Starting phenix.real_space_refine on Sat Oct 24 11:15:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.map" model { file = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kew_22841/10_2026/7kew_22841.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8325 2.51 5 N 2235 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13173 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, H, I, K, L, E, F, N, Q, P, R Time building chain proxies: 2.38, per 1000 atoms: 0.18 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 B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.10 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.08 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.10 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: 1.21 Conformation dependent library (CDL) restraints added in 530.3 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: 0.43 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: 2.37 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2227 1.31 - 1.45: 4355 1.45 - 1.59: 6747 1.59 - 1.73: 66 1.73 - 1.87: 78 Bond restraints: 13473 Sorted by residual: bond pdb=" CB ILE C 33 " pdb=" CG1 ILE C 33 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" NE1 TRP I 103 " pdb=" CE2 TRP I 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.34e+01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" NE1 TRP G 103 " pdb=" CE2 TRP G 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.23e+01 ... (remaining 13468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 15954 2.60 - 5.21: 1932 5.21 - 7.81: 363 7.81 - 10.42: 35 10.42 - 13.02: 16 Bond angle restraints: 18300 Sorted by residual: angle pdb=" N GLU C 71 " pdb=" CA GLU C 71 " pdb=" C GLU C 71 " ideal model delta sigma weight residual 114.62 104.18 10.44 1.14e+00 7.69e-01 8.39e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 114.62 104.26 10.36 1.14e+00 7.69e-01 8.26e+01 angle pdb=" N GLU A 71 " pdb=" CA GLU A 71 " pdb=" C GLU A 71 " ideal model delta sigma weight residual 114.62 104.27 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" N ARG C 247 " pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 114.75 104.25 10.50 1.26e+00 6.30e-01 6.95e+01 angle pdb=" N ARG A 247 " pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.86e+01 ... (remaining 18295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7536 17.10 - 34.19: 177 34.19 - 51.29: 48 51.29 - 68.39: 33 68.39 - 85.48: 6 Dihedral angle restraints: 7800 sinusoidal: 3093 harmonic: 4707 Sorted by residual: dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " pdb=" CB CYS G 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.17 40.83 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.18 40.82 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 7797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1453 0.103 - 0.207: 482 0.207 - 0.310: 128 0.310 - 0.414: 30 0.414 - 0.517: 13 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 ... (remaining 2103 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 103 " -0.065 2.00e-02 2.50e+03 3.04e-02 2.31e+01 pdb=" CG TRP H 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 103 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 103 " -0.065 2.00e-02 2.50e+03 3.03e-02 2.29e+01 pdb=" CG TRP I 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP I 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 103 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 103 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 103 " -0.065 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CG TRP G 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP G 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 103 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP