Starting phenix.real_space_refine on Fri Jul 3 09:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_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_2026/7kew_22841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.map" model { file = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kew_22841/07_2026/7kew_22841.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: "J" 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: "D" 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 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 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 chiralities: 1 Restraints were copied for chains: B, C, H, I, K, L, E, F, N, Q, P, R Time building chain proxies: 1.98, per 1000 atoms: 0.15 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=21, 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 B 53 " - pdb=" SG CYS E 609 " distance=2.08 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.08 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.10 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.10 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.04 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " 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: 0.98 Conformation dependent library (CDL) restraints added in 373.5 milliseconds 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: 0.49 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: 2.24 Time building geometry restraints manager: 1.23 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 - 17.10: 7536 17.10 - 34.19: 177 34.19 - 51.29: 48 51.29 - 68.39: 33 68.39 - 85.48: 6 Dihedral angle restraints: 7800 sinusoidal: 3093 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 7797 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: 2.40 - 2.90: 5329 2.90 - 3.40: 12294 3.40 - 3.90: 23301 3.90 - 4.40: 26627 4.40 - 4.90: 41730 Nonbonded interactions: 109281 Sorted by model distance: nonbonded pdb=" N PRO B 187 " pdb=" O PRO B 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO C 187 " pdb=" O PRO C 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO A 187 " pdb=" O PRO A 187 " model vdw 2.403 2.496 nonbonded pdb=" N ARG C 247 " pdb=" N PHE C 248 " model vdw 2.443 2.560 nonbonded pdb=" N ARG B 247 " pdb=" N PHE B 248 " model vdw 2.444 2.560 ... (remaining 109276 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'E' 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 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 13518 Z= 1.151 Angle : 1.895 13.024 18414 Z= 1.237 Chirality : 0.117 0.517 2106 Planarity : 0.009 0.037 2310 Dihedral : 9.668 85.481 4725 Min Nonbonded Distance : 2.402 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG F 559 TYR 0.066 0.013 TYR D 534 PHE 0.031 0.007 PHE H 29 TRP 0.065 0.013 TRP H 103 HIS 0.008 0.002 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.02171 / 1.14 (13473) covalent geometry : angle 1.88152 / 1.24 (18300) SS BOND : bond 0.03240 / 2.10 ( 21) SS BOND : angle 2.70477 / 1.80 ( 42) hydrogen bonds : bond 0.17125 / 11.63 ( 461) hydrogen bonds : angle 7.86842 / 5.62 ( 1302) link_ALPHA1-3 : bond 0.08348 / 3.86 ( 3) link_ALPHA1-3 : angle 3.75787 / 1.85 ( 9) link_ALPHA1-6 : bond 0.05519 / 2.55 ( 3) link_ALPHA1-6 : angle 3.13911 / 1.55 ( 9) link_BETA1-4 : bond 0.07290 / 3.94 ( 9) link_BETA1-4 : angle 5.30207 / 3.17 ( 27) link_NAG-ASN : bond 0.07894 / 4.20 ( 9) link_NAG-ASN : angle 1.59115 / 1.05 ( 27) *********************** 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 : 0.486 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: 0.6661 (tp30) REVERT: A 230 THR cc_start: 0.7277 (m) cc_final: 0.6754 (m) REVERT: A 235 GLN cc_start: 0.9171 (tt0) cc_final: 0.8889 (tm-30) REVERT: G 48 MET cc_start: 0.8819 (mtp) cc_final: 0.8365 (mtp) REVERT: J 70 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8776 (mm-30) REVERT: J 97 THR cc_start: 0.7532 (t) cc_final: 0.6248 (p) REVERT: B 156 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6769 (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: 0.8330 (mtp) REVERT: H 101 ASP cc_start: 0.7210 (m-30) cc_final: 0.6878 (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: 0.6527 (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: 0.6466 (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: 0.8358 (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: 0.7234 (mt-10) REVERT: I 101 ASP cc_start: 0.7397 (m-30) cc_final: 0.6887 (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: 0.1192 time to fit residues: 84.2270 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 : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 GLN J 32 ASN D 602 HIS H 64 GLN K 32 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS L 6 GLN L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.130413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097155 restraints weight = 33313.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101297 restraints weight = 19360.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104266 restraints weight = 10252.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105966 restraints weight = 7695.