Starting phenix.real_space_refine on Wed Mar 4 11:45:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kew_22841/03_2026/7kew_22841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kew_22841/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kew_22841/03_2026/7kew_22841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kew_22841/03_2026/7kew_22841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kew_22841/03_2026/7kew_22841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kew_22841/03_2026/7kew_22841.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, H, I, K, L, E, F, N, Q, P, R Time building chain proxies: 2.51, per 1000 atoms: 0.19 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: 1.20 Conformation dependent library (CDL) restraints added in 600.0 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: 0.55 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: 2.48 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2227 1.31 - 1.45: 4355 1.45 - 1.59: 6747 1.59 - 1.73: 66 1.73 - 1.87: 78 Bond restraints: 13473 Sorted by residual: bond pdb=" CB ILE C 33 " pdb=" CG1 ILE C 33 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" NE1 TRP I 103 " pdb=" CE2 TRP I 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.34e+01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" NE1 TRP G 103 " pdb=" CE2 TRP G 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.23e+01 ... (remaining 13468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 15954 2.60 - 5.21: 1932 5.21 - 7.81: 363 7.81 - 10.42: 35 10.42 - 13.02: 16 Bond angle restraints: 18300 Sorted by residual: angle pdb=" N GLU C 71 " pdb=" CA GLU C 71 " pdb=" C GLU C 71 " ideal model delta sigma weight residual 114.62 104.18 10.44 1.14e+00 7.69e-01 8.39e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 114.62 104.26 10.36 1.14e+00 7.69e-01 8.26e+01 angle pdb=" N GLU A 71 " pdb=" CA GLU A 71 " pdb=" C GLU A 71 " ideal model delta sigma weight residual 114.62 104.27 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" N ARG C 247 " pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 114.75 104.25 10.50 1.26e+00 6.30e-01 6.95e+01 angle pdb=" N ARG A 247 " pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.86e+01 ... (remaining 18295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 8046 21.41 - 42.81: 156 42.81 - 64.22: 45 64.22 - 85.63: 27 85.63 - 107.03: 12 Dihedral angle restraints: 8286 sinusoidal: 3579 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 8283 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.136 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 : 11.742 107.032 5211 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 covalent geometry : bond 0.02171 (13473) covalent geometry : angle 1.88152 (18300) SS BOND : bond 0.03240 ( 21) SS BOND : angle 2.70477 ( 42) hydrogen bonds : bond 0.17125 ( 461) hydrogen bonds : angle 7.86842 ( 1302) link_ALPHA1-3 : bond 0.08348 ( 3) link_ALPHA1-3 : angle 3.75787 ( 9) link_ALPHA1-6 : bond 0.05519 ( 3) link_ALPHA1-6 : angle 3.13911 ( 9) link_BETA1-4 : bond 0.07290 ( 9) link_BETA1-4 : angle 5.30207 ( 27) link_NAG-ASN : bond 0.07894 ( 9) link_NAG-ASN : angle 1.59115 ( 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 : 0.536 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: 0.1403 time to fit residues: 98.2945 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 : 0.487 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4243 r_free = 0.4243 target = 0.130635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.097427 restraints weight = 33300.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.101528 restraints weight = 19355.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104480 restraints weight = 10289.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.106180 restraints weight = 7681.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.106279 restraints weight = 7035.416| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4022 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= 0.203 Angle : 0.842 9.293 18414 Z= 0.442 Chirality : 0.050 0.242 2106 Planarity : 0.006 0.052 2310 Dihedral : 10.474 86.168 2268 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % 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: -0.35 (0.20), residues: 1614 helix: 0.52 (0.34), residues: 231 sheet: -0.02 (0.26), residues: 405 loop : -0.46 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.033 0.003 TYR D 534 PHE 0.046 0.003 PHE G 29 TRP 0.018 0.003 TRP C 275 HIS 0.006 0.002 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00463 (13473) covalent geometry : angle 0.81940 (18300) SS BOND : bond 0.00653 ( 21) SS BOND : angle 2.01433 ( 42) hydrogen bonds : bond 0.05057 ( 461) hydrogen bonds : angle 6.50495 ( 1302) link_ALPHA1-3 : bond 0.01616 ( 3) link_ALPHA1-3 : angle 2.32007 ( 9) link_ALPHA1-6 : bond 0.00714 ( 3) link_ALPHA1-6 : angle 2.23348 ( 9) link_BETA1-4 : bond 0.00890 ( 9) link_BETA1-4 : angle 3.17102 ( 27) link_NAG-ASN : bond 0.00633 ( 9) link_NAG-ASN : angle 2.98078 ( 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 334 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8539 (mttm) REVERT: A 126 PRO cc_start: 0.8007 (Cg_exo) cc_final: 0.7604 (Cg_endo) REVERT: A 235 GLN cc_start: 0.9143 (tt0) cc_final: 0.8751 (tm-30) REVERT: G 23 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8499 (ttm-80) REVERT: G 37 VAL cc_start: 0.8435 (m) cc_final: 0.8190 (m) REVERT: G 46 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7311 (mm-30) REVERT: G 48 MET cc_start: 0.8635 (mtp) cc_final: 0.8162 (mtp) REVERT: G 52 MET cc_start: 0.7792 (mmm) cc_final: 0.7436 (mmm) REVERT: G 90 TYR cc_start: 0.8200 (m-80) cc_final: 0.7966 (m-80) REVERT: J 70 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9041 (mm-30) REVERT: J 97 THR cc_start: 0.6179 (t) cc_final: 0.5185 (p) REVERT: B 120 GLU cc_start: 0.7288 (pp20) cc_final: 0.7059 (pp20) REVERT: B 130 ARG cc_start: 0.6868 (ptt-90) cc_final: 0.6397 (ptt90) REVERT: B 156 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6964 (tp30) REVERT: B 235 GLN cc_start: 0.9182 (tt0) cc_final: 0.8597 (tm-30) REVERT: H 20 VAL cc_start: 0.8694 (t) cc_final: 0.8392 (p) REVERT: H 33 TYR cc_start: 0.7651 (m-80) cc_final: 0.7353 (m-80) REVERT: H 46 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7136 (mm-30) REVERT: H 48 MET cc_start: 0.8534 (mtp) cc_final: 0.8262 (mtp) REVERT: K 18 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7767 (tmm-80) REVERT: K 97 THR cc_start: 0.6558 (t) cc_final: 0.6297 (p) REVERT: C 130 ARG cc_start: 0.6886 (mtm-85) cc_final: 0.6492 (ptt-90) REVERT: C 156 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6935 (tp30) REVERT: C 235 GLN cc_start: 0.9198 (tt0) cc_final: 0.8813 (tm-30) REVERT: C 258 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8875 (mt-10) REVERT: I 20 VAL cc_start: 0.8733 (t) cc_final: 0.8462 (t) REVERT: I 46 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7177 (mm-30) REVERT: I 48 MET cc_start: 0.8631 (mtp) cc_final: 0.8226 (mtp) REVERT: I 53 ILE cc_start: 0.8100 (tt) cc_final: 0.7845 (mm) REVERT: I 90 TYR cc_start: 0.8259 (m-80) cc_final: 0.8045 (m-80) REVERT: L 70 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9096 (mm-30) REVERT: L 97 THR cc_start: 0.6265 (t) cc_final: 0.5980 (p) REVERT: L 103 LYS cc_start: 0.8189 (tttt) cc_final: 0.7943 (tttm) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.1320 time to fit residues: 60.5529 Evaluate side-chains 221 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 9.9990 chunk 111 optimal weight: 4.9990 chunk 146 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** 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 = 0.4103 r_free = 0.4103 target = 0.120660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.088482 restraints weight = 33979.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.091046 restraints weight = 16479.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.091912 restraints weight = 11121.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092700 restraints weight = 9523.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093025 restraints weight = 8530.361| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 13518 Z= 0.306 Angle : 0.902 8.819 18414 Z= 0.468 Chirality : 0.052 0.230 2106 Planarity : 0.006 0.079 2310 Dihedral : 9.720 76.535 2268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.79 % 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: -0.87 (0.20), residues: 1614 helix: 0.40 (0.35), residues: 231 sheet: -0.37 (0.22), residues: 495 loop : -0.92 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 24 TYR 0.031 0.003 TYR E 534 PHE 0.037 0.003 PHE E 592 TRP 0.027 0.004 TRP B 275 HIS 0.008 0.003 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00696 (13473) covalent geometry : angle 0.88501 (18300) SS BOND : bond 0.00693 ( 21) SS BOND : angle 2.25507 ( 42) hydrogen bonds : bond 0.05347 ( 461) hydrogen bonds : angle 6.62159 ( 1302) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 2.04886 ( 9) link_ALPHA1-6 : bond 0.00524 ( 3) link_ALPHA1-6 : angle 2.96070 ( 9) link_BETA1-4 : bond 0.00401 ( 9) link_BETA1-4 : angle 2.63283 ( 27) link_NAG-ASN : bond 0.00752 ( 9) link_NAG-ASN : angle 2.23984 ( 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 309 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.501 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: 0.7435 (p) cc_final: 0.6663 (t) REVERT: A 167 SER cc_start: 0.8371 (m) cc_final: 0.8067 (p) REVERT: A 229 MET cc_start: 0.8478 (pmm) cc_final: 0.8205 (pmm) REVERT: A 235 GLN cc_start: 0.9132 (tt0) cc_final: 0.8447 (tm-30) REVERT: G 19 LYS cc_start: 0.8919 (tptt) cc_final: 0.8511 (tptp) REVERT: G 32 LYS cc_start: 0.9198 (tmtt) cc_final: 0.8806 (tptt) REVERT: G 48 MET cc_start: 0.8920 (mtp) cc_final: 0.8432 (mtp) REVERT: G 96 GLU cc_start: 0.7438 (tt0) cc_final: 0.7176 (tp30) REVERT: J 70 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9190 (tp30) REVERT: J 71 PHE cc_start: 0.8568 (m-80) cc_final: 0.7426 (m-10) REVERT: D 564 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 229 MET cc_start: 0.8537 (pmm) cc_final: 0.8263 (pmm) REVERT: B 235 GLN cc_start: 0.9150 (tt0) cc_final: 0.8636 (tm-30) REVERT: H 19 LYS cc_start: 0.8757 (tptt) cc_final: 0.8188 (tptp) REVERT: H 20 VAL cc_start: 0.8598 (t) cc_final: 0.8067 (t) REVERT: H 33 TYR cc_start: 0.7428 (m-80) cc_final: 0.7080 (m-80) REVERT: H 48 MET cc_start: 0.8195 (mtp) cc_final: 0.7906 (mtp) REVERT: H 90 TYR cc_start: 0.8376 (m-10) cc_final: 0.8012 (m-80) REVERT: H 100 TRP cc_start: 0.6067 (p90) cc_final: 0.5718 (p90) REVERT: K 18 ARG cc_start: 0.8373 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: K 35 TRP cc_start: 0.5776 (m-90) cc_final: 0.5390 (m-90) REVERT: K 48 ILE cc_start: 0.7500 (mm) cc_final: 0.7217 (mm) REVERT: K 90 GLN cc_start: 0.7468 (tt0) cc_final: 0.6733 (tt0) REVERT: K 97 THR cc_start: 0.6800 (t) cc_final: 0.6145 (p) REVERT: C 229 MET cc_start: 0.8544 (pmm) cc_final: 0.8243 (pmm) REVERT: C 230 THR cc_start: 0.6695 (m) cc_final: 0.6399 (m) REVERT: C 235 GLN cc_start: 0.9240 (tt0) cc_final: 0.8490 (tm-30) REVERT: I 19 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8677 (mmmt) REVERT: I 32 LYS cc_start: 0.9238 (tmtt) cc_final: 0.9020 (tptt) REVERT: I 46 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7698 (mm-30) REVERT: I 48 MET cc_start: 0.8938 (mtp) cc_final: 0.8586 (mtp) REVERT: I 96 GLU cc_start: 0.7395 (tt0) cc_final: 0.7082 (tt0) REVERT: L 90 GLN cc_start: 0.7487 (tt0) cc_final: 0.6890 (tt0) REVERT: L 97 THR cc_start: 0.6597 (t) cc_final: 0.5816 (p) REVERT: F 545 GLU cc_start: 0.7517 (pm20) cc_final: 0.7264 (mt-10) REVERT: F 564 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8537 (tm-30) outliers start: 2 outliers final: 2 residues processed: 309 average time/residue: 0.1374 time to fit residues: 58.0728 Evaluate side-chains 207 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 1.9990 chunk 95 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 263 ASN D 521 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.125084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093006 restraints weight = 34810.