G 103 " -0.027 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5329 2.90 - 3.40: 12294 3.40 - 3.90: 23301 3.90 - 4.40: 26627 4.40 - 4.90: 41730 Nonbonded interactions: 109281 Sorted by model distance: nonbonded pdb=" N PRO B 187 " pdb=" O PRO B 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO C 187 " pdb=" O PRO C 187 " model vdw 2.402 2.496 nonbonded pdb=" N PRO A 187 " pdb=" O PRO A 187 " model vdw 2.403 2.496 nonbonded pdb=" N ARG C 247 " pdb=" N PHE C 248 " model vdw 2.443 2.560 nonbonded pdb=" N ARG B 247 " pdb=" N PHE B 248 " model vdw 2.444 2.560 ... (remaining 109276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 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: 2.310 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.136 13518 Z= 1.151 Angle : 1.895 13.024 18414 Z= 1.237 Chirality : 0.117 0.517 2106 Planarity : 0.009 0.037 2310 Dihedral : 9.668 85.481 4725 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.16 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1614 helix: -0.03 (0.30), residues: 210 sheet: -0.04 (0.25), residues: 438 loop : 0.31 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 559 TYR 0.066 0.013 TYR D 534 PHE 0.031 0.007 PHE H 29 TRP 0.065 0.013 TRP H 103 HIS 0.008 0.002 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.02171 / 1.14 (13473) covalent geometry : angle 1.88152 / 1.24 (18300) SS BOND : bond 0.03240 / 2.10 ( 21) SS BOND : angle 2.70477 / 1.86 ( 42) hydrogen bonds : bond 0.17125 / 11.63 ( 461) hydrogen bonds : angle 7.86842 / 5.62 ( 1302) link_ALPHA1-3 : bond 0.08348 / 3.86 ( 3) link_ALPHA1-3 : angle 3.75787 / 1.85 ( 9) link_ALPHA1-6 : bond 0.05519 / 2.55 ( 3) link_ALPHA1-6 : angle 3.13911 / 1.55 ( 9) link_BETA1-4 : bond 0.07290 / 3.94 ( 9) link_BETA1-4 : angle 5.30207 / 3.17 ( 27) link_NAG-ASN : bond 0.07894 / 4.20 ( 9) link_NAG-ASN : angle 1.59115 / 1.05 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.540 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: 0.1313 time to fit residues: 93.1550 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 6 GLN J 32 ASN D 602 HIS H 64 GLN K 32 ASN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS L 6 GLN L 32 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.130413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097155 restraints weight = 33313.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101297 restraints weight = 19360.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104266 restraints weight = 10252.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105966 restraints weight = 7695.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106074 restraints weight = 7034.089| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13518 Z= 0.209 Angle : 0.841 9.471 18414 Z= 0.442 Chirality : 0.049 0.243 2106 Planarity : 0.006 0.051 2310 Dihedral : 6.153 31.914 1782 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1614 helix: 0.54 (0.34), residues: 231 sheet: 0.11 (0.27), residues: 387 loop : -0.47 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.034 0.003 TYR D 534 PHE 0.047 0.003 PHE G 29 TRP 0.021 0.003 TRP C 275 HIS 0.006 0.002 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (13473) covalent geometry : angle 0.81976 / 0.44 (18300) SS BOND : bond 0.00524 / 0.29 ( 21) SS BOND : angle 2.07854 / 1.37 ( 42) hydrogen bonds : bond 0.05107 / 3.41 ( 461) hydrogen bonds : angle 6.51005 / 4.69 ( 1302) link_ALPHA1-3 : bond 0.01009 / 0.46 ( 3) link_ALPHA1-3 : angle 1.70946 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00643 / 0.30 ( 3) link_ALPHA1-6 : angle 1.62798 / 0.87 ( 9) link_BETA1-4 : bond 0.00783 / 0.43 ( 9) link_BETA1-4 : angle 3.01548 / 2.01 ( 27) link_NAG-ASN : bond 0.00524 / 0.31 ( 9) link_NAG-ASN : angle 3.01410 / 1.82 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8528 (mttm) REVERT: A 126 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7587 (Cg_endo) REVERT: A 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8750 (tm-30) REVERT: G 37 VAL cc_start: 0.8429 (m) cc_final: 0.8196 (m) REVERT: G 46 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7302 (mm-30) REVERT: G 48 MET cc_start: 0.8620 (mtp) cc_final: 0.8131 (mtp) REVERT: G 52 MET cc_start: 0.7806 (mmm) cc_final: 0.7428 (mmm) REVERT: G 53 ILE cc_start: 0.8109 (tt) cc_final: 0.7792 (mm) REVERT: J 70 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8911 (mm-30) REVERT: J 97 THR cc_start: 0.6182 (t) cc_final: 0.4979 (p) REVERT: B 120 GLU cc_start: 0.7256 (pp20) cc_final: 0.7021 (pp20) REVERT: B 130 ARG cc_start: 0.6869 (ptt-90) cc_final: 0.6399 (ptt90) REVERT: B 156 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6980 (tp30) REVERT: B 235 GLN cc_start: 0.9184 (tt0) cc_final: 0.8596 (tm-30) REVERT: H 20 VAL cc_start: 0.8722 (t) cc_final: 0.8412 (p) REVERT: H 32 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8728 (tptp) REVERT: H 33 TYR cc_start: 0.7649 (m-80) cc_final: 0.7357 (m-80) REVERT: H 46 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7135 (mm-30) REVERT: H 96 GLU cc_start: 0.7696 (tt0) cc_final: 0.7294 (tp30) REVERT: K 18 ARG cc_start: 0.8010 (tmm-80) cc_final: 0.7794 (tmm-80) REVERT: K 97 THR cc_start: 0.6553 (t) cc_final: 0.6286 (p) REVERT: C 130 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6494 (ptt-90) REVERT: C 156 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6960 (tp30) REVERT: C 235 GLN cc_start: 0.9199 (tt0) cc_final: 0.8810 (tm-30) REVERT: C 258 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8857 (mt-10) REVERT: I 32 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8899 (tptp) REVERT: I 46 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7182 (mm-30) REVERT: I 48 MET cc_start: 0.8614 (mtp) cc_final: 0.8198 (mtp) REVERT: I 68 THR cc_start: 0.7761 (m) cc_final: 0.7527 (p) REVERT: I 81 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7153 (mt-10) REVERT: L 70 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8984 (mm-30) REVERT: L 97 THR cc_start: 0.6239 (t) cc_final: 0.5958 (p) REVERT: L 103 LYS cc_start: 0.8199 (tttt) cc_final: 0.7943 (tttm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1267 time to fit residues: 59.4266 Evaluate side-chains 229 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [69, 111, 146, 122, 80, 36, 95, 26, 157, 131, 54] chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095592 restraints weight = 34480.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098067 restraints weight = 18452.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100093 restraints weight = 11191.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.101075 restraints weight = 8787.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101184 restraints weight = 7876.543| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13518 Z= 0.197 Angle : 0.771 10.391 18414 Z= 0.401 Chirality : 0.048 0.300 2106 Planarity : 0.005 0.055 2310 Dihedral : 5.956 34.610 1782 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1614 helix: 0.73 (0.36), residues: 234 sheet: -0.38 (0.23), residues: 483 loop : -0.71 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 596 TYR 0.029 0.002 TYR E 534 PHE 0.030 0.002 PHE H 29 TRP 0.031 0.003 TRP B 275 HIS 0.006 0.002 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (13473) covalent geometry : angle 0.75372 / 0.40 (18300) SS BOND : bond 0.00712 / 0.49 ( 21) SS BOND : angle 2.31417 / 1.67 ( 42) hydrogen bonds : bond 0.04597 / 3.10 ( 461) hydrogen bonds : angle 6.20822 / 4.49 ( 1302) link_ALPHA1-3 : bond 0.00919 / 0.41 ( 3) link_ALPHA1-3 : angle 1.31230 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00413 / 0.19 ( 3) link_ALPHA1-6 : angle 1.79624 / 0.95 ( 9) link_BETA1-4 : bond 0.00407 / 0.24 ( 9) link_BETA1-4 : angle 2.35370 / 1.53 ( 27) link_NAG-ASN : bond 0.00390 / 0.18 ( 9) link_NAG-ASN : angle 2.16849 / 1.33 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8211 (pmm) cc_final: 0.7968 (pmm) REVERT: A 235 GLN cc_start: 0.9128 (tt0) cc_final: 0.8585 (tm-30) REVERT: G 19 LYS cc_start: 0.8877 (tptt) cc_final: 0.8511 (tptp) REVERT: G 23 ARG cc_start: 0.8666 (tpt-90) cc_final: 0.8459 (tpp80) REVERT: G 48 MET cc_start: 0.8703 (mtp) cc_final: 0.8347 (mtp) REVERT: J 70 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9135 (mm-30) REVERT: J 71 PHE cc_start: 0.8315 (m-10) cc_final: 0.7260 (m-10) REVERT: B 156 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7195 (tp30) REVERT: B 229 MET cc_start: 0.8361 (pmm) cc_final: 0.8129 (pmm) REVERT: B 235 GLN cc_start: 0.9147 (tt0) cc_final: 0.8438 (tm-30) REVERT: H 20 VAL cc_start: 0.8575 (t) cc_final: 0.8257 (t) REVERT: H 32 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8793 (tptp) REVERT: H 35 SER cc_start: 0.8556 (t) cc_final: 0.8248 (m) REVERT: H 96 GLU cc_start: 0.7526 (tt0) cc_final: 0.7293 (tp30) REVERT: H 97 ILE cc_start: 0.8456 (tp) cc_final: 0.8143 (tp) REVERT: K 89 LEU cc_start: 0.8452 (tt) cc_final: 0.8247 (tt) REVERT: K 90 GLN cc_start: 0.7053 (tt0) cc_final: 0.6510 (tt0) REVERT: K 97 THR cc_start: 0.6874 (t) cc_final: 0.5910 (p) REVERT: C 130 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6734 (ptt-90) REVERT: C 235 GLN cc_start: 0.9216 (tt0) cc_final: 0.8732 (tm-30) REVERT: I 19 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8461 (mmmt) REVERT: I 20 VAL cc_start: 0.8735 (t) cc_final: 0.8400 (t) REVERT: I 23 ARG cc_start: 0.8597 (tpt-90) cc_final: 0.8373 (tpp80) REVERT: I 46 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7689 (mm-30) REVERT: I 48 MET cc_start: 0.8744 (mtp) cc_final: 0.8328 (mtp) REVERT: I 96 GLU cc_start: 0.7372 (tt0) cc_final: 0.7116 (tt0) REVERT: L 58 ILE cc_start: 0.7335 (tt) cc_final: 0.6476 (tt) REVERT: L 70 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9120 (mm-30) REVERT: L 71 PHE cc_start: 0.8367 (m-10) cc_final: 0.8021 (m-10) REVERT: L 90 GLN cc_start: 0.7292 (tt0) cc_final: 0.6755 (tt0) REVERT: L 97 THR cc_start: 0.6244 (t) cc_final: 0.5479 (p) REVERT: F 596 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6944 (mmm160) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1288 time to fit residues: 57.4845 Evaluate side-chains 213 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [115, 95, 144, 37, 76, 135, 69, 99, 121, 4, 98] chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 121 optimal weight: 0.0870 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.125306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.093644 restraints weight = 31283.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.096991 restraints weight = 16915.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.097907 restraints weight = 9724.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099312 restraints weight = 8750.