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106074 restraints weight = 7034.089| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13518 Z= 0.209 Angle : 0.841 9.471 18414 Z= 0.442 Chirality : 0.049 0.243 2106 Planarity : 0.006 0.051 2310 Dihedral : 6.153 31.914 1782 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1614 helix: 0.54 (0.34), residues: 231 sheet: 0.11 (0.27), residues: 387 loop : -0.47 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.034 0.003 TYR D 534 PHE 0.047 0.003 PHE G 29 TRP 0.021 0.003 TRP C 275 HIS 0.006 0.002 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (13473) covalent geometry : angle 0.81976 / 0.44 (18300) SS BOND : bond 0.00524 / 0.29 ( 21) SS BOND : angle 2.07854 / 1.50 ( 42) hydrogen bonds : bond 0.05107 / 3.41 ( 461) hydrogen bonds : angle 6.51005 / 4.69 ( 1302) link_ALPHA1-3 : bond 0.01009 / 0.46 ( 3) link_ALPHA1-3 : angle 1.70946 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00643 / 0.30 ( 3) link_ALPHA1-6 : angle 1.62798 / 0.87 ( 9) link_BETA1-4 : bond 0.00783 / 0.43 ( 9) link_BETA1-4 : angle 3.01548 / 2.01 ( 27) link_NAG-ASN : bond 0.00524 / 0.31 ( 9) link_NAG-ASN : angle 3.01410 / 1.82 ( 27) *********************** 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 : 0.368 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8528 (mttm) REVERT: A 126 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: A 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8750 (tm-30) REVERT: G 37 VAL cc_start: 0.8429 (m) cc_final: 0.8196 (m) REVERT: G 46 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7302 (mm-30) REVERT: G 48 MET cc_start: 0.8620 (mtp) cc_final: 0.8131 (mtp) REVERT: G 52 MET cc_start: 0.7806 (mmm) cc_final: 0.7428 (mmm) REVERT: G 53 ILE cc_start: 0.8109 (tt) cc_final: 0.7792 (mm) REVERT: J 70 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8911 (mm-30) REVERT: J 97 THR cc_start: 0.6182 (t) cc_final: 0.4979 (p) REVERT: B 120 GLU cc_start: 0.7256 (pp20) cc_final: 0.7021 (pp20) REVERT: B 130 ARG cc_start: 0.6869 (ptt-90) cc_final: 0.6399 (ptt90) REVERT: B 156 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6980 (tp30) REVERT: B 235 GLN cc_start: 0.9184 (tt0) cc_final: 0.8596 (tm-30) REVERT: H 20 VAL cc_start: 0.8722 (t) cc_final: 0.8412 (p) REVERT: H 32 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8728 (tptp) REVERT: H 33 TYR cc_start: 0.7649 (m-80) cc_final: 0.7357 (m-80) REVERT: H 46 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7135 (mm-30) REVERT: H 96 GLU cc_start: 0.7696 (tt0) cc_final: 0.7294 (tp30) REVERT: K 18 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7794 (tmm-80) REVERT: K 97 THR cc_start: 0.6553 (t) cc_final: 0.6286 (p) REVERT: C 130 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6494 (ptt-90) REVERT: C 156 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6960 (tp30) REVERT: C 235 GLN cc_start: 0.9199 (tt0) cc_final: 0.8810 (tm-30) REVERT: C 258 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8857 (mt-10) REVERT: I 32 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8899 (tptp) REVERT: I 46 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7182 (mm-30) REVERT: I 48 MET cc_start: 0.8614 (mtp) cc_final: 0.8198 (mtp) REVERT: I 68 THR cc_start: 0.7761 (m) cc_final: 0.7527 (p) REVERT: I 81 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7153 (mt-10) REVERT: L 70 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8984 (mm-30) REVERT: L 97 THR cc_start: 0.6239 (t) cc_final: 0.5958 (p) REVERT: L 103 LYS cc_start: 0.8199 (tttt) cc_final: 0.7943 (tttm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1131 time to fit residues: 53.0310 Evaluate side-chains 229 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 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** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095590 restraints weight = 34480.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098121 restraints weight = 18455.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100153 restraints weight = 11197.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.101136 restraints weight = 8727.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101239 restraints weight = 7826.452| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13518 Z= 0.197 Angle : 0.771 10.391 18414 Z= 0.401 Chirality : 0.048 0.300 2106 Planarity : 0.005 0.055 2310 Dihedral : 5.956 34.610 1782 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1614 helix: 0.73 (0.36), residues: 234 sheet: -0.38 (0.23), residues: 483 loop : -0.71 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 596 TYR 0.029 0.002 TYR E 534 PHE 0.030 0.002 PHE H 29 TRP 0.031 0.003 TRP B 275 HIS 0.006 0.002 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (13473) covalent geometry : angle 0.75372 / 0.40 (18300) SS BOND : bond 0.00712 / 0.49 ( 21) SS BOND : angle 2.31416 / 1.60 ( 42) hydrogen bonds : bond 0.04597 / 3.10 ( 461) hydrogen bonds : angle 6.20822 / 4.49 ( 1302) link_ALPHA1-3 : bond 0.00919 / 0.41 ( 3) link_ALPHA1-3 : angle 1.31229 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00413 / 0.19 ( 3) link_ALPHA1-6 : angle 1.79623 / 0.95 ( 9) link_BETA1-4 : bond 0.00407 / 0.24 ( 9) link_BETA1-4 : angle 2.35370 / 1.53 ( 27) link_NAG-ASN : bond 0.00390 / 0.18 ( 9) link_NAG-ASN : angle 2.16849 / 1.33 ( 27) *********************** 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 321 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.343 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 229 MET cc_start: 0.8198 (pmm) cc_final: 0.7956 (pmm) REVERT: A 235 GLN cc_start: 0.9127 (tt0) cc_final: 0.8587 (tm-30) REVERT: G 19 LYS cc_start: 0.8880 (tptt) cc_final: 0.8515 (tptp) REVERT: G 23 ARG cc_start: 0.8661 (tpt-90) cc_final: 0.8454 (tpp80) REVERT: G 48 MET cc_start: 0.8705 (mtp) cc_final: 0.8349 (mtp) REVERT: J 70 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9135 (mm-30) REVERT: J 71 PHE cc_start: 0.8306 (m-10) cc_final: 0.7257 (m-10) REVERT: B 156 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7196 (tp30) REVERT: B 229 MET cc_start: 0.8351 (pmm) cc_final: 0.8120 (pmm) REVERT: B 235 GLN cc_start: 0.9147 (tt0) cc_final: 0.8439 (tm-30) REVERT: H 20 VAL cc_start: 0.8582 (t) cc_final: 0.8266 (t) REVERT: H 32 LYS cc_start: 0.9201 (tmtt) cc_final: 0.8796 (tptp) REVERT: H 35 SER cc_start: 0.8559 (t) cc_final: 0.8251 (m) REVERT: H 96 GLU cc_start: 0.7529 (tt0) cc_final: 0.7295 (tp30) REVERT: H 97 ILE cc_start: 0.8454 (tp) cc_final: 0.8145 (tp) REVERT: K 89 LEU cc_start: 0.8453 (tt) cc_final: 0.8247 (tt) REVERT: K 90 GLN cc_start: 0.7058 (tt0) cc_final: 0.6518 (tt0) REVERT: K 97 THR cc_start: 0.6888 (t) cc_final: 0.5923 (p) REVERT: C 130 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6738 (ptt-90) REVERT: C 235 GLN cc_start: 0.9217 (tt0) cc_final: 0.8734 (tm-30) REVERT: I 19 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8459 (mmmt) REVERT: I 20 VAL cc_start: 0.8738 (t) cc_final: 0.8406 (t) REVERT: I 23 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8367 (tpp80) REVERT: I 46 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7690 (mm-30) REVERT: I 48 MET cc_start: 0.8745 (mtp) cc_final: 0.8329 (mtp) REVERT: I 96 GLU cc_start: 0.7376 (tt0) cc_final: 0.7119 (tt0) REVERT: L 58 ILE cc_start: 0.7337 (tt) cc_final: 0.6487 (tt) REVERT: L 70 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9120 (mm-30) REVERT: L 71 PHE cc_start: 0.8356 (m-10) cc_final: 0.8015 (m-10) REVERT: L 90 GLN cc_start: 0.7298 (tt0) cc_final: 0.6761 (tt0) REVERT: L 97 THR cc_start: 0.6259 (t) cc_final: 0.5493 (p) REVERT: F 596 ARG cc_start: 0.7247 (mmm160) cc_final: 0.6951 (mmm160) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1155 time to fit residues: 51.3959 Evaluate side-chains 213 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 135 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.124429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.092722 restraints weight = 31381.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096014 restraints weight = 16914.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097026 restraints weight = 9838.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097651 restraints weight = 8741.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.097930 restraints weight = 7594.052| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13518 Z= 0.209 Angle : 0.763 8.526 18414 Z= 0.397 Chirality : 0.048 0.270 2106 Planarity : 0.006 0.065 2310 Dihedral : 5.896 32.929 1782 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1614 helix: 0.47 (0.35), residues: 234 sheet: -0.48 (0.23), residues: 504 loop : -0.95 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 94 TYR 0.022 0.002 TYR E 534 PHE 0.033 0.002 PHE H 63 TRP 0.026 0.003 TRP G 103 HIS 0.006 0.002 HIS I 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (13473) covalent geometry : angle 0.74680 / 0.39 (18300) SS BOND : bond 0.00424 / 0.28 ( 21) SS BOND : angle 2.17207 / 1.51 ( 42) hydrogen bonds : bond 0.04663 / 3.18 ( 461) hydrogen bonds : angle 6.07261 / 4.38 ( 1302) link_ALPHA1-3 : bond 0.00539 / 0.25 ( 3) link_ALPHA1-3 : angle 1.52021 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00252 / 0.12 ( 3) link_ALPHA1-6 : angle 1.97333 / 1.05 ( 9) link_BETA1-4 : bond 0.00343 / 0.20 ( 9) link_BETA1-4 : angle 2.32802 / 1.53 ( 27) link_NAG-ASN : bond 0.00306 / 0.14 ( 9) link_NAG-ASN : angle 1.93181 / 1.13 ( 27) *********************** 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 301 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.523 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: A 77 THR cc_start: 0.7436 (p) cc_final: 0.6694 (t) REVERT: A 148 PRO cc_start: 0.8348 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: A 167 SER cc_start: 0.8513 (m) cc_final: 0.8189 (p) REVERT: A 229 MET cc_start: 0.8438 (pmm) cc_final: 0.8194 (pmm) REVERT: A 230 THR cc_start: 0.6959 (m) cc_final: 0.6755 (m) REVERT: A 235 GLN cc_start: 0.9108 (tt0) cc_final: 0.8383 (tm-30) REVERT: G 19 LYS cc_start: 0.8912 (tptt) cc_final: 0.8469 (tptp) REVERT: G 48 MET cc_start: 0.8853 (mtp) cc_final: 0.8563 (mtp) REVERT: G 90 TYR cc_start: 0.8718 (m-10) cc_final: 0.8085 (m-80) REVERT: J 71 PHE cc_start: 0.8415 (m-80) cc_final: 0.7504 (m-10) REVERT: D 596 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7362 (mmm160) REVERT: B 44 GLN cc_start: 0.6143 (tm-30) cc_final: 0.5836 (tm-30) REVERT: B 130 ARG cc_start: 0.7610 (ptt90) cc_final: 0.6536 (ptt-90) REVERT: B 229 MET cc_start: 0.8472 (pmm) cc_final: 0.8218 (pmm) REVERT: B 235 GLN cc_start: 0.9133 (tt0) cc_final: 0.8401 (tm-30) REVERT: B 236 VAL cc_start: 0.7294 (t) cc_final: 0.6895 (t) REVERT: H 19 LYS cc_start: 0.8906 (tptt) cc_final: 0.8356 (tptp) REVERT: H 20 VAL cc_start: 0.8701 (t) cc_final: 0.8180 (t) REVERT: H 35 SER cc_start: 0.8557 (t) cc_final: 0.8322 (m) REVERT: H 48 MET cc_start: 0.8355 (mmt) cc_final: 0.8098 (mmm) REVERT: K 27 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7142 (tm-30) REVERT: K 71 PHE cc_start: 0.8353 (m-10) cc_final: 0.8117 (m-10) REVERT: K 90 GLN cc_start: 0.7429 (tt0) cc_final: 0.6591 (tt0) REVERT: K 97 THR cc_start: 0.7263 (t) cc_final: 0.6051 (p) REVERT: C 77 THR cc_start: 0.7514 (p) cc_final: 0.6856 (t) REVERT: C 229 MET cc_start: 0.8473 (pmm) cc_final: 0.8219 (pmm) REVERT: C 230 THR cc_start: 0.6629 (m) cc_final: 0.6381 (m) REVERT: C 235 GLN cc_start: 0.9236 (tt0) cc_final: 0.8431 (tm-30) REVERT: I 20 VAL cc_start: 0.8504 (t) cc_final: 0.7963 (t) REVERT: I 23 ARG cc_start: 0.8565 (tpt-90) cc_final: 0.8348 (tpp80) REVERT: I 46 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7678 (mm-30) REVERT: I 52 MET cc_start: 0.8139 (mpp) cc_final: 0.7515 (mpp) REVERT: L 33 LEU cc_start: 0.8783 (tp) cc_final: 0.8532 (tp) REVERT: L 70 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9140 (mm-30) REVERT: L 71 PHE cc_start: 0.8408 (m-10) cc_final: 0.8084 (m-10) REVERT: L 75 ILE cc_start: 0.9453 (mt) cc_final: 0.9188 (tt) REVERT: L 90 GLN cc_start: 0.7606 (tt0) cc_final: 0.6970 (tt0) REVERT: L 97 THR cc_start: 0.6833 (t) cc_final: 0.5987 (p) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.1072 time to fit residues: 45.6494 Evaluate side-chains 198 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** 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 = 0.4087 r_free = 0.4087 target = 0.119135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087360 restraints weight = 33599.