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.097416 restraints weight = 16944.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.098757 restraints weight = 9535.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.098949 restraints weight = 8241.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099322 restraints weight = 7817.020| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13518 Z= 0.154 Angle : 0.735 8.808 18414 Z= 0.385 Chirality : 0.049 0.240 2106 Planarity : 0.005 0.045 2310 Dihedral : 8.833 69.526 2268 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.07 % 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: -0.95 (0.20), residues: 1614 helix: 0.68 (0.36), residues: 234 sheet: -0.51 (0.22), residues: 501 loop : -1.03 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 94 TYR 0.038 0.002 TYR H 33 PHE 0.035 0.002 PHE H 29 TRP 0.031 0.002 TRP F 597 HIS 0.006 0.002 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00337 (13473) covalent geometry : angle 0.71630 (18300) SS BOND : bond 0.00312 ( 21) SS BOND : angle 2.32469 ( 42) hydrogen bonds : bond 0.04347 ( 461) hydrogen bonds : angle 5.98913 ( 1302) link_ALPHA1-3 : bond 0.01239 ( 3) link_ALPHA1-3 : angle 1.46702 ( 9) link_ALPHA1-6 : bond 0.01022 ( 3) link_ALPHA1-6 : angle 2.31605 ( 9) link_BETA1-4 : bond 0.00489 ( 9) link_BETA1-4 : angle 2.41335 ( 27) link_NAG-ASN : bond 0.00393 ( 9) link_NAG-ASN : angle 2.03082 ( 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 295 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.474 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: 0.7386 (p) cc_final: 0.6635 (t) REVERT: A 148 PRO cc_start: 0.8313 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: A 167 SER cc_start: 0.8442 (m) cc_final: 0.8093 (p) REVERT: A 229 MET cc_start: 0.8370 (pmm) cc_final: 0.8159 (pmm) REVERT: A 235 GLN cc_start: 0.9111 (tt0) cc_final: 0.8286 (tm-30) REVERT: G 23 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8615 (ttm-80) REVERT: G 48 MET cc_start: 0.8824 (mtp) cc_final: 0.8441 (mtp) REVERT: G 81 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7437 (tp30) REVERT: J 39 LYS cc_start: 0.8714 (mptt) cc_final: 0.8485 (mptt) REVERT: J 71 PHE cc_start: 0.8322 (m-80) cc_final: 0.7251 (m-10) REVERT: B 130 ARG cc_start: 0.7622 (ptt90) cc_final: 0.6438 (ptt-90) REVERT: B 229 MET cc_start: 0.8336 (pmm) cc_final: 0.8085 (pmm) REVERT: B 235 GLN cc_start: 0.9136 (tt0) cc_final: 0.8369 (tm-30) REVERT: H 20 VAL cc_start: 0.8787 (t) cc_final: 0.8480 (t) REVERT: H 35 ILE cc_start: 0.8833 (mm) cc_final: 0.8239 (tp) REVERT: H 48 MET cc_start: 0.8323 (mtp) cc_final: 0.7752 (mtp) REVERT: H 81 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7261 (tp30) REVERT: H 90 TYR cc_start: 0.8274 (m-10) cc_final: 0.7986 (m-10) REVERT: H 100 TRP cc_start: 0.5844 (p90) cc_final: 0.5410 (p90) REVERT: K 90 GLN cc_start: 0.7458 (tt0) cc_final: 0.6757 (tt0) REVERT: K 97 THR cc_start: 0.7125 (t) cc_final: 0.5784 (t) REVERT: C 229 MET cc_start: 0.8418 (pmm) cc_final: 0.8131 (pmm) REVERT: C 235 GLN cc_start: 0.9190 (tt0) cc_final: 0.8480 (tm-30) REVERT: I 23 ARG cc_start: 0.8754 (tpt170) cc_final: 0.8345 (tpm170) REVERT: I 46 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7243 (mm-30) REVERT: I 48 MET cc_start: 0.8918 (mtp) cc_final: 0.8541 (mtp) REVERT: I 81 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7692 (tp30) REVERT: I 96 GLU cc_start: 0.6669 (tt0) cc_final: 0.6425 (tt0) REVERT: L 90 GLN cc_start: 0.7630 (tt0) cc_final: 0.6891 (tt0) REVERT: L 97 THR cc_start: 0.6812 (t) cc_final: 0.5373 (p) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1191 time to fit residues: 49.8318 Evaluate side-chains 196 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 8.9990 chunk 76 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN A 263 ASN B 235 GLN B 263 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 263 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.083299 restraints weight = 36460.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.085649 restraints weight = 17699.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.086941 restraints weight = 11920.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.087515 restraints weight = 9726.