cc_final: 0.7181 (t) REVERT: B 230 THR cc_start: 0.7080 (m) cc_final: 0.6813 (m) REVERT: B 235 GLN cc_start: 0.9165 (tt0) cc_final: 0.8273 (tm-30) REVERT: H 19 LYS cc_start: 0.8857 (tptt) cc_final: 0.8236 (tptp) REVERT: H 20 VAL cc_start: 0.8653 (t) cc_final: 0.8247 (t) REVERT: H 35 ILE cc_start: 0.8866 (mm) cc_final: 0.8487 (tp) REVERT: H 46 GLU cc_start: 0.8292 (tp30) cc_final: 0.7920 (mp0) REVERT: H 48 MET cc_start: 0.8565 (mtp) cc_final: 0.7949 (mtp) REVERT: H 53 ILE cc_start: 0.7851 (tt) cc_final: 0.7617 (pt) REVERT: H 80 MET cc_start: 0.8217 (mtp) cc_final: 0.7873 (mtp) REVERT: H 90 TYR cc_start: 0.8454 (m-10) cc_final: 0.8026 (m-80) REVERT: H 97 ILE cc_start: 0.8749 (tp) cc_final: 0.8473 (tp) REVERT: K 70 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8632 (mm-30) REVERT: K 90 GLN cc_start: 0.7787 (tt0) cc_final: 0.7060 (tt0) REVERT: K 97 THR cc_start: 0.7107 (t) cc_final: 0.5792 (p) REVERT: C 77 THR cc_start: 0.7695 (p) cc_final: 0.7031 (t) REVERT: C 230 THR cc_start: 0.6960 (m) cc_final: 0.6652 (m) REVERT: C 235 GLN cc_start: 0.9210 (tt0) cc_final: 0.8430 (tm-30) REVERT: I 23 ARG cc_start: 0.8841 (tpt170) cc_final: 0.8467 (tpp-160) REVERT: I 46 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7475 (mm-30) REVERT: I 48 MET cc_start: 0.9098 (mtp) cc_final: 0.8796 (mtp) REVERT: I 52 MET cc_start: 0.8024 (mpp) cc_final: 0.7388 (mpp) REVERT: I 64 GLN cc_start: 0.8330 (mt0) cc_final: 0.8130 (tp40) REVERT: I 80 MET cc_start: 0.8903 (ptp) cc_final: 0.8369 (mtm) REVERT: L 27 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7485 (tm-30) REVERT: L 33 LEU cc_start: 0.8789 (tp) cc_final: 0.8440 (tp) REVERT: L 71 PHE cc_start: 0.8691 (m-80) cc_final: 0.7106 (m-10) REVERT: L 90 GLN cc_start: 0.7241 (tt0) cc_final: 0.6732 (tt0) REVERT: L 97 THR cc_start: 0.6934 (p) cc_final: 0.6251 (p) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2902 time to fit residues: 118.3384 Evaluate side-chains 212 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 41 optimal weight: 0.3980 chunk 140 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.121913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.088885 restraints weight = 34668.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092191 restraints weight = 17226.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.092882 restraints weight = 11049.678| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13510 Z= 0.127 Angle : 0.684 11.817 18398 Z= 0.347 Chirality : 0.047 0.244 2106 Planarity : 0.005 0.099 2310 Dihedral : 7.347 51.819 2268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1614 helix: 1.83 (0.39), residues: 198 sheet: -0.44 (0.23), residues: 501 loop : -1.21 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 275 HIS 0.009 0.001 HIS G 100C PHE 0.038 0.002 PHE I 29 TYR 0.021 0.002 TYR H 33 ARG 0.006 0.001 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 1.81264 ( 27) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 2.43231 ( 9) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 2.20788 ( 27) link_ALPHA1-3 : bond 0.01002 ( 3) link_ALPHA1-3 : angle 1.31365 ( 9) hydrogen bonds : bond 0.03729 ( 461) hydrogen bonds : angle 5.51860 ( 1302) SS BOND : bond 0.00348 ( 13) SS BOND : angle 1.66959 ( 26) covalent geometry : bond 0.00292 (13473) covalent geometry : angle 0.67091 (18300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7952 (p) cc_final: 0.7255 (t) REVERT: A 148 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8028 (Cg_endo) REVERT: A 230 THR cc_start: 0.7221 (m) cc_final: 0.6974 (m) REVERT: A 235 GLN cc_start: 0.9074 (tt0) cc_final: 0.8352 (tm-30) REVERT: G 46 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7079 (mm-30) REVERT: G 48 MET cc_start: 0.9086 (mtp) cc_final: 0.8519 (mtp) REVERT: G 52 MET cc_start: 0.8371 (mmp) cc_final: 0.8077 (mmm) REVERT: G 80 MET cc_start: 0.8889 (ptp) cc_final: 0.8360 (ptm) REVERT: G 81 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7634 (tp30) REVERT: G 90 TYR cc_start: 0.8549 (m-80) cc_final: 0.8061 (m-80) REVERT: J 70 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9118 (mm-30) REVERT: J 71 PHE cc_start: 0.8521 (m-10) cc_final: 0.7930 (m-10) REVERT: B 77 THR cc_start: 0.7725 (p) cc_final: 0.7179 (t) REVERT: B 229 MET cc_start: 0.8569 (pmm) cc_final: 0.8312 (pmm) REVERT: B 230 THR cc_start: 0.7120 (m) cc_final: 0.6862 (m) REVERT: B 235 GLN cc_start: 0.9137 (tt0) cc_final: 0.8064 (tm-30) REVERT: H 19 LYS cc_start: 0.8836 (tptt) cc_final: 0.8183 (tptp) REVERT: H 20 VAL cc_start: 0.8679 (t) cc_final: 0.8291 (t) REVERT: H 35 ILE cc_start: 0.9050 (mm) cc_final: 0.8595 (tp) REVERT: H 46 GLU cc_start: 0.8280 (tp30) cc_final: 0.7893 (mp0) REVERT: H 48 MET cc_start: 0.8562 (mtp) cc_final: 0.7986 (mtp) REVERT: H 80 MET cc_start: 0.8192 (mtp) cc_final: 0.7808 (mtp) REVERT: H 90 TYR cc_start: 0.8506 (m-10) cc_final: 0.8081 (m-80) REVERT: K 90 GLN cc_start: 0.7789 (tt0) cc_final: 0.7173 (tt0) REVERT: K 97 THR cc_start: 0.7078 (t) cc_final: 0.5643 (p) REVERT: E 583 SER cc_start: 0.7793 (m) cc_final: 0.7518 (p) REVERT: C 77 THR cc_start: 0.7644 (p) cc_final: 0.6969 (t) REVERT: C 122 LEU cc_start: 0.9347 (mm) cc_final: 0.8985 (mm) REVERT: C 148 PRO cc_start: 0.8110 (Cg_exo) cc_final: 0.7844 (Cg_endo) REVERT: C 229 MET cc_start: 0.8501 (pmm) cc_final: 0.8215 (pmm) REVERT: C 230 THR cc_start: 0.6883 (m) cc_final: 0.6549 (m) REVERT: C 235 GLN cc_start: 0.9176 (tt0) cc_final: 0.8371 (tm-30) REVERT: I 19 LYS cc_start: 0.8950 (tptt) cc_final: 0.8333 (tptp) REVERT: I 23 ARG cc_start: 0.8753 (tpt170) cc_final: 0.8403 (tpp-160) REVERT: I 48 MET cc_start: 0.9092 (mtp) cc_final: 0.8726 (mtp) REVERT: I 52 MET cc_start: 0.8171 (mpp) cc_final: 0.7583 (mpp) REVERT: I 80 MET cc_start: 0.8866 (ptp) cc_final: 0.8357 (ptm) REVERT: L 27 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7526 (tm-30) REVERT: L 71 PHE cc_start: 0.8621 (m-80) cc_final: 0.7080 (m-10) REVERT: L 90 GLN cc_start: 0.7215 (tt0) cc_final: 0.6599 (tt0) REVERT: L 97 THR cc_start: 0.6944 (p) cc_final: 0.6194 (p) REVERT: F 583 SER cc_start: 0.7760 (m) cc_final: 0.7240 (p) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2753 time to fit residues: 107.8530 Evaluate side-chains 206 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.0000 chunk 129 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 140 optimal weight: 30.