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.089355 restraints weight = 16511.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.090334 restraints weight = 11222.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.090795 restraints weight = 10054.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091063 restraints weight = 9051.535| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13518 Z= 0.260 Angle : 0.829 9.518 18414 Z= 0.422 Chirality : 0.050 0.272 2106 Planarity : 0.006 0.052 2310 Dihedral : 6.081 31.675 1782 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1614 helix: 0.76 (0.36), residues: 216 sheet: -0.61 (0.23), residues: 519 loop : -1.37 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 38 TYR 0.042 0.003 TYR D 534 PHE 0.024 0.003 PHE E 592 TRP 0.028 0.003 TRP A 104 HIS 0.010 0.002 HIS A 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.26 (13473) covalent geometry : angle 0.81521 / 0.42 (18300) SS BOND : bond 0.00558 / 0.36 ( 21) SS BOND : angle 2.29708 / 1.63 ( 42) hydrogen bonds : bond 0.04742 / 3.24 ( 461) hydrogen bonds : angle 6.15345 / 4.36 ( 1302) link_ALPHA1-3 : bond 0.00397 / 0.18 ( 3) link_ALPHA1-3 : angle 1.57518 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00077 / 0.04 ( 3) link_ALPHA1-6 : angle 2.14387 / 1.14 ( 9) link_BETA1-4 : bond 0.00258 / 0.13 ( 9) link_BETA1-4 : angle 2.20275 / 1.43 ( 27) link_NAG-ASN : bond 0.00348 / 0.18 ( 9) link_NAG-ASN : angle 1.74705 / 1.01 ( 27) *********************** 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 283 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.493 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: 0.7979 (p) cc_final: 0.7307 (t) REVERT: A 229 MET cc_start: 0.8545 (pmm) cc_final: 0.8316 (pmm) REVERT: A 230 THR cc_start: 0.7136 (m) cc_final: 0.6863 (m) REVERT: A 235 GLN cc_start: 0.9113 (tt0) cc_final: 0.8346 (tm-30) REVERT: A 236 VAL cc_start: 0.7530 (t) cc_final: 0.7014 (t) REVERT: G 19 LYS cc_start: 0.8876 (tptt) cc_final: 0.8185 (tptp) REVERT: G 29 PHE cc_start: 0.6635 (m-10) cc_final: 0.6189 (m-80) REVERT: G 48 MET cc_start: 0.8968 (mtp) cc_final: 0.8762 (mtp) REVERT: G 90 TYR cc_start: 0.8637 (m-10) cc_final: 0.8149 (m-80) REVERT: J 90 GLN cc_start: 0.7705 (tt0) cc_final: 0.6928 (tt0) REVERT: J 97 THR cc_start: 0.7129 (p) cc_final: 0.6414 (p) REVERT: B 77 THR cc_start: 0.7758 (p) cc_final: 0.7187 (t) REVERT: B 229 MET cc_start: 0.8617 (pmm) cc_final: 0.8357 (pmm) REVERT: B 230 THR cc_start: 0.6993 (m) cc_final: 0.6734 (m) REVERT: B 235 GLN cc_start: 0.9121 (tt0) cc_final: 0.8343 (tm-30) REVERT: B 236 VAL cc_start: 0.7389 (t) cc_final: 0.7027 (t) REVERT: H 19 LYS cc_start: 0.8913 (tptt) cc_final: 0.8265 (tptp) REVERT: H 20 VAL cc_start: 0.8750 (t) cc_final: 0.8377 (t) REVERT: H 32 LYS cc_start: 0.9118 (tptp) cc_final: 0.8849 (tppt) REVERT: H 80 MET cc_start: 0.8483 (mtp) cc_final: 0.8252 (mtp) REVERT: H 90 TYR cc_start: 0.8406 (m-80) cc_final: 0.8190 (m-80) REVERT: K 27 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7239 (tm-30) REVERT: K 71 PHE cc_start: 0.8474 (m-10) cc_final: 0.8237 (m-10) REVERT: K 90 GLN cc_start: 0.7856 (tt0) cc_final: 0.7232 (tt0) REVERT: K 97 THR cc_start: 0.7456 (t) cc_final: 0.6785 (p) REVERT: C 77 THR cc_start: 0.7709 (p) cc_final: 0.7055 (t) REVERT: C 229 MET cc_start: 0.8657 (pmm) cc_final: 0.8374 (pmm) REVERT: C 230 THR cc_start: 0.6821 (m) cc_final: 0.6510 (m) REVERT: C 235 GLN cc_start: 0.9187 (tt0) cc_final: 0.8334 (tm-30) REVERT: I 19 LYS cc_start: 0.8712 (tptt) cc_final: 0.8420 (tptp) REVERT: I 46 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7760 (mm-30) REVERT: I 48 MET cc_start: 0.9002 (mtt) cc_final: 0.8574 (mpp) REVERT: L 70 GLU cc_start: 0.9402 (mt-10) cc_final: 0.9134 (mm-30) REVERT: L 71 PHE cc_start: 0.8520 (m-10) cc_final: 0.8024 (m-10) REVERT: L 90 GLN cc_start: 0.7938 (tt0) cc_final: 0.7339 (tt0) REVERT: L 97 THR cc_start: 0.7122 (t) cc_final: 0.6349 (p) REVERT: F 596 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7295 (mmm160) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1089 time to fit residues: 43.6339 Evaluate side-chains 202 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN C 69 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.121522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090445 restraints weight = 32322.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091992 restraints weight = 16890.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093235 restraints weight = 11435.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.094065 restraints weight = 9529.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.094385 restraints weight = 8490.705| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13518 Z= 0.162 Angle : 0.724 10.525 18414 Z= 0.373 Chirality : 0.047 0.275 2106 Planarity : 0.006 0.103 2310 Dihedral : 5.805 29.974 1782 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.20), residues: 1614 helix: 1.50 (0.37), residues: 198 sheet: -0.57 (0.22), residues: 504 loop : -1.36 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 94 TYR 0.023 0.002 TYR E 534 PHE 0.043 0.002 PHE G 29 TRP 0.028 0.002 TRP I 103 HIS 0.008 0.001 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13473) covalent geometry : angle 0.71123 / 0.37 (18300) SS BOND : bond 0.00383 / 0.26 ( 21) SS BOND : angle 1.98810 / 1.45 ( 42) hydrogen bonds : bond 0.04180 / 2.88 ( 461) hydrogen bonds : angle 5.82539 / 4.18 ( 1302) link_ALPHA1-3 : bond 0.00556 / 0.25 ( 3) link_ALPHA1-3 : angle 1.48801 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00237 / 0.11 ( 