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.087709 restraints weight = 8873.471| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13518 Z= 0.286 Angle : 0.870 9.638 18414 Z= 0.444 Chirality : 0.053 0.265 2106 Planarity : 0.006 0.073 2310 Dihedral : 8.715 63.124 2268 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -1.23 (0.20), residues: 1614 helix: 0.79 (0.35), residues: 213 sheet: -0.62 (0.22), residues: 513 loop : -1.34 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 596 TYR 0.028 0.003 TYR E 534 PHE 0.019 0.003 PHE L 71 TRP 0.031 0.004 TRP C 104 HIS 0.010 0.002 HIS H 100C Details of bonding type rmsd covalent geometry : bond 0.00650 (13473) covalent geometry : angle 0.85233 (18300) SS BOND : bond 0.00721 ( 21) SS BOND : angle 2.34577 ( 42) hydrogen bonds : bond 0.05100 ( 461) hydrogen bonds : angle 6.36059 ( 1302) link_ALPHA1-3 : bond 0.00946 ( 3) link_ALPHA1-3 : angle 2.47760 ( 9) link_ALPHA1-6 : bond 0.00453 ( 3) link_ALPHA1-6 : angle 2.94236 ( 9) link_BETA1-4 : bond 0.00507 ( 9) link_BETA1-4 : angle 2.54281 ( 27) link_NAG-ASN : bond 0.00528 ( 9) link_NAG-ASN : angle 2.03208 ( 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 267 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.538 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: 0.7981 (p) cc_final: 0.7428 (t) REVERT: A 167 SER cc_start: 0.8411 (m) cc_final: 0.8115 (p) REVERT: A 223 ASP cc_start: 0.7337 (m-30) cc_final: 0.7012 (m-30) REVERT: A 229 MET cc_start: 0.8537 (pmm) cc_final: 0.8323 (pmm) REVERT: A 230 THR cc_start: 0.7262 (m) cc_final: 0.6883 (m) REVERT: A 231 ASN cc_start: 0.8418 (t0) cc_final: 0.7512 (p0) REVERT: A 235 GLN cc_start: 0.9139 (tt0) cc_final: 0.8379 (tm-30) REVERT: G 46 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7193 (mm-30) REVERT: G 48 MET cc_start: 0.9038 (mtp) cc_final: 0.8770 (mtp) REVERT: G 64 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7594 (mm-40) REVERT: G 80 MET cc_start: 0.8782 (ptp) cc_final: 0.8502 (mtm) REVERT: G 81 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7321 (tp30) REVERT: D 564 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8510 (tm-30) REVERT: B 77 THR cc_start: 0.7837 (p) cc_final: 0.7339 (t) REVERT: B 229 MET cc_start: 0.8593 (pmm) cc_final: 0.8367 (pmm) REVERT: B 230 THR cc_start: 0.7168 (m) cc_final: 0.6897 (m) REVERT: B 235 GLN cc_start: 0.9153 (tt0) cc_final: 0.8458 (tm-30) REVERT: H 19 LYS cc_start: 0.8165 (tptp) cc_final: 0.7898 (tptp) REVERT: H 35 ILE cc_start: 0.8840 (mm) cc_final: 0.8261 (tp) REVERT: H 46 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7659 (mm-30) REVERT: H 48 MET cc_start: 0.8442 (mtp) cc_final: 0.8029 (mtp) REVERT: H 80 MET cc_start: 0.7882 (mtm) cc_final: 0.7646 (mtp) REVERT: H 90 TYR cc_start: 0.8596 (m-10) cc_final: 0.8215 (m-80) REVERT: K 27 GLN cc_start: 0.7413 (tm-30) cc_final: 0.7134 (tm-30) REVERT: K 48 ILE cc_start: 0.7925 (tt) cc_final: 0.7560 (tp) REVERT: K 70 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8816 (mm-30) REVERT: K 90 GLN cc_start: 0.7866 (tt0) cc_final: 0.7159 (tt0) REVERT: K 97 THR cc_start: 0.7236 (t) cc_final: 0.6618 (p) REVERT: C 77 THR cc_start: 0.7652 (p) cc_final: 0.6989 (t) REVERT: C 229 MET cc_start: 0.8642 (pmm) cc_final: 0.8412 (pmm) REVERT: C 230 THR cc_start: 0.6871 (m) cc_final: 0.6528 (m) REVERT: C 235 GLN cc_start: 0.9177 (tt0) cc_final: 0.8890 (tt0) REVERT: I 23 ARG cc_start: 0.8837 (tpt170) cc_final: 0.8503 (tpp-160) REVERT: I 32 LYS cc_start: 0.9310 (tmtt) cc_final: 0.9064 (tptp) REVERT: I 48 MET cc_start: 0.9094 (mtp) cc_final: 0.8887 (mtp) REVERT: I 52 MET cc_start: 0.8190 (mpp) cc_final: 0.7868 (mpp) REVERT: I 68 THR cc_start: 0.8592 (m) cc_final: 0.8186 (p) REVERT: I 81 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7355 (tp30) REVERT: I 94 ARG cc_start: 0.4862 (tmt170) cc_final: 0.4509 (ptm-80) REVERT: L 27 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7363 (tm-30) REVERT: L 71 PHE cc_start: 0.8776 (m-10) cc_final: 0.7754 (m-10) REVERT: L 90 GLN cc_start: 0.7805 (tt0) cc_final: 0.7179 (tt0) REVERT: L 97 THR cc_start: 0.7024 (t) cc_final: 0.6255 (p) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1057 time to fit residues: 40.7146 Evaluate side-chains 194 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.120473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.087608 restraints weight = 35945.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090337 restraints weight = 19491.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.092337 restraints weight = 11658.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.092541 restraints weight = 9639.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092741 restraints weight = 8789.107| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13518 Z= 0.160 Angle : 0.734 10.495 18414 Z= 0.376 Chirality : 0.049 0.250 2106 Planarity : 0.005 0.050 2310 Dihedral : 8.076 57.677 2268 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.08 (0.20), residues: 1614 helix: 1.32 (0.37), residues: 198 sheet: -0.54 (0.23), residues: 498 loop : -1.29 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 130 TYR 0.016 0.002 TYR E 534 PHE 0.042 0.002 PHE H 29 TRP 0.030 0.002 TRP K 35 HIS 0.010 0.002 HIS G 100C Details of bonding type rmsd covalent geometry : bond 0.00367 (13473) covalent geometry : angle 0.71850 (18300) SS BOND : bond 0.00319 ( 21) SS BOND : angle 2.07748 ( 42) hydrogen bonds : bond 0.04288 ( 461) hydrogen bonds : angle 5.88375 ( 1302) link_ALPHA1-3 : bond 0.01017 ( 3) link_ALPHA1-3 : angle 1.30441 ( 9) link_ALPHA1-6 : bond 0.00909 ( 3) link_ALPHA1-6 : angle 2.51507 ( 9) link_BETA1-4 : bond 0.00333 ( 9) link_BETA1-4 : angle 2.27435 ( 27) link_NAG-ASN : bond 0.00257 ( 9) link_NAG-ASN : angle 1.80444 ( 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 289 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8066 (p) cc_final: 0.7523 (t) REVERT: A 167 SER cc_start: 0.8558 (m) cc_final: 0.8182 (p) REVERT: A 223 ASP cc_start: 0.7471 (m-30) cc_final: 0.7112 (m-30) REVERT: A 229 MET cc_start: 0.8539 (pmm) cc_final: 0.8335 (pmm) REVERT: A 230 THR cc_start: 0.7165 (m) cc_final: 0.6753 (m) REVERT: A 231 ASN cc_start: 0.8379 (t0) cc_final: 0.7426 (p0) REVERT: A 235 GLN cc_start: 0.9118 (tt0) cc_final: 0.8391 (tm-30) REVERT: A 236 VAL cc_start: 0.7277 (t) cc_final: 0.7011 (t) REVERT: G 23 ARG cc_start: 0.8851 (ttt180) cc_final: 0.8624 (ttm-80) REVERT: G 29 PHE cc_start: 0.5572 (m-80) cc_final: 0.5220 (m-80) REVERT: G 46 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7112 (mm-30) REVERT: G 48 MET cc_start: 0.9030 (mtp) cc_final: 0.8734 (mtp) REVERT: G 52 