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN J 32 ASN J 37 GLN B 263 ASN H 64 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.122719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087342 restraints weight = 36230.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091270 restraints weight = 18468.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.093912 restraints weight = 11690.733| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13510 Z= 0.130 Angle : 0.683 7.883 18398 Z= 0.348 Chirality : 0.047 0.239 2106 Planarity : 0.005 0.052 2310 Dihedral : 7.023 46.853 2268 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.21), residues: 1614 helix: 1.75 (0.39), residues: 198 sheet: -0.50 (0.22), residues: 498 loop : -1.11 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 104 HIS 0.009 0.001 HIS H 100C PHE 0.011 0.001 PHE H 100E TYR 0.018 0.002 TYR E 534 ARG 0.008 0.001 ARG A 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 9) link_NAG-ASN : angle 1.70413 ( 27) link_ALPHA1-6 : bond 0.01008 ( 3) link_ALPHA1-6 : angle 2.41377 ( 9) link_BETA1-4 : bond 0.00460 ( 9) link_BETA1-4 : angle 2.19755 ( 27) link_ALPHA1-3 : bond 0.01059 ( 3) link_ALPHA1-3 : angle 1.23170 ( 9) hydrogen bonds : bond 0.03766 ( 461) hydrogen bonds : angle 5.43267 ( 1302) SS BOND : bond 0.00337 ( 13) SS BOND : angle 1.87860 ( 26) covalent geometry : bond 0.00299 (13473) covalent geometry : angle 0.66974 (18300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7947 (p) cc_final: 0.7253 (t) REVERT: A 119 SER cc_start: 0.8736 (m) cc_final: 0.8214 (p) REVERT: A 230 THR cc_start: 0.7166 (m) cc_final: 0.6945 (m) REVERT: A 235 GLN cc_start: 0.9083 (tt0) cc_final: 0.8274 (tm-30) REVERT: G 46 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7107 (mm-30) REVERT: G 48 MET cc_start: 0.9106 (mtp) cc_final: 0.8547 (mtp) REVERT: G 53 ILE cc_start: 0.8313 (tt) cc_final: 0.7715 (pt) REVERT: G 80 MET cc_start: 0.8668 (ptp) cc_final: 0.8251 (ptm) REVERT: G 90 TYR cc_start: 0.8512 (m-80) cc_final: 0.8063 (m-80) REVERT: J 70 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9091 (mm-30) REVERT: J 71 PHE cc_start: 0.8519 (m-10) cc_final: 0.7950 (m-10) REVERT: B 77 THR cc_start: 0.7746 (p) cc_final: 0.7195 (t) REVERT: B 229 MET cc_start: 0.8444 (pmm) cc_final: 0.8167 (pmm) REVERT: B 230 THR cc_start: 0.7263 (m) cc_final: 0.7027 (m) REVERT: B 235 GLN cc_start: 0.9144 (tt0) cc_final: 0.7992 (tm-30) REVERT: H 19 LYS cc_start: 0.8655 (tptt) cc_final: 0.8391 (tptp) REVERT: H 20 VAL cc_start: 0.8693 (t) cc_final: 0.8090 (t) REVERT: H 35 ILE cc_start: 0.8877 (mm) cc_final: 0.8356 (tp) REVERT: H 46 GLU cc_start: 0.8314 (tp30) cc_final: 0.7896 (mp0) REVERT: H 48 MET cc_start: 0.8608 (mtp) cc_final: 0.8096 (mtp) REVERT: H 80 MET cc_start: 0.8273 (mtp) cc_final: 0.7813 (mtp) REVERT: H 90 TYR cc_start: 0.8546 (m-10) cc_final: 0.8099 (m-80) REVERT: K 73 LEU cc_start: 0.8936 (tp) cc_final: 0.7556 (tp) REVERT: K 90 GLN cc_start: 0.7853 (tt0) cc_final: 0.7240 (tt0) REVERT: K 97 THR cc_start: 0.6887 (t) cc_final: 0.5510 (p) REVERT: E 583 SER cc_start: 0.7934 (m) cc_final: 0.7662 (p) REVERT: C 77 THR cc_start: 0.7636 (p) cc_final: 0.6942 (t) REVERT: C 122 LEU cc_start: 0.9336 (mm) cc_final: 0.8797 (mm) REVERT: C 148 PRO cc_start: 0.8186 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: C 229 MET cc_start: 0.8364 (pmm) cc_final: 0.8135 (pmm) REVERT: C 235 GLN cc_start: 0.9153 (tt0) cc_final: 0.8304 (tm-30) REVERT: I 20 VAL cc_start: 0.8216 (t) cc_final: 0.8005 (t) REVERT: I 23 ARG cc_start: 0.8809 (tpt170) cc_final: 0.8460 (tpp-160) REVERT: I 48 MET cc_start: 0.9115 (mtp) cc_final: 0.8772 (mtp) REVERT: I 59 SER cc_start: 0.7837 (p) cc_final: 0.7605 (p) REVERT: I 80 MET cc_start: 0.8833 (ptp) cc_final: 0.8622 (ptp) REVERT: I 81 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7297 (tp30) REVERT: L 27 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7503 (tm-30) REVERT: L 33 LEU cc_start: 0.8789 (tp) cc_final: 0.8582 (tp) REVERT: L 42 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8646 (mp10) REVERT: L 71 PHE cc_start: 0.8653 (m-80) cc_final: 0.7074 (m-10) REVERT: L 90 GLN cc_start: 0.7146 (tt0) cc_final: 0.6560 (tt0) REVERT: L 97 THR cc_start: 0.6723 (p) cc_final: 0.5954 (p) REVERT: F 583 SER cc_start: 0.7799 (m) cc_final: 0.7503 (p) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2754 time to fit residues: 110.4988 Evaluate side-chains 212 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 116 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 72 optimal weight: 0.0670 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 263 ASN J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN H 64 GLN H 79 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.121572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.085938 restraints weight = 36225.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.089752 restraints weight = 18599.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092334 restraints weight = 11899.279| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13510 Z= 0.155 Angle : 0.712 12.815 18398 Z= 0.360 Chirality : 0.047 0.225 2106 Planarity : 0.008 0.294 2310 Dihedral : 7.582 144.076 2268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1614 helix: 1.87 (0.39), residues: 198 sheet: -0.85 (0.21), residues: 543 loop : -1.08 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP K 35 HIS 0.013 0.002 HIS H 100C PHE 0.020 0.002 PHE H 100E TYR 0.028 0.002 TYR G 33 ARG 0.010 0.001 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 9) link_NAG-ASN : angle 1.60794 ( 27) link_ALPHA1-6 : bond 0.00768 ( 3) link_ALPHA1-6 : angle 2.49053 ( 9) link_BETA1-4 : bond 0.00428 ( 9) link_BETA1-4 : angle 2.19921 ( 27) link_ALPHA1-3 : bond 0.00888 ( 3) link_ALPHA1-3 : angle 1.31961 ( 9) hydrogen bonds : bond 0.03808 ( 461) hydrogen