3) link_ALPHA1-6 : angle 1.76784 / 0.95 ( 9) link_BETA1-4 : bond 0.00406 / 0.22 ( 9) link_BETA1-4 : angle 2.01512 / 1.33 ( 27) link_NAG-ASN : bond 0.00228 / 0.11 ( 9) link_NAG-ASN : angle 1.63920 / 0.99 ( 27) *********************** 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 278 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.530 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: 0.7986 (p) cc_final: 0.7451 (t) REVERT: A 230 THR cc_start: 0.7221 (m) cc_final: 0.6949 (m) REVERT: A 235 GLN cc_start: 0.9049 (tt0) cc_final: 0.8372 (tm-30) REVERT: A 236 VAL cc_start: 0.7266 (t) cc_final: 0.7032 (t) REVERT: G 19 LYS cc_start: 0.8893 (tptt) cc_final: 0.8176 (tptp) REVERT: G 52 MET cc_start: 0.8525 (mmp) cc_final: 0.8056 (mmm) REVERT: G 90 TYR cc_start: 0.8608 (m-10) cc_final: 0.8157 (m-80) REVERT: J 18 ARG cc_start: 0.8298 (tmm-80) cc_final: 0.8020 (tmm-80) REVERT: J 90 GLN cc_start: 0.7687 (tt0) cc_final: 0.6824 (tt0) REVERT: J 97 THR cc_start: 0.7079 (p) cc_final: 0.6326 (p) REVERT: B 77 THR cc_start: 0.7894 (p) cc_final: 0.7371 (t) REVERT: B 229 MET cc_start: 0.8562 (pmm) cc_final: 0.8321 (pmm) REVERT: B 230 THR cc_start: 0.6938 (m) cc_final: 0.6685 (m) REVERT: B 235 GLN cc_start: 0.9143 (tt0) cc_final: 0.8230 (tm-30) REVERT: H 19 LYS cc_start: 0.8879 (tptt) cc_final: 0.8217 (tptp) REVERT: H 20 VAL cc_start: 0.8792 (t) cc_final: 0.8307 (t) REVERT: H 32 LYS cc_start: 0.9118 (tptp) cc_final: 0.8891 (tppt) REVERT: H 35 ILE cc_start: 0.8892 (mm) cc_final: 0.8342 (tp) REVERT: H 52 MET cc_start: 0.8420 (mmp) cc_final: 0.8001 (mmm) REVERT: K 73 LEU cc_start: 0.8866 (tp) cc_final: 0.7346 (tp) REVERT: K 90 GLN cc_start: 0.7809 (tt0) cc_final: 0.7443 (tt0) REVERT: K 97 THR cc_start: 0.7439 (t) cc_final: 0.6644 (p) REVERT: C 77 THR cc_start: 0.7664 (p) cc_final: 0.7011 (t) REVERT: C 229 MET cc_start: 0.8548 (pmm) cc_final: 0.8297 (pmm) REVERT: C 230 THR cc_start: 0.6851 (m) cc_final: 0.6529 (m) REVERT: C 235 GLN cc_start: 0.9185 (tt0) cc_final: 0.8414 (tm-30) REVERT: I 20 VAL cc_start: 0.8530 (t) cc_final: 0.8260 (t) REVERT: I 32 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8902 (tptt) REVERT: I 48 MET cc_start: 0.9099 (mtt) cc_final: 0.8554 (mpp) REVERT: I 52 MET cc_start: 0.8089 (mmm) cc_final: 0.7876 (mmm) REVERT: I 81 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7037 (tp30) REVERT: L 42 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8619 (mm110) REVERT: L 70 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9118 (mm-30) REVERT: L 71 PHE cc_start: 0.8355 (m-10) cc_final: 0.7958 (m-10) REVERT: L 90 GLN cc_start: 0.7858 (tt0) cc_final: 0.7098 (tt0) REVERT: L 97 THR cc_start: 0.7274 (t) cc_final: 0.5889 (p) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.0957 time to fit residues: 39.0319 Evaluate side-chains 203 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 0.0270 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.121643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.089692 restraints weight = 32468.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.092409 restraints weight = 16548.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.093478 restraints weight = 10353.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.094141 restraints weight = 9414.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.094332 restraints weight = 8356.853| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13518 Z= 0.165 Angle : 0.721 12.073 18414 Z= 0.368 Chirality : 0.047 0.254 2106 Planarity : 0.006 0.101 2310 Dihedral : 5.680 28.666 1782 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.21), residues: 1614 helix: 1.55 (0.37), residues: 198 sheet: -0.73 (0.22), residues: 522 loop : -1.29 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 172 TYR 0.024 0.002 TYR H 33 PHE 0.033 0.002 PHE G 29 TRP 0.047 0.002 TRP K 35 HIS 0.009 0.001 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (13473) covalent geometry : angle 0.70784 / 0.36 (18300) SS BOND : bond 0.00430 / 0.29 ( 21) SS BOND : angle 2.09761 / 1.49 ( 42) hydrogen bonds : bond 0.04125 / 2.85 ( 461) hydrogen bonds : angle 5.76614 / 4.10 ( 1302) link_ALPHA1-3 : bond 0.00345 / 0.16 ( 3) link_ALPHA1-3 : angle 1.44473 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00245 / 0.11 ( 3) link_ALPHA1-6 : angle 1.75680 / 0.95 ( 9) link_BETA1-4 : bond 0.00267 / 0.17 ( 9) link_BETA1-4 : angle 2.01342 / 1.33 ( 27) link_NAG-ASN : bond 0.00239 / 0.12 ( 9) link_NAG-ASN : angle 1.57865 / 0.99 ( 27) *********************** 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 291 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.400 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: A 77 THR cc_start: 0.7995 (p) cc_final: 0.7482 (t) REVERT: A 167 SER cc_start: 0.8437 (t) cc_final: 0.7836 (p) REVERT: A 229 MET cc_start: 0.8483 (pmm) cc_final: 0.8171 (pmm) REVERT: A 230 THR cc_start: 0.7242 (m) cc_final: 0.6959 (m) REVERT: A 235 GLN cc_start: 0.9076 (tt0) cc_final: 0.8356 (tm-30) REVERT: G 19 LYS cc_start: 0.8892 (tptt) cc_final: 0.8179 (tptp) REVERT: G 53 ILE cc_start: 0.8132 (tt) cc_final: 0.7891 (pt) REVERT: G 90 TYR cc_start: 0.8538 (m-10) cc_final: 0.8041 (m-80) REVERT: J 90 GLN cc_start: 0.7832 (tt0) cc_final: 0.6999 (tt0) REVERT: J 97 THR cc_start: 0.7214 (p) cc_final: 0.6442 (p) REVERT: B 77 THR cc_start: 0.7964 (p) cc_final: 0.7464 (t) REVERT: B 229 MET cc_start: 0.8570 (pmm) cc_final: 0.8339 (pmm) REVERT: B 230 THR cc_start: 0.7062 (m) cc_final: 0.6795 (m) REVERT: B 235 GLN cc_start: 0.9164 (tt0) cc_final: 0.8186 (tm-30) REVERT: H 19 LYS cc_start: 0.8894 (tptt) cc_final: 0.8239 (tptp) REVERT: H 20 VAL cc_start: 0.8766 (t) cc_final: 0.8333 (t) REVERT: H 32 LYS cc_start: 0.9113 (tptp) cc_final: 0.8865 (tptt) REVERT: H 35 ILE cc_start: 0.8916 (mm) cc_final: 0.8403 (tp) REVERT: H 48 