MET cc_start: 0.8345 (mmp) cc_final: 0.8051 (mmm) REVERT: G 53 ILE cc_start: 0.8124 (tt) cc_final: 0.7861 (pt) REVERT: G 64 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7623 (mm-40) REVERT: G 81 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7809 (tp30) REVERT: B 77 THR cc_start: 0.7941 (p) cc_final: 0.7439 (t) REVERT: B 229 MET cc_start: 0.8574 (pmm) cc_final: 0.8347 (pmm) REVERT: B 230 THR cc_start: 0.6999 (m) cc_final: 0.6731 (m) REVERT: B 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8246 (tm-30) REVERT: B 236 VAL cc_start: 0.7203 (t) cc_final: 0.6804 (t) REVERT: H 46 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7216 (mp0) REVERT: H 48 MET cc_start: 0.8365 (mtp) cc_final: 0.7902 (mtp) REVERT: H 80 MET cc_start: 0.7767 (mtm) cc_final: 0.7436 (mtp) REVERT: H 90 TYR cc_start: 0.8490 (m-10) cc_final: 0.8080 (m-80) REVERT: K 48 ILE cc_start: 0.7673 (tt) cc_final: 0.6962 (tp) REVERT: K 70 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8758 (mm-30) REVERT: K 90 GLN cc_start: 0.7937 (tt0) cc_final: 0.7187 (tt0) REVERT: K 97 THR cc_start: 0.7434 (t) cc_final: 0.6319 (p) REVERT: C 77 THR cc_start: 0.7685 (p) cc_final: 0.7030 (t) REVERT: C 230 THR cc_start: 0.6755 (m) cc_final: 0.6416 (m) REVERT: C 235 GLN cc_start: 0.9210 (tt0) cc_final: 0.8387 (tm-30) REVERT: C 258 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8688 (mt-10) REVERT: I 19 LYS cc_start: 0.8764 (tptt) cc_final: 0.8506 (tptp) REVERT: I 23 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8388 (tpp-160) REVERT: I 48 MET cc_start: 0.9132 (mtp) cc_final: 0.8875 (mtp) REVERT: I 52 MET cc_start: 0.8265 (mpp) cc_final: 0.7803 (mpp) REVERT: I 53 ILE cc_start: 0.8188 (tt) cc_final: 0.7977 (pt) REVERT: I 68 THR cc_start: 0.8547 (m) cc_final: 0.8164 (p) REVERT: I 81 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7296 (tp30) REVERT: I 97 ILE cc_start: 0.8348 (tp) cc_final: 0.8018 (tp) REVERT: L 27 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7363 (tm-30) REVERT: L 33 LEU cc_start: 0.8743 (tp) cc_final: 0.8524 (tp) REVERT: L 71 PHE cc_start: 0.8415 (m-10) cc_final: 0.7213 (m-10) REVERT: L 90 GLN cc_start: 0.7790 (tt0) cc_final: 0.6977 (tt0) REVERT: L 97 THR cc_start: 0.7276 (t) cc_final: 0.5909 (p) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1190 time to fit residues: 48.8145 Evaluate side-chains 205 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 5.9990 chunk 86 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 138 optimal weight: 0.1980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN J 32 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN H 64 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.121013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.086412 restraints weight = 35286.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090103 restraints weight = 18126.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.092625 restraints weight = 11495.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094309 restraints weight = 8449.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.095387 restraints weight = 6867.356| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13518 Z= 0.157 Angle : 0.735 11.611 18414 Z= 0.374 Chirality : 0.049 0.238 2106 Planarity : 0.006 0.076 2310 Dihedral : 7.673 52.622 2268 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.05 (0.20), residues: 1614 helix: 1.57 (0.38), residues: 198 sheet: -0.58 (0.22), residues: 504 loop : -1.29 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 172 TYR 0.017 0.002 TYR E 534 PHE 0.022 0.002 PHE H 29 TRP 0.030 0.002 TRP I 103 HIS 0.009 0.001 HIS G 100C Details of bonding type rmsd covalent geometry : bond 0.00365 (13473) covalent geometry : angle 0.71819 (18300) SS BOND : bond 0.00395 ( 21) SS BOND : angle 2.28966 ( 42) hydrogen bonds : bond 0.04039 ( 461) hydrogen bonds : angle 5.76152 ( 1302) link_ALPHA1-3 : bond 0.00909 ( 3) link_ALPHA1-3 : angle 1.39299 ( 9) link_ALPHA1-6 : bond 0.00885 ( 3) link_ALPHA1-6 : angle 2.57544 ( 9) link_BETA1-4 : bond 0.00358 ( 9) link_BETA1-4 : angle 2.22806 ( 27) link_NAG-ASN : bond 0.00307 ( 9) link_NAG-ASN : angle 1.72032 ( 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 272 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.497 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: 0.8052 (p) cc_final: 0.7520 (t) REVERT: A 167 SER cc_start: 0.8434 (m) cc_final: 0.8106 (p) REVERT: A 223 ASP cc_start: 0.7656 (m-30) cc_final: 0.7215 (m-30) REVERT: A 230 THR cc_start: 0.7192 (m) cc_final: 0.6846 (m) REVERT: A 231 ASN cc_start: 0.8393 (t0) cc_final: 0.7422 (p0) REVERT: A 235 GLN cc_start: 0.9092 (tt0) cc_final: 0.8349 (tm-30) REVERT: G 46 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7119 (mm-30) REVERT: G 48 MET cc_start: 0.9124 (mtp) cc_final: 0.8920 (mtp) REVERT: G 64 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7621 (mm-40) REVERT: G 80 MET cc_start: 0.8494 (pmm) cc_final: 0.8187 (pmm) REVERT: G 81 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8080 (tp30) REVERT: J 13 VAL cc_start: 0.6815 (t) cc_final: 0.6187 (t) REVERT: J 33 LEU cc_start: 0.8927 (tp) cc_final: 0.8440 (tp) REVERT: J 91 TYR cc_start: 0.6797 (p90) cc_final: 0.5528 (p90) REVERT: B 77 THR cc_start: 0.7989 (p) cc_final: 0.7509 (t) REVERT: B 230 THR cc_start: 0.7149 (m) cc_final: 0.6896 (m) REVERT: B 235 GLN cc_start: 0.9166 (tt0) cc_final: 0.8159 (tm-30) REVERT: H 20 VAL cc_start: 0.8560 (t) cc_final: 0.8196 (t) REVERT: H 46 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7254 (mp0) REVERT: H 48 MET cc_start: 0.8302 (mtp) cc_final: 0.7875 (mtp) REVERT: H 52 MET cc_start: 0.8335 (mmm) cc_final: 0.8073 (mmm) REVERT: H 80 MET cc_start: 0.7781 (mtm) cc_final: 0.7468 (mtp) REVERT: H 90 TYR cc_start: 