bonds : angle 5.54554 ( 1302) SS BOND : bond 0.00361 ( 13) SS BOND : angle 1.96832 ( 26) covalent geometry : bond 0.00358 (13473) covalent geometry : angle 0.69903 (18300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7987 (p) cc_final: 0.7430 (t) REVERT: A 119 SER cc_start: 0.8898 (m) cc_final: 0.8411 (p) REVERT: A 230 THR cc_start: 0.7247 (m) cc_final: 0.7019 (m) REVERT: A 235 GLN cc_start: 0.9101 (tt0) cc_final: 0.8364 (tm-30) REVERT: G 46 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7128 (mm-30) REVERT: G 48 MET cc_start: 0.9157 (mtp) cc_final: 0.8708 (mtp) REVERT: G 80 MET cc_start: 0.8697 (ptp) cc_final: 0.8334 (ptm) REVERT: G 90 TYR cc_start: 0.8574 (m-80) cc_final: 0.8171 (m-80) REVERT: J 70 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9078 (mm-30) REVERT: J 71 PHE cc_start: 0.8604 (m-10) cc_final: 0.8055 (m-10) REVERT: J 75 ILE cc_start: 0.9209 (tt) cc_final: 0.8827 (tt) REVERT: B 69 ASN cc_start: 0.8188 (m-40) cc_final: 0.7950 (m110) REVERT: B 77 THR cc_start: 0.7828 (p) cc_final: 0.7304 (t) REVERT: B 229 MET cc_start: 0.8463 (pmm) cc_final: 0.8184 (pmm) REVERT: B 230 THR cc_start: 0.7399 (m) cc_final: 0.7155 (m) REVERT: B 235 GLN cc_start: 0.9141 (tt0) cc_final: 0.8053 (tm-30) REVERT: H 20 VAL cc_start: 0.8557 (t) cc_final: 0.8017 (t) REVERT: H 35 ILE cc_start: 0.8866 (mm) cc_final: 0.8383 (tp) REVERT: H 46 GLU cc_start: 0.8327 (tp30) cc_final: 0.7890 (mp0) REVERT: H 48 MET cc_start: 0.8632 (mtp) cc_final: 0.8111 (mtp) REVERT: H 80 MET cc_start: 0.8228 (mtp) cc_final: 0.7814 (mtp) REVERT: H 90 TYR cc_start: 0.8540 (m-10) cc_final: 0.8124 (m-80) REVERT: K 42 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8599 (mm110) REVERT: K 90 GLN cc_start: 0.7844 (tt0) cc_final: 0.7093 (tt0) REVERT: K 97 THR cc_start: 0.6933 (t) cc_final: 0.5654 (p) REVERT: E 583 SER cc_start: 0.7986 (m) cc_final: 0.7774 (p) REVERT: C 77 THR cc_start: 0.7628 (p) cc_final: 0.6973 (t) REVERT: C 148 PRO cc_start: 0.8290 (Cg_exo) cc_final: 0.8039 (Cg_endo) REVERT: C 229 MET cc_start: 0.8402 (pmm) cc_final: 0.8180 (pmm) REVERT: C 235 GLN cc_start: 0.9174 (tt0) cc_final: 0.8271 (tm-30) REVERT: I 23 ARG cc_start: 0.8806 (tpt170) cc_final: 0.8446 (tpp-160) REVERT: I 48 MET cc_start: 0.9130 (mtp) cc_final: 0.8898 (mtp) REVERT: I 52 MET cc_start: 0.7805 (mmp) cc_final: 0.7600 (mmp) REVERT: I 59 SER cc_start: 0.7760 (p) cc_final: 0.7518 (p) REVERT: I 81 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7431 (tp30) REVERT: L 42 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8652 (mp10) REVERT: L 90 GLN cc_start: 0.7175 (tt0) cc_final: 0.6834 (tt0) REVERT: L 97 THR cc_start: 0.6703 (p) cc_final: 0.5910 (p) REVERT: F 583 SER cc_start: 0.7914 (m) cc_final: 0.7623 (p) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.2533 time to fit residues: 103.9572 Evaluate side-chains 221 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 100 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN E 521 GLN C 69 ASN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.085005 restraints weight = 36246.