MET cc_start: 0.8444 (mmp) cc_final: 0.8204 (mmm) REVERT: H 52 MET cc_start: 0.8373 (mmp) cc_final: 0.8097 (mmm) REVERT: H 80 MET cc_start: 0.8330 (mtp) cc_final: 0.8072 (mtp) REVERT: H 90 TYR cc_start: 0.8327 (m-10) cc_final: 0.7965 (m-80) REVERT: K 90 GLN cc_start: 0.8121 (tt0) cc_final: 0.7613 (tt0) REVERT: K 97 THR cc_start: 0.7621 (t) cc_final: 0.6909 (p) REVERT: E 583 SER cc_start: 0.7796 (m) cc_final: 0.7558 (p) REVERT: C 54 ARG cc_start: 0.7927 (mmp-170) cc_final: 0.7494 (mmp80) REVERT: C 77 THR cc_start: 0.7666 (p) cc_final: 0.7001 (t) REVERT: C 229 MET cc_start: 0.8509 (pmm) cc_final: 0.8302 (pmm) REVERT: C 235 GLN cc_start: 0.9230 (tt0) cc_final: 0.8426 (tm-30) REVERT: I 19 LYS cc_start: 0.8689 (tptt) cc_final: 0.8471 (tptp) REVERT: I 20 VAL cc_start: 0.8428 (t) cc_final: 0.7937 (t) REVERT: I 48 MET cc_start: 0.9088 (mtt) cc_final: 0.8493 (mpp) REVERT: I 81 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7296 (tp30) REVERT: I 94 ARG cc_start: 0.6624 (mtp180) cc_final: 0.6213 (mtp180) REVERT: L 42 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8570 (mm110) REVERT: L 70 GLU cc_start: 0.9394 (mt-10) cc_final: 0.9081 (mm-30) REVERT: L 71 PHE cc_start: 0.8286 (m-10) cc_final: 0.7954 (m-10) REVERT: L 90 GLN cc_start: 0.8163 (tt0) cc_final: 0.7493 (tt0) REVERT: L 97 THR cc_start: 0.7502 (t) cc_final: 0.6178 (p) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1047 time to fit residues: 44.2200 Evaluate side-chains 209 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 3 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN K 32 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.113649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.079413 restraints weight = 33744.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.082389 restraints weight = 18452.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.084479 restraints weight = 12250.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085839 restraints weight = 9303.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086693 restraints weight = 7750.167| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 13518 Z= 0.343 Angle : 0.945 13.170 18414 Z= 0.482 Chirality : 0.053 0.303 2106 Planarity : 0.007 0.085 2310 Dihedral : 6.600 31.849 1782 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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 : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.20), residues: 1614 helix: 0.72 (0.37), residues: 180 sheet: -1.08 (0.22), residues: 525 loop : -1.42 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 31 TYR 0.026 0.003 TYR I 33 PHE 0.031 0.003 PHE G 29 TRP 0.046 0.004 TRP G 103 HIS 0.016 0.003 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.34 (13473) covalent geometry : angle 0.93129 / 0.48 (18300) SS BOND : bond 0.00590 / 0.38 ( 21) SS BOND : angle 2.50567 / 1.75 ( 42) hydrogen bonds : bond 0.05560 / 3.90 ( 461) hydrogen bonds : angle 6.37212 / 4.50 ( 1302) link_ALPHA1-3 : bond 0.00027 / 0.01 ( 3) link_ALPHA1-3 : angle 1.86161 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00179 / 0.08 ( 3) link_ALPHA1-6 : angle 2.40421 / 1.28 ( 9) link_BETA1-4 : bond 0.00459 / 0.26 ( 9) link_BETA1-4 : angle 2.26493 / 1.45 ( 27) link_NAG-ASN : bond 0.00550 / 0.30 ( 9) link_NAG-ASN : angle 1.81833 / 1.05 ( 27) *********************** 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 256 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.440 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: A 77 THR cc_start: 0.8190 (p) cc_final: 0.7763 (t) REVERT: A 229 MET cc_start: 0.8514 (pmm) cc_final: 0.8274 (pmm) REVERT: A 230 THR cc_start: 0.7530 (m) cc_final: 0.7176 (m) REVERT: A 231 ASN cc_start: 0.8662 (t0) cc_final: 0.7808 (p0) REVERT: A 235 GLN cc_start: 0.9136 (tt0) cc_final: 0.8460 (tm-30) REVERT: G 19 LYS cc_start: 0.8840 (tptt) cc_final: 0.8090 (tptp) REVERT: G 48 MET cc_start: 0.9011 (mtt) cc_final: 0.8499 (mpp) REVERT: G 90 TYR cc_start: 0.8598 (m-10) cc_final: 0.8386 (m-80) REVERT: J 18 ARG cc_start: 0.8318 (tmm-80) cc_final: 0.7745 (tmm-80) REVERT: J 90 GLN cc_start: 0.7764 (tt0) cc_final: 0.7099 (tt0) REVERT: J 97 THR cc_start: 0.7259 (p) cc_final: 0.6942 (p) REVERT: D 517 TYR cc_start: 0.8206 (p90) cc_final: 0.7907 (p90) REVERT: B 77 THR cc_start: 0.8367 (p) cc_final: 0.7924 (t) REVERT: B 122 LEU cc_start: 0.9114 (mm) cc_final: 0.8912 (mm) REVERT: B 130 ARG cc_start: 0.7624 (ptt-90) cc_final: 0.6727 (ptt-90) REVERT: B 230 THR cc_start: 0.7534 (m) cc_final: 0.7295 (m) REVERT: B 235 GLN cc_start: 0.9078 (tt0) cc_final: 0.8320 (tm-30) REVERT: B 236 VAL cc_start: 0.7612 (t) cc_final: 0.7246 (t) REVERT: H 19 LYS cc_start: 0.8885 (tptt) cc_final: 0.8241 (tptp) REVERT: H 20 VAL cc_start: 0.8691 (t) cc_final: 0.8172 (t) REVERT: H 35 ILE cc_start: 0.8886 (mm) cc_final: 0.8509 (tp) REVERT: H 64 GLN cc_start: 0.8765 (mt0) cc_final: 0.8465 (mt0) REVERT: H 80 MET cc_start: 0.8299 (mtp) cc_final: 0.7976 (mtp) REVERT: K 42 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8397 (mm110) REVERT: K 48 ILE cc_start: 0.8132 (tp) cc_final: 0.7744 (tp) REVERT: K 70 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8922 (mm-30) REVERT: K 90 GLN cc_start: 0.8302 (tt0) cc_final: 0.7691 (tt0) REVERT: K 97 THR cc_start: 0.7751 (t) cc_final: 0.7094 (p) REVERT: E 517 TYR cc_start: 0.8207 (p90) cc_final: 0.7936 (p90) REVERT: E 583 SER cc_start: 0.8174 (m) cc_final: 0.7885 (p) REVERT: C 55 ASP cc_start: 0.7875 (m-30) cc_final: 0.7660 (m-30) REVERT: C 77 THR cc_start: 0.8102 (p) cc_final: 0.7601 (t) REVERT: C 122 LEU cc_start: 0.8980 (mm) cc_final: 0.8600 (mm) REVERT: C 235 GLN cc_start: 0.9214 (tt0) cc_final: 0.8468 (tm-30) REVERT: I 19 LYS cc_start: 0.8713 (tptt) cc_final: 0.8210 (tptp) REVERT: I 48 MET cc_start: 0.9254 (mtt) cc_final: 0.8584 (mpp) REVERT: L 70 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9198 (mm-30) REVERT: L 71 PHE cc_start: 0.8681 (m-10) cc_final: 0.8440 (m-10) REVERT: L 90 GLN cc_start: 0.8528 (tt0) cc_final: 0.7743 (tt0) REVERT: L 97 THR cc_start: 0.7583 (t) cc_final: 0.6386 (p) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.0913 time to fit residues: 34.6850 Evaluate side-chains 190 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 141 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN D 516 HIS ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.116468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.081911 restraints weight = 35835.