0.8505 (m-10) cc_final: 0.8090 (m-80) REVERT: K 18 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7596 (ttp80) REVERT: K 48 ILE cc_start: 0.7875 (tt) cc_final: 0.7321 (tp) REVERT: K 90 GLN cc_start: 0.8274 (tt0) cc_final: 0.7587 (tt0) REVERT: K 97 THR cc_start: 0.7356 (t) cc_final: 0.6249 (p) REVERT: E 583 SER cc_start: 0.7875 (m) cc_final: 0.7570 (p) REVERT: C 77 THR cc_start: 0.7693 (p) cc_final: 0.7029 (t) REVERT: C 229 MET cc_start: 0.8328 (pmm) cc_final: 0.8078 (pmm) REVERT: C 235 GLN cc_start: 0.9209 (tt0) cc_final: 0.8416 (tm-30) REVERT: C 258 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8656 (mt-10) REVERT: I 19 LYS cc_start: 0.8750 (tptt) cc_final: 0.8398 (tptp) REVERT: I 23 ARG cc_start: 0.8775 (tpt170) cc_final: 0.8300 (tpp-160) REVERT: I 48 MET cc_start: 0.9106 (mtp) cc_final: 0.8782 (mtp) REVERT: I 68 THR cc_start: 0.8561 (m) cc_final: 0.8289 (p) REVERT: I 81 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7644 (mm-30) REVERT: I 100 PHE cc_start: 0.6521 (p90) cc_final: 0.6224 (p90) REVERT: L 42 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8522 (mm110) REVERT: L 71 PHE cc_start: 0.8483 (m-80) cc_final: 0.7255 (m-10) REVERT: L 90 GLN cc_start: 0.8089 (tt0) cc_final: 0.7437 (tt0) REVERT: L 97 THR cc_start: 0.7128 (t) cc_final: 0.5793 (p) REVERT: F 583 SER cc_start: 0.7899 (m) cc_final: 0.7357 (p) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1086 time to fit residues: 43.3254 Evaluate side-chains 208 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 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 = 0.4044 r_free = 0.4044 target = 0.116220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080606 restraints weight = 35287.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.084066 restraints weight = 18444.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086332 restraints weight = 11938.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.087884 restraints weight = 8972.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.088897 restraints weight = 7410.694| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13518 Z= 0.235 Angle : 0.809 11.253 18414 Z= 0.413 Chirality : 0.050 0.245 2106 Planarity : 0.006 0.070 2310 Dihedral : 7.829 49.428 2268 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.29 (0.21), residues: 1614 helix: 1.44 (0.38), residues: 198 sheet: -0.90 (0.21), residues: 555 loop : -1.36 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.025 0.002 TYR G 33 PHE 0.033 0.002 PHE G 29 TRP 0.041 0.003 TRP H 103 HIS 0.012 0.002 HIS G 100C Details of bonding type rmsd covalent geometry : bond 0.00538 (13473) covalent geometry : angle 0.79168 (18300) SS BOND : bond 0.00624 ( 21) SS BOND : angle 2.38992 ( 42) hydrogen bonds : bond 0.04555 ( 461) hydrogen bonds : angle 6.05188 ( 1302) link_ALPHA1-3 : bond 0.00721 ( 3) link_ALPHA1-3 : angle 1.79875 ( 9) link_ALPHA1-6 : bond 0.00547 ( 3) link_ALPHA1-6 : angle 3.07595 ( 9) link_BETA1-4 : bond 0.00310 ( 9) link_BETA1-4 : angle 2.28049 ( 27) link_NAG-ASN : bond 0.00290 ( 9) link_NAG-ASN : angle 1.86405 ( 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 270 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 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: A 77 THR cc_start: 0.8216 (p) cc_final: 0.7722 (t) REVERT: A 167 SER cc_start: 0.8412 (m) cc_final: 0.8123 (p) REVERT: A 223 ASP cc_start: 0.7993 (m-30) cc_final: 0.7538 (m-30) REVERT: A 229 MET cc_start: 0.8456 (pmm) cc_final: 0.7985 (pmm) REVERT: A 230 THR cc_start: 0.7373 (m) cc_final: 0.6987 (m) REVERT: A 231 ASN cc_start: 0.8545 (t0) cc_final: 0.7545 (p0) REVERT: A 235 GLN cc_start: 0.9119 (tt0) cc_final: 0.8343 (tm-30) REVERT: G 48 MET cc_start: 0.9104 (mtp) cc_final: 0.8866 (mtp) REVERT: G 52 MET cc_start: 0.8509 (mmp) cc_final: 0.8257 (mmm) REVERT: G 64 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7796 (mm-40) REVERT: G 79 HIS cc_start: 0.8099 (m-70) cc_final: 0.7527 (m-70) REVERT: G 80 MET cc_start: 0.8392 (pmm) cc_final: 0.8016 (pmm) REVERT: G 81 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7707 (tp30) REVERT: J 13 VAL cc_start: 0.6269 (t) cc_final: 0.5998 (p) REVERT: J 42 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8595 (mp-120) REVERT: D 517 TYR cc_start: 0.7989 (p90) cc_final: 0.7780 (p90) REVERT: B 77 THR cc_start: 0.8215 (p) cc_final: 0.7758 (t) REVERT: B 229 MET cc_start: 0.8517 (pmm) cc_final: 0.8150 (pmm) REVERT: B 230 THR cc_start: 0.7458 (m) cc_final: 0.7138 (m) REVERT: B 231 ASN cc_start: 0.8754 (t0) cc_final: 0.7803 (p0) REVERT: B 235 GLN cc_start: 0.9135 (tt0) cc_final: 0.8320 (tm-30) REVERT: B 236 VAL cc_start: 0.7351 (t) cc_final: 0.6988 (t) REVERT: H 46 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7273 (mp0) REVERT: H 48 MET cc_start: 0.8472 (mtp) cc_final: 0.8074 (mtp) REVERT: H 52 MET cc_start: 0.8342 (mmm) cc_final: 0.8014 (mmm) REVERT: H 81 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7374 (tp30) REVERT: K 18 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7497 (ttp80) REVERT: K 42 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8441 (mm110) REVERT: K 48 ILE cc_start: 0.7956 (tt) cc_final: 0.7497 (tp) REVERT: K 70 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8794 (mm-30) REVERT: K 90 GLN cc_start: 0.8318 (tt0) cc_final: 0.7620 (tt0) REVERT: K 97 THR cc_start: 0.7378 (t) cc_final: 0.6316 (p) REVERT: E 583 SER cc_start: 0.8030 (m) cc_final: 0.7739 (p) REVERT: C 77 THR cc_start: 0.7823 (p) cc_final: 0.7241 (t) REVERT: C 229 MET cc_start: 0.8432 (pmm) cc_final: 0.8192 (pmm) REVERT: C 235 GLN cc_start: 0.9190 (tt0) cc_final: 0.8376 (tm-30) REVERT: I 19 LYS cc_start: 0.8725 (tptt) cc_final: 0.8481 (tptp) REVERT: I 48 MET cc_start: 0.9157 (mtp) cc_final: 0.8874 (mtp) REVERT: I 68 THR