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.088725 restraints weight = 18814.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091213 restraints weight = 12029.875| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.7646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13510 Z= 0.160 Angle : 0.712 8.129 18398 Z= 0.365 Chirality : 0.047 0.241 2106 Planarity : 0.006 0.148 2310 Dihedral : 7.312 162.267 2268 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.21), residues: 1614 helix: 1.90 (0.39), residues: 198 sheet: -0.85 (0.22), residues: 516 loop : -1.11 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP I 103 HIS 0.013 0.002 HIS H 100C PHE 0.015 0.002 PHE G 100E TYR 0.018 0.002 TYR G 33 ARG 0.006 0.001 ARG C 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 9) link_NAG-ASN : angle 1.52630 ( 27) link_ALPHA1-6 : bond 0.00549 ( 3) link_ALPHA1-6 : angle 2.05273 ( 9) link_BETA1-4 : bond 0.00477 ( 9) link_BETA1-4 : angle 2.22290 ( 27) link_ALPHA1-3 : bond 0.00813 ( 3) link_ALPHA1-3 : angle 1.28101 ( 9) hydrogen bonds : bond 0.03885 ( 461) hydrogen bonds : angle 5.58039 ( 1302) SS BOND : bond 0.00408 ( 13) SS BOND : angle 2.01398 ( 26) covalent geometry : bond 0.00369 (13473) covalent geometry : angle 0.69998 (18300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8012 (p) cc_final: 0.7480 (t) REVERT: A 119 SER cc_start: 0.9015 (m) cc_final: 0.8504 (p) REVERT: A 167 SER cc_start: 0.8398 (t) cc_final: 0.7779 (p) REVERT: A 229 MET cc_start: 0.8445 (pmm) cc_final: 0.8226 (pmm) REVERT: A 230 THR cc_start: 0.7372 (m) cc_final: 0.7104 (m) REVERT: A 235 GLN cc_start: 0.9095 (tt0) cc_final: 0.8338 (tm-30) REVERT: G 35 ILE cc_start: 0.8826 (mm) cc_final: 0.8508 (tp) REVERT: G 46 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7145 (mm-30) REVERT: G 48 MET cc_start: 0.9141 (mtp) cc_final: 0.8693 (mtp) REVERT: G 53 ILE cc_start: 0.8435 (tt) cc_final: 0.7803 (pt) REVERT: G 80 MET cc_start: 0.8773 (ptp) cc_final: 0.8494 (ptm) REVERT: G 81 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7190 (tp30) REVERT: G 90 TYR cc_start: 0.8650 (m-80) cc_final: 0.8286 (m-80) REVERT: J 42 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8545 (mp10) REVERT: J 70 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9084 (mm-30) REVERT: J 71 PHE cc_start: 0.8585 (m-10) cc_final: 0.8112 (m-10) REVERT: J 75 ILE cc_start: 0.9139 (tt) cc_final: 0.8863 (tp) REVERT: B 77 THR cc_start: 0.7938 (p) cc_final: 0.7435 (t) REVERT: B 229 MET cc_start: 0.8486 (pmm) cc_final: 0.8180 (pmm) REVERT: B 230 THR cc_start: 0.7468 (m) cc_final: 0.7196 (m) REVERT: B 235 GLN cc_start: 0.9141 (tt0) cc_final: 0.8082 (tm-30) REVERT: H 20 VAL cc_start: 0.8296 (t) cc_final: 0.8059 (t) REVERT: H 35 ILE cc_start: 0.8791 (mm) cc_final: 0.8350 (tp) REVERT: H 46 GLU cc_start: 0.8322 (tp30) cc_final: 0.7889 (mp0) REVERT: H 48 MET cc_start: 0.8766 (mtp) cc_final: 0.8383 (mtp) REVERT: H 80 MET cc_start: 0.7955 (mtp) cc_final: 0.7649 (mtt) REVERT: H 90 TYR cc_start: 0.8540 (m-10) cc_final: 0.8240 (m-80) REVERT: K 42 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8570 (mm110) REVERT: K 90 GLN cc_start: 0.7966 (tt0) cc_final: 0.7268 (tt0) REVERT: K 97 THR cc_start: 0.7121 (t) cc_final: 0.5816 (p) REVERT: E 583 SER cc_start: 0.8054 (m) cc_final: 0.7816 (p) REVERT: C 77 THR cc_start: 0.7613 (p) cc_final: 0.6957 (t) REVERT: C 122 LEU cc_start: 0.9318 (mm) cc_final: 0.8948 (mm) REVERT: C 148 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.7994 (Cg_endo) REVERT: C 229 MET cc_start: 0.8427 (pmm) cc_final: 0.8219 (pmm) REVERT: C 235 GLN cc_start: 0.9206 (tt0) cc_final: 0.8309 (tm-30) REVERT: I 19 LYS cc_start: 0.8874 (tptt) cc_final: 0.8327 (tptp) REVERT: I 23 ARG cc_start: 0.8823 (tpt170) cc_final: 0.8483 (tpp-160) REVERT: I 48 MET cc_start: 0.9177 (mtp) cc_final: 0.8857 (mtp) REVERT: I 59 SER cc_start: 0.7705 (p) cc_final: 0.7448 (p) REVERT: I 79 HIS cc_start: 0.8050 (m90) cc_final: 0.7581 (m90) REVERT: I 80 MET cc_start: 0.8649 (pmm) cc_final: 0.7827 (pmm) REVERT: L 42 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8566 (mm110) REVERT: L 75 ILE cc_start: 0.9212 (tt) cc_final: 0.8925 (tt) REVERT: L 90 GLN cc_start: 0.7363 (tt0) cc_final: 0.6715 (tt0) REVERT: L 97 THR cc_start: 0.6808 (p) cc_final: 0.6043 (p) REVERT: F 583 SER cc_start: 0.7914 (m) cc_final: 0.7640 (p) outliers start: 1 outliers final: 1 residues processed: 271 average time/residue: 0.2687 time to fit residues: 106.1749 Evaluate side-chains 208 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 HIS J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN I 79 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.118623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082977 restraints weight = 36978.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.086525 restraints weight = 19434.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088934 restraints weight = 12608.952| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13510 Z= 0.178 Angle : 0.725 9.315 18398 Z= 0.371 Chirality : 0.047 0.246 2106 Planarity : 0.006 0.059 2310 Dihedral : 6.940 173.400 2268 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -1.04 (0.21), residues: 1614 helix: 1.84 (0.38), residues: 198 sheet: -0.99 (0.21), residues: 531 loop : -1.06 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 103 HIS 0.016 0.002 HIS G 100C PHE 0.019 0.002 PHE L 83 TYR 0.038 0.002 TYR I 33 ARG 0.010 0.001 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 9) link_NAG-ASN : angle 1.51136 ( 27) link_ALPHA1-6 : bond 0.00163 ( 3) link_ALPHA1-6 : angle 1.94583 ( 9) link_BETA1-4 : bond 0.00445 ( 9) link_BETA1-4 : angle 2.26340 ( 27) link_ALPHA1-3 : bond 0.00769 ( 3) link_ALPHA1-3 : angle 1.36668 ( 9) hydrogen bonds : bond 0.03967 ( 461) hydrogen bonds : angle 5.63403 ( 1302) SS BOND : bond 0.00365 ( 13) SS BOND : angle 1.75944 ( 26) covalent geometry : bond 0.00412 (13473) covalent geometry : angle 0.71458 (18300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5103.55 seconds wall clock time: 91 minutes 30.78 seconds (5490.78 seconds total)