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085260 restraints weight = 18992.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.087491 restraints weight = 12337.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.088997 restraints weight = 9210.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.089906 restraints weight = 7622.273| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13518 Z= 0.198 Angle : 0.797 13.910 18414 Z= 0.403 Chirality : 0.050 0.278 2106 Planarity : 0.006 0.061 2310 Dihedral : 6.186 29.568 1782 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1614 helix: 0.95 (0.36), residues: 198 sheet: -1.01 (0.22), residues: 501 loop : -1.48 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 172 TYR 0.032 0.002 TYR F 534 PHE 0.028 0.002 PHE G 29 TRP 0.031 0.003 TRP K 35 HIS 0.014 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (13473) covalent geometry : angle 0.78327 / 0.40 (18300) SS BOND : bond 0.00417 / 0.28 ( 21) SS BOND : angle 2.33027 / 1.63 ( 42) hydrogen bonds : bond 0.04504 / 3.15 ( 461) hydrogen bonds : angle 5.97653 / 4.26 ( 1302) link_ALPHA1-3 : bond 0.00097 / 0.05 ( 3) link_ALPHA1-3 : angle 1.49411 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00137 / 0.07 ( 3) link_ALPHA1-6 : angle 1.85916 / 1.00 ( 9) link_BETA1-4 : bond 0.00255 / 0.14 ( 9) link_BETA1-4 : angle 1.96759 / 1.32 ( 27) link_NAG-ASN : bond 0.00218 / 0.11 ( 9) link_NAG-ASN : angle 1.75980 / 1.10 ( 27) *********************** 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 253 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.504 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: A 77 THR cc_start: 0.8162 (p) cc_final: 0.7652 (t) REVERT: A 229 MET cc_start: 0.8617 (pmm) cc_final: 0.8383 (pmm) REVERT: A 230 THR cc_start: 0.7353 (m) cc_final: 0.7029 (m) REVERT: A 235 GLN cc_start: 0.9098 (tt0) cc_final: 0.8325 (tm-30) REVERT: G 19 LYS cc_start: 0.8879 (tptt) cc_final: 0.8136 (tptp) REVERT: G 48 MET cc_start: 0.9120 (mtt) cc_final: 0.8557 (mpp) REVERT: G 52 MET cc_start: 0.8335 (mmm) cc_final: 0.7949 (mmm) REVERT: G 90 TYR cc_start: 0.8623 (m-10) cc_final: 0.8350 (m-80) REVERT: J 39 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8754 (mptt) REVERT: J 90 GLN cc_start: 0.8169 (tt0) cc_final: 0.7600 (tt0) REVERT: J 97 THR cc_start: 0.6890 (p) cc_final: 0.6627 (p) REVERT: B 77 THR cc_start: 0.8441 (p) cc_final: 0.8004 (t) REVERT: B 130 ARG cc_start: 0.7807 (ptt-90) cc_final: 0.6894 (ptt-90) REVERT: B 229 MET cc_start: 0.8625 (pmm) cc_final: 0.8312 (pmm) REVERT: B 230 THR cc_start: 0.7252 (m) cc_final: 0.6871 (m) REVERT: B 231 ASN cc_start: 0.8659 (t0) cc_final: 0.7606 (p0) REVERT: B 235 GLN cc_start: 0.9111 (tt0) cc_final: 0.8309 (tm-30) REVERT: B 236 VAL cc_start: 0.6941 (t) cc_final: 0.6573 (t) REVERT: H 19 LYS cc_start: 0.8877 (tptt) cc_final: 0.8201 (tptp) REVERT: H 20 VAL cc_start: 0.8629 (t) cc_final: 0.8122 (t) REVERT: H 35 ILE cc_start: 0.8872 (mm) cc_final: 0.8453 (tp) REVERT: H 80 MET cc_start: 0.8294 (mtp) cc_final: 0.7697 (mtp) REVERT: H 90 TYR cc_start: 0.8404 (m-80) cc_final: 0.8054 (m-80) REVERT: K 48 ILE cc_start: 0.8194 (tp) cc_final: 0.7885 (tp) REVERT: K 70 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8788 (mm-30) REVERT: K 71 PHE cc_start: 0.9100 (m-10) cc_final: 0.8665 (m-10) REVERT: K 90 GLN cc_start: 0.8296 (tt0) cc_final: 0.7445 (tt0) REVERT: K 97 THR cc_start: 0.7517 (t) cc_final: 0.6423 (p) REVERT: E 517 TYR cc_start: 0.7910 (p90) cc_final: 0.7700 (p90) REVERT: E 583 SER cc_start: 0.8099 (m) cc_final: 0.7786 (p) REVERT: C 77 THR cc_start: 0.8058 (p) cc_final: 0.7501 (t) REVERT: C 229 MET cc_start: 0.8453 (pmm) cc_final: 0.8186 (pmm) REVERT: C 231 ASN cc_start: 0.8758 (t0) cc_final: 0.7710 (p0) REVERT: C 235 GLN cc_start: 0.9186 (tt0) cc_final: 0.8850 (tt0) REVERT: I 19 LYS cc_start: 0.8740 (tptt) cc_final: 0.8360 (tptp) REVERT: I 29 PHE cc_start: 0.6316 (m-10) cc_final: 0.5940 (m-10) REVERT: I 32 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8610 (ttpp) REVERT: I 48 MET cc_start: 0.9278 (mtt) cc_final: 0.8431 (mpp) REVERT: L 70 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9170 (mm-30) REVERT: L 71 PHE cc_start: 0.8822 (m-10) cc_final: 0.8545 (m-10) REVERT: L 90 GLN cc_start: 0.8467 (tt0) cc_final: 0.7756 (tt0) REVERT: L 97 THR cc_start: 0.7270 (t) cc_final: 0.6160 (p) REVERT: F 583 SER cc_start: 0.7937 (m) cc_final: 0.7574 (p) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.0824 time to fit residues: 31.9110 Evaluate side-chains 180 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 56 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 123 optimal weight: 0.0070 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084828 restraints weight = 35260.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088265 restraints weight = 18577.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090661 restraints weight = 12014.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092208 restraints weight = 8907.