cc_start: 0.8642 (m) cc_final: 0.8281 (p) REVERT: I 81 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7333 (tp30) REVERT: I 100 PHE cc_start: 0.6601 (p90) cc_final: 0.5710 (p90) REVERT: L 42 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8497 (mm110) REVERT: L 71 PHE cc_start: 0.8591 (m-80) cc_final: 0.7563 (m-10) REVERT: L 90 GLN cc_start: 0.8350 (tt0) cc_final: 0.7560 (tt0) REVERT: L 97 THR cc_start: 0.7185 (t) cc_final: 0.5966 (p) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1089 time to fit residues: 43.4453 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 : 0.604 ------------------------------------------------------------------------------- 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: 8.9990 chunk 137 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 39 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.113620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.079688 restraints weight = 35798.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.082928 restraints weight = 18778.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085102 restraints weight = 12181.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.086534 restraints weight = 9122.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087399 restraints weight = 7542.897| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.8084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13518 Z= 0.323 Angle : 0.925 13.825 18414 Z= 0.468 Chirality : 0.053 0.231 2106 Planarity : 0.007 0.074 2310 Dihedral : 8.460 56.429 2268 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -1.52 (0.20), residues: 1614 helix: 0.89 (0.37), residues: 180 sheet: -1.14 (0.21), residues: 537 loop : -1.29 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 18 TYR 0.041 0.003 TYR F 534 PHE 0.031 0.003 PHE I 29 TRP 0.041 0.004 TRP G 103 HIS 0.016 0.003 HIS I 100C Details of bonding type rmsd covalent geometry : bond 0.00736 (13473) covalent geometry : angle 0.90828 (18300) SS BOND : bond 0.00521 ( 21) SS BOND : angle 2.44232 ( 42) hydrogen bonds : bond 0.05215 ( 461) hydrogen bonds : angle 6.44205 ( 1302) link_ALPHA1-3 : bond 0.00531 ( 3) link_ALPHA1-3 : angle 1.98453 ( 9) link_ALPHA1-6 : bond 0.00220 ( 3) link_ALPHA1-6 : angle 3.48672 ( 9) link_BETA1-4 : bond 0.00423 ( 9) link_BETA1-4 : angle 2.38175 ( 27) link_NAG-ASN : bond 0.00438 ( 9) link_NAG-ASN : angle 2.06957 ( 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 250 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.443 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: A 77 THR cc_start: 0.8403 (p) cc_final: 0.7986 (t) REVERT: A 229 MET cc_start: 0.8635 (pmm) cc_final: 0.8400 (pmm) REVERT: A 230 THR cc_start: 0.7652 (m) cc_final: 0.7320 (m) REVERT: A 231 ASN cc_start: 0.8662 (t0) cc_final: 0.7821 (p0) REVERT: A 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8396 (tm-30) REVERT: G 23 ARG cc_start: 0.8891 (ttt180) cc_final: 0.8661 (ttp-110) REVERT: G 35 ILE cc_start: 0.8833 (mm) cc_final: 0.8473 (tp) REVERT: G 64 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7929 (mm-40) REVERT: G 79 HIS cc_start: 0.8120 (m-70) cc_final: 0.7661 (m-70) REVERT: G 80 MET cc_start: 0.8206 (pmm) cc_final: 0.7698 (pmm) REVERT: G 81 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7912 (tp30) REVERT: J 11 MET cc_start: 0.5400 (ttp) cc_final: 0.5037 (ttt) REVERT: J 13 VAL cc_start: 0.6530 (t) cc_final: 0.6209 (p) REVERT: J 42 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8492 (mm110) REVERT: J 78 LEU cc_start: 0.8302 (pp) cc_final: 0.8051 (pp) REVERT: D 517 TYR cc_start: 0.8261 (p90) cc_final: 0.8009 (p90) REVERT: B 55 ASP cc_start: 0.7974 (m-30) cc_final: 0.7733 (m-30) REVERT: B 77 THR cc_start: 0.8590 (p) cc_final: 0.8194 (t) REVERT: B 229 MET cc_start: 0.8684 (pmm) cc_final: 0.8406 (pmm) REVERT: B 230 THR cc_start: 0.7488 (m) cc_final: 0.7181 (m) REVERT: B 231 ASN cc_start: 0.8826 (t0) cc_final: 0.8129 (p0) REVERT: B 235 GLN cc_start: 0.9168 (tt0) cc_final: 0.8486 (tm-30) REVERT: H 19 LYS cc_start: 0.8703 (tptt) cc_final: 0.8364 (tptp) REVERT: K 18 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7483 (ttp80) REVERT: K 42 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8461 (mm110) REVERT: K 48 ILE cc_start: 0.8118 (tt) cc_final: 0.7728 (tp) REVERT: K 70 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8742 (mm-30) REVERT: K 90 GLN cc_start: 0.8452 (tt0) cc_final: 0.7676 (tt0) REVERT: K 97 THR cc_start: 0.7696 (t) cc_final: 0.6730 (p) REVERT: C 77 THR cc_start: 0.8198 (p) cc_final: 0.7666 (t) REVERT: C 122 LEU cc_start: 0.9262 (mm) cc_final: 0.8845 (mm) REVERT: C 229 MET cc_start: 0.8538 (pmm) cc_final: 0.8297 (pmm) REVERT: C 231 ASN cc_start: 0.8729 (t0) cc_final: 0.7760 (p0) REVERT: C 235 GLN cc_start: 0.9193 (tt0) cc_final: 0.8459 (tm-30) REVERT: I 19 LYS cc_start: 0.8674 (tptt) cc_final: 0.8453 (tptp) REVERT: I 48 MET cc_start: 0.9247 (mtp) cc_final: 0.8983 (mtp) REVERT: I 80 MET cc_start: 0.8992 (ptp) cc_final: 0.8629 (ptp) REVERT: I 81 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7508 (tp30) REVERT: L 13 VAL cc_start: 0.6792 (t) cc_final: 0.6011 (t) REVERT: L 42 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8527 (mm110) REVERT: L 71 PHE cc_start: 0.8851 (m-80) cc_final: 0.7685 (m-10) REVERT: L 90 GLN cc_start: 0.8456 (tt0) cc_final: 0.7742 (tt0) REVERT: L 97 THR cc_start: 0.7372 (t) cc_final: 0.6328 (p) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1036 time to fit residues: 38.3504 Evaluate side-chains 182 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 1.9990 chunk 134 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.086474 restraints weight = 39428.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.089943 restraints weight = 21458.