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099324 restraints weight = 7426.593| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13518 Z= 0.202 Angle : 0.747 8.571 18414 Z= 0.389 Chirality : 0.048 0.279 2106 Planarity : 0.006 0.066 2310 Dihedral : 5.848 33.027 1782 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z 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: -0.89 (0.21), residues: 1614 helix: 0.53 (0.36), residues: 234 sheet: -0.47 (0.23), residues: 504 loop : -0.92 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 94 TYR 0.022 0.002 TYR E 534 PHE 0.029 0.002 PHE H 63 TRP 0.024 0.003 TRP G 103 HIS 0.006 0.002 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (13473) covalent geometry : angle 0.73172 / 0.39 (18300) SS BOND : bond 0.00616 / 0.43 ( 21) SS BOND : angle 2.05333 / 1.47 ( 42) hydrogen bonds : bond 0.04589 / 3.12 ( 461) hydrogen bonds : angle 6.03668 / 4.35 ( 1302) link_ALPHA1-3 : bond 0.00545 / 0.25 ( 3) link_ALPHA1-3 : angle 1.45851 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00290 / 0.13 ( 3) link_ALPHA1-6 : angle 1.94035 / 1.03 ( 9) link_BETA1-4 : bond 0.00346 / 0.21 ( 9) link_BETA1-4 : angle 2.34139 / 1.54 ( 27) link_NAG-ASN : bond 0.00265 / 0.12 ( 9) link_NAG-ASN : angle 1.93058 / 1.15 ( 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 302 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 0.511 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: 0.7336 (p) cc_final: 0.6604 (t) REVERT: A 148 PRO cc_start: 0.8251 (Cg_exo) cc_final: 0.7849 (Cg_endo) REVERT: A 167 SER cc_start: 0.8452 (m) cc_final: 0.8146 (p) REVERT: A 229 MET cc_start: 0.8360 (pmm) cc_final: 0.8128 (pmm) REVERT: A 235 GLN cc_start: 0.9096 (tt0) cc_final: 0.8391 (tm-30) REVERT: G 19 LYS cc_start: 0.8914 (tptt) cc_final: 0.8478 (tptp) REVERT: G 48 MET cc_start: 0.8824 (mtp) cc_final: 0.8534 (mtp) REVERT: G 52 MET cc_start: 0.7997 (mmt) cc_final: 0.7719 (mmm) REVERT: G 53 ILE cc_start: 0.8165 (tt) cc_final: 0.7813 (pt) REVERT: G 90 TYR cc_start: 0.8702 (m-10) cc_final: 0.8097 (m-10) REVERT: J 71 PHE cc_start: 0.8374 (m-80) cc_final: 0.7424 (m-10) REVERT: D 602 HIS cc_start: 0.7123 (t-90) cc_final: 0.6748 (m170) REVERT: B 130 ARG cc_start: 0.7593 (ptt90) cc_final: 0.6535 (ptt-90) REVERT: B 229 MET cc_start: 0.8406 (pmm) cc_final: 0.8156 (pmm) REVERT: B 235 GLN cc_start: 0.9125 (tt0) cc_final: 0.8422 (tm-30) REVERT: H 19 LYS cc_start: 0.8922 (tptt) cc_final: 0.8378 (tptp) REVERT: H 20 VAL cc_start: 0.8726 (t) cc_final: 0.8219 (t) REVERT: H 35 SER cc_start: 0.8549 (t) cc_final: 0.8320 (m) REVERT: H 48 MET cc_start: 0.8345 (mmt) cc_final: 0.8111 (mmm) REVERT: K 90 GLN cc_start: 0.7416 (tt0) cc_final: 0.6561 (tt0) REVERT: K 97 THR cc_start: 0.7198 (t) cc_final: 0.5908 (p) REVERT: E 602 HIS cc_start: 0.6681 (t70) cc_final: 0.6474 (m170) REVERT: C 229 MET cc_start: 0.8425 (pmm) cc_final: 0.8212 (pmm) REVERT: C 230 THR cc_start: 0.6613 (m) cc_final: 0.6380 (m) REVERT: C 235 GLN cc_start: 0.9212 (tt0) cc_final: 0.8437 (tm-30) REVERT: C 258 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8740 (mt-10) REVERT: I 20 VAL cc_start: 0.8552 (t) cc_final: 0.8000 (t) REVERT: I 23 ARG cc_start: 0.8554 (tpt-90) cc_final: 0.8337 (tpp80) REVERT: I 46 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7677 (mm-30) REVERT: I 52 MET cc_start: 0.8151 (mpp) cc_final: 0.7550 (mpp) REVERT: L 33 LEU cc_start: 0.8796 (tp) cc_final: 0.8565 (tp) REVERT: L 71 PHE cc_start: 0.8363 (m-10) cc_final: 0.7992 (m-10) REVERT: L 90 GLN cc_start: 0.7567 (tt0) cc_final: 0.6900 (tt0) REVERT: L 97 THR cc_start: 0.6732 (t) cc_final: 0.5909 (p) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1217 time to fit residues: 52.0544 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [142, 76, 155, 34, 21, 48, 81, 77, 29, 156, 30] chunk 142 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.118548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.086890 restraints weight = 33672.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089200 restraints weight = 15967.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.090007 restraints weight = 10912.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.090458 restraints weight = 9930.