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093262 restraints weight = 7300.964| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13518 Z= 0.141 Angle : 0.728 12.565 18414 Z= 0.374 Chirality : 0.048 0.272 2106 Planarity : 0.006 0.058 2310 Dihedral : 5.844 30.460 1782 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1614 helix: 1.31 (0.38), residues: 198 sheet: -1.16 (0.21), residues: 540 loop : -1.36 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 172 TYR 0.035 0.002 TYR K 36 PHE 0.018 0.002 PHE G 29 TRP 0.042 0.002 TRP G 103 HIS 0.011 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13473) covalent geometry : angle 0.71523 / 0.37 (18300) SS BOND : bond 0.00359 / 0.25 ( 21) SS BOND : angle 2.04215 / 1.45 ( 42) hydrogen bonds : bond 0.04076 / 2.86 ( 461) hydrogen bonds : angle 5.72628 / 4.07 ( 1302) link_ALPHA1-3 : bond 0.00266 / 0.13 ( 3) link_ALPHA1-3 : angle 1.49910 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00252 / 0.12 ( 3) link_ALPHA1-6 : angle 1.60962 / 0.88 ( 9) link_BETA1-4 : bond 0.00307 / 0.18 ( 9) link_BETA1-4 : angle 1.86795 / 1.28 ( 27) link_NAG-ASN : bond 0.00311 / 0.15 ( 9) link_NAG-ASN : angle 1.67197 / 1.08 ( 27) ********************** 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 250 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.503 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: 0.8048 (p) cc_final: 0.7549 (t) REVERT: A 148 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7992 (Cg_endo) REVERT: A 230 THR cc_start: 0.7348 (m) cc_final: 0.7104 (m) REVERT: A 235 GLN cc_start: 0.9034 (tt0) cc_final: 0.8341 (tm-30) REVERT: G 19 LYS cc_start: 0.8934 (tptt) cc_final: 0.8203 (tptp) REVERT: G 48 MET cc_start: 0.9025 (mtt) cc_final: 0.8549 (mpp) REVERT: G 53 ILE cc_start: 0.8351 (tt) cc_final: 0.7763 (pt) REVERT: G 80 MET cc_start: 0.8388 (mtp) cc_final: 0.8184 (mtp) REVERT: G 90 TYR cc_start: 0.8492 (m-10) cc_final: 0.8196 (m-80) REVERT: J 39 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8613 (mptt) REVERT: J 71 PHE cc_start: 0.8627 (m-10) cc_final: 0.8232 (m-10) REVERT: J 90 GLN cc_start: 0.8136 (tt0) cc_final: 0.7677 (tt0) REVERT: J 97 THR cc_start: 0.6882 (p) cc_final: 0.6585 (p) REVERT: B 77 THR cc_start: 0.8338 (p) cc_final: 0.7920 (t) REVERT: B 229 MET cc_start: 0.8517 (pmm) cc_final: 0.8241 (pmm) REVERT: B 230 THR cc_start: 0.7359 (m) cc_final: 0.7047 (m) REVERT: B 231 ASN cc_start: 0.8618 (t0) cc_final: 0.7631 (p0) REVERT: B 235 GLN cc_start: 0.9170 (tt0) cc_final: 0.8171 (tm-30) REVERT: H 19 LYS cc_start: 0.8883 (tptt) cc_final: 0.8219 (tptp) REVERT: H 20 VAL cc_start: 0.8648 (t) cc_final: 0.8320 (t) REVERT: H 35 ILE cc_start: 0.8840 (mm) cc_final: 0.8413 (tp) REVERT: H 80 MET cc_start: 0.8254 (mtp) cc_final: 0.7582 (mtp) REVERT: H 90 TYR cc_start: 0.8318 (m-80) cc_final: 0.8112 (m-80) REVERT: H 101 ASP cc_start: 0.7750 (m-30) cc_final: 0.7472 (m-30) REVERT: K 70 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8732 (mm-30) REVERT: K 71 PHE cc_start: 0.8913 (m-10) cc_final: 0.8448 (m-10) REVERT: K 90 GLN cc_start: 0.8354 (tt0) cc_final: 0.7572 (tt0) REVERT: K 97 THR cc_start: 0.7515 (t) cc_final: 0.6398 (p) REVERT: E 517 TYR cc_start: 0.8021 (p90) cc_final: 0.7808 (p90) REVERT: E 583 SER cc_start: 0.7892 (m) cc_final: 0.7685 (p) REVERT: C 77 THR cc_start: 0.7878 (p) cc_final: 0.7322 (t) REVERT: C 148 PRO cc_start: 0.8227 (Cg_exo) cc_final: 0.7901 (Cg_endo) REVERT: C 231 ASN cc_start: 0.8482 (t0) cc_final: 0.7803 (p0) REVERT: C 235 GLN cc_start: 0.9192 (tt0) cc_final: 0.8394 (tm-30) REVERT: C 236 VAL cc_start: 0.7755 (t) cc_final: 0.7214 (t) REVERT: I 19 LYS cc_start: 0.8732 (tptt) cc_final: 0.8335 (tptp) REVERT: I 48 MET cc_start: 0.9276 (mtt) cc_final: 0.8334 (mpp) REVERT: L 39 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8675 (mptt) REVERT: L 70 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9102 (mm-30) REVERT: L 71 PHE cc_start: 0.8704 (m-10) cc_final: 0.8449 (m-10) REVERT: L 90 GLN cc_start: 0.8507 (tt0) cc_final: 0.7771 (tt0) REVERT: L 97 THR cc_start: 0.7344 (t) cc_final: 0.6228 (p) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.0869 time to fit residues: 32.5350 Evaluate side-chains 185 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 100CHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.119783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.088587 restraints weight = 31823.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.090240 restraints weight = 14840.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090882 restraints weight = 10649.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.091398 restraints weight = 9970.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091739 restraints weight = 8664.232| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13518 Z= 0.163 Angle : 0.734 12.467 18414 Z= 0.375 Chirality : 0.048 0.266 2106 Planarity : 0.006 0.051 2310 Dihedral : 5.793 30.148 1782 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1614 helix: 1.34 (0.38), residues: 198 sheet: -1.19 (0.21), residues: 540 loop : -1.36 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 172 TYR 0.036 0.002 TYR K 36 PHE 0.020 0.002 PHE G 29 TRP 0.036 0.002 TRP G 103 HIS 0.012 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (13473) covalent geometry : angle 0.72132 / 0.37 (18300) SS BOND : bond 0.00372 / 0.25 ( 21) SS BOND : angle 2.13715 / 1.44 ( 42) hydrogen bonds : bond 0.04082 / 2.84 ( 461) hydrogen bonds : angle 5.75923 / 4.09 ( 1302) link_ALPHA1-3 : bond 0.00130 / 0.06 ( 3) link_ALPHA1-3 : angle 1.46449 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00167 / 0.08 ( 3) link_ALPHA1-6 : angle 1.67062 / 0.91 ( 9) link_BETA1-4 : bond 0.00240 / 0.14 ( 9) link_BETA1-4 : angle 1.91396 / 1.29 ( 27) link_NAG-ASN : bond 0.00287 / 0.13 ( 9) link_NAG-ASN : angle 1.66411 / 1.07 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.02 seconds wall clock time: 34 minutes 50.52 seconds (2090.52 seconds total)