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.092283 restraints weight = 14203.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.093838 restraints weight = 10777.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.094775 restraints weight = 8967.926| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.8115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13518 Z= 0.141 Angle : 0.762 13.945 18414 Z= 0.386 Chirality : 0.049 0.225 2106 Planarity : 0.006 0.056 2310 Dihedral : 7.079 58.943 2268 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -1.28 (0.21), residues: 1614 helix: 1.40 (0.37), residues: 198 sheet: -1.16 (0.21), residues: 531 loop : -1.13 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 18 TYR 0.029 0.002 TYR D 534 PHE 0.022 0.002 PHE H 29 TRP 0.032 0.002 TRP K 35 HIS 0.006 0.002 HIS G 100C Details of bonding type rmsd covalent geometry : bond 0.00321 (13473) covalent geometry : angle 0.74958 (18300) SS BOND : bond 0.00351 ( 21) SS BOND : angle 1.92531 ( 42) hydrogen bonds : bond 0.04049 ( 461) hydrogen bonds : angle 5.82199 ( 1302) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.09403 ( 9) link_ALPHA1-6 : bond 0.00712 ( 3) link_ALPHA1-6 : angle 1.86088 ( 9) link_BETA1-4 : bond 0.00598 ( 9) link_BETA1-4 : angle 2.28404 ( 27) link_NAG-ASN : bond 0.00448 ( 9) link_NAG-ASN : angle 1.66226 ( 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 258 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.468 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: 0.8158 (p) cc_final: 0.7708 (t) REVERT: A 229 MET cc_start: 0.8338 (pmm) cc_final: 0.7942 (pmm) REVERT: A 230 THR cc_start: 0.7461 (m) cc_final: 0.7209 (m) REVERT: A 235 GLN cc_start: 0.9035 (tt0) cc_final: 0.8332 (tm-30) REVERT: G 79 HIS cc_start: 0.8152 (m-70) cc_final: 0.7754 (m-70) REVERT: G 80 MET cc_start: 0.8193 (pmm) cc_final: 0.7776 (pmm) REVERT: G 81 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7593 (tp30) REVERT: J 11 MET cc_start: 0.5295 (ttp) cc_final: 0.5001 (ttt) REVERT: J 13 VAL cc_start: 0.6673 (t) cc_final: 0.6372 (p) REVERT: B 77 THR cc_start: 0.8372 (p) cc_final: 0.7972 (t) REVERT: B 229 MET cc_start: 0.8339 (pmm) cc_final: 0.8076 (pmm) REVERT: B 231 ASN cc_start: 0.8865 (t0) cc_final: 0.8191 (p0) REVERT: B 235 GLN cc_start: 0.9164 (tt0) cc_final: 0.8215 (tm-30) REVERT: H 35 ILE cc_start: 0.8866 (mm) cc_final: 0.8451 (tp) REVERT: H 48 MET cc_start: 0.8748 (mtp) cc_final: 0.8536 (mtp) REVERT: H 80 MET cc_start: 0.8425 (pmm) cc_final: 0.7968 (pmm) REVERT: H 81 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7431 (tp30) REVERT: K 48 ILE cc_start: 0.7645 (tt) cc_final: 0.7335 (tp) REVERT: K 70 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8722 (mm-30) REVERT: K 71 PHE cc_start: 0.8836 (m-10) cc_final: 0.8387 (m-10) REVERT: K 90 GLN cc_start: 0.8507 (tt0) cc_final: 0.7853 (tt0) REVERT: K 97 THR cc_start: 0.7734 (t) cc_final: 0.6928 (p) REVERT: C 77 THR cc_start: 0.7722 (p) cc_final: 0.7200 (t) REVERT: C 122 LEU cc_start: 0.9226 (mm) cc_final: 0.8979 (mm) REVERT: C 231 ASN cc_start: 0.8858 (t0) cc_final: 0.7857 (p0) REVERT: C 235 GLN cc_start: 0.9121 (tt0) cc_final: 0.8241 (tm-30) REVERT: C 236 VAL cc_start: 0.7699 (t) cc_final: 0.7245 (t) REVERT: I 48 MET cc_start: 0.9103 (mtp) cc_final: 0.8839 (mtp) REVERT: I 51 ILE cc_start: 0.8485 (mm) cc_final: 0.8235 (mt) REVERT: I 80 MET cc_start: 0.8923 (ptp) cc_final: 0.8663 (ptp) REVERT: I 81 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7377 (tp30) REVERT: L 23 CYS cc_start: 0.6300 (m) cc_final: 0.5060 (m) REVERT: L 33 LEU cc_start: 0.8743 (tp) cc_final: 0.8430 (tp) REVERT: L 42 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8527 (mm110) REVERT: L 71 PHE cc_start: 0.8725 (m-80) cc_final: 0.7401 (m-10) REVERT: L 85 VAL cc_start: 0.8848 (t) cc_final: 0.8643 (p) REVERT: L 90 GLN cc_start: 0.8495 (tt0) cc_final: 0.8005 (tt0) REVERT: L 97 THR cc_start: 0.7404 (t) cc_final: 0.6617 (p) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1083 time to fit residues: 40.7357 Evaluate side-chains 181 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.129351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.090692 restraints weight = 39662.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.094066 restraints weight = 21281.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.096337 restraints weight = 14044.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.097811 restraints weight = 10627.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.098814 restraints weight = 8853.697| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13518 Z= 0.138 Angle : 0.735 13.478 18414 Z= 0.372 Chirality : 0.048 0.228 2106 Planarity : 0.006 0.061 2310 Dihedral : 6.417 57.930 2268 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % 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: -1.21 (0.21), residues: 1614 helix: 1.48 (0.38), residues: 198 sheet: -1.09 (0.22), residues: 525 loop : -1.11 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 172 TYR 0.036 0.002 TYR L 36 PHE 0.028 0.002 PHE E 592 TRP 0.041 0.003 TRP H 103 HIS 0.008 0.001 HIS G 100C Details of bonding type rmsd covalent geometry : bond 0.00315 (13473) covalent geometry : angle 0.72216 (18300) SS BOND : bond 0.00318 ( 21) SS BOND : angle 1.81124 ( 42) hydrogen bonds : bond 0.04014 ( 461) hydrogen bonds : angle 5.70496 ( 1302) link_ALPHA1-3 : bond 0.00782 ( 3) link_ALPHA1-3 : angle 1.20052 ( 9) link_ALPHA1-6 : bond 0.00368 ( 3) link_ALPHA1-6 : angle 1.82017 ( 9) link_BETA1-4 : bond 0.00561 ( 9) link_BETA1-4 : angle 2.32233 ( 27) link_NAG-ASN : bond 0.00385 ( 9) link_NAG-ASN : angle 1.58556 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.46 seconds wall clock time: 40 minutes 49.58 seconds (2449.58 seconds total)