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.090695 restraints weight = 8957.699| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.6523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13518 Z= 0.276 Angle : 0.845 9.717 18414 Z= 0.432 Chirality : 0.051 0.284 2106 Planarity : 0.006 0.053 2310 Dihedral : 6.141 31.933 1782 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % 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 : 0.39 % 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: -1.12 (0.21), residues: 1614 helix: 1.13 (0.37), residues: 198 sheet: -0.57 (0.23), residues: 519 loop : -1.28 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 38 TYR 0.042 0.003 TYR D 534 PHE 0.021 0.003 PHE H 63 TRP 0.028 0.003 TRP A 104 HIS 0.010 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (13473) covalent geometry : angle 0.83127 / 0.43 (18300) SS BOND : bond 0.00556 / 0.36 ( 21) SS BOND : angle 2.28982 / 1.62 ( 42) hydrogen bonds : bond 0.04925 / 3.39 ( 461) hydrogen bonds : angle 6.22067 / 4.42 ( 1302) link_ALPHA1-3 : bond 0.00436 / 0.19 ( 3) link_ALPHA1-3 : angle 1.49516 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00131 / 0.06 ( 3) link_ALPHA1-6 : angle 2.18707 / 1.17 ( 9) link_BETA1-4 : bond 0.00269 / 0.14 ( 9) link_BETA1-4 : angle 2.22689 / 1.45 ( 27) link_NAG-ASN : bond 0.00399 / 0.22 ( 9) link_NAG-ASN : angle 1.79373 / 1.04 ( 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 279 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.451 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: 0.7959 (p) cc_final: 0.7278 (t) REVERT: A 223 ASP cc_start: 0.7568 (m-30) cc_final: 0.7102 (m-30) REVERT: A 229 MET cc_start: 0.8534 (pmm) cc_final: 0.8313 (pmm) REVERT: A 230 THR cc_start: 0.7285 (m) cc_final: 0.6888 (m) REVERT: A 231 ASN cc_start: 0.8361 (t0) cc_final: 0.7385 (p0) REVERT: A 235 GLN cc_start: 0.9139 (tt0) cc_final: 0.8324 (tm-30) REVERT: A 236 VAL cc_start: 0.7628 (t) cc_final: 0.7172 (t) REVERT: G 19 LYS cc_start: 0.8875 (tptt) cc_final: 0.8199 (tptp) REVERT: G 48 MET cc_start: 0.8967 (mtp) cc_final: 0.8746 (mtp) REVERT: G 90 TYR cc_start: 0.8649 (m-10) cc_final: 0.8142 (m-80) REVERT: J 90 GLN cc_start: 0.7725 (tt0) cc_final: 0.6943 (tt0) REVERT: J 97 THR cc_start: 0.7191 (p) cc_final: 0.6472 (p) REVERT: D 602 HIS cc_start: 0.6956 (t-90) cc_final: 0.6515 (m170) REVERT: B 77 THR cc_start: 0.7707 (p) cc_final: 0.7140 (t) REVERT: B 229 MET cc_start: 0.8608 (pmm) cc_final: 0.8343 (pmm) REVERT: B 230 THR cc_start: 0.7014 (m) cc_final: 0.6750 (m) REVERT: B 235 GLN cc_start: 0.9147 (tt0) cc_final: 0.8352 (tm-30) REVERT: B 236 VAL cc_start: 0.7437 (t) cc_final: 0.7080 (t) REVERT: H 19 LYS cc_start: 0.8922 (tptt) cc_final: 0.8287 (tptp) REVERT: H 20 VAL cc_start: 0.8764 (t) cc_final: 0.8390 (t) REVERT: H 32 LYS cc_start: 0.9017 (tptp) cc_final: 0.8734 (tppt) REVERT: H 80 MET cc_start: 0.8478 (mtp) cc_final: 0.8255 (mtp) REVERT: H 90 TYR cc_start: 0.8414 (m-80) cc_final: 0.8196 (m-80) REVERT: K 27 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6954 (tm-30) REVERT: K 90 GLN cc_start: 0.7793 (tt0) cc_final: 0.7177 (tt0) REVERT: K 97 THR cc_start: 0.7465 (t) cc_final: 0.6770 (p) REVERT: C 77 THR cc_start: 0.7718 (p) cc_final: 0.7047 (t) REVERT: C 229 MET cc_start: 0.8615 (pmm) cc_final: 0.8322 (pmm) REVERT: C 230 THR cc_start: 0.6854 (m) cc_final: 0.6539 (m) REVERT: C 235 GLN cc_start: 0.9191 (tt0) cc_final: 0.8411 (tm-30) REVERT: I 19 LYS cc_start: 0.8698 (tptt) cc_final: 0.8453 (tptp) REVERT: I 46 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7725 (mm-30) REVERT: I 48 MET cc_start: 0.9027 (mtt) cc_final: 0.8578 (mpp) REVERT: L 90 GLN cc_start: 0.7924 (tt0) cc_final: 0.7408 (tt0) REVERT: L 97 THR cc_start: 0.7121 (t) cc_final: 0.6363 (p) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1164 time to fit residues: 46.3512 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [22, 127, 14, 80, 110, 104, 100, 70, 43, 103, 32] chunk 22 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN C 69 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** 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 = 0.4110 r_free = 0.4110 target = 0.120745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088627 restraints weight = 33490.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091566 restraints weight = 17298.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.092917 restraints weight = 10322.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.093367 restraints weight = 9033.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.093653 restraints weight = 8188.432| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13518 Z= 0.164 Angle : 0.725 10.499 18414 Z= 0.375 Chirality : 0.047 0.256 2106 Planarity : 0.005 0.049 2310 Dihedral : 5.848 30.364 1782 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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 : 0.26 % 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: -1.17 (0.20), residues: 1614 helix: 1.33 (0.37), residues: 198 sheet: -0.60 (0.22), residues: 507 loop : -1.38 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 94 TYR 0.034 0.002 TYR H 33 PHE 0.033 0.002 PHE I 29 TRP 0.028 0.002 TRP I 103 HIS 0.008 0.001 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (13473) covalent geometry : angle 0.71232 / 0.37 (18300) SS BOND : bond 0.00408 / 0.28 ( 21) SS BOND : angle 2.03083 / 1.45 ( 42) hydrogen bonds : bond 0.04233 / 2.92 ( 461) hydrogen bonds : angle 5.81140 / 4.18 ( 1302) link_ALPHA1-3 : bond 0.00493 / 0.23 ( 3) link_ALPHA1-3 : angle 1.45812 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00292 / 0.13 ( 3) link_ALPHA1-6 : angle 1.80153 / 0.98 ( 9) link_BETA1-4 : bond 0.00313 / 0.17 ( 9) link_BETA1-4 : angle 2.03341 / 1.36 ( 27) link_NAG-ASN : bond 0.00217 / 0.10 ( 9) link_NAG-ASN : angle 1.64118 / 1.00 ( 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 274 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.7943 (p) cc_final: 0.7381 (t) REVERT: A 148 PRO cc_start: 0.8447 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: A 223 ASP cc_start: 0.7734 (m-30) cc_final: 0.7245 (m-30) REVERT: A 229 MET cc_start: 0.8482 (pmm) cc_final: 0.8277 (pmm) REVERT: A 230 THR cc_start: 0.7210 (m) cc_final: 0.6828 (m) REVERT: A 231 ASN cc_start: 0.8373 (t0) cc_final: 0.7400 (p0) REVERT: A 235 GLN cc_start: 0.9068 (tt0) cc_final: 0.8389 (tm-30) REVERT: A 236 VAL cc_start: 0.7285 (t) cc_final: 0.7036 (t) REVERT: G 19 LYS cc_start: 0.8884 (tptt) cc_final: 0.8184 (tptp) REVERT: G 48 MET cc_start: 0.8945 (mtp) cc_final: 0.8723 (mtp) REVERT: G 90 TYR cc_start: 0.8649 (m-10) cc_final: 0.8179 (m-80) REVERT: J 18 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.8002 (tmm-80) REVERT: J 71 PHE cc_start: 0.8253 (m-80) cc_final: 0.8028 (m-10) REVERT: J 90 GLN cc_start: 0.7672 (tt0) cc_final: 0.6857 (tt0) REVERT: J 97 THR cc_start: 0.7129 (p) cc_final: 0.6379 (p) REVERT: D 602 HIS cc_start: 0.6806 (t-90) cc_final: 0.6435 (m170) REVERT: B 77 THR cc_start: 0.7845 (p) cc_final: 0.7271 (t) REVERT: B 229 MET cc_start: 0.8545 (pmm) cc_final: 0.8308 (pmm) REVERT: B 230 THR cc_start: 0.7007 (m) cc_final: 0.6766 (m) REVERT: B 235 GLN cc_start: 0.9138 (tt0) cc_final: 0.8266 (tm-30) REVERT: H 19 LYS cc_start: 0.8877 (tptt) cc_final: 0.8211 (tptp) REVERT: H 20 VAL cc_start: 0.8800 (t) cc_final: 0.8355 (t) REVERT: H 35 ILE cc_start: 0.8882 (mm) cc_final: 0.8274 (tp) REVERT: H 48 MET cc_start: 0.8396 (mmp) cc_final: 0.8163 (mmm) REVERT: H 52 MET cc_start: 0.8505 (mmp) cc_final: 0.8217 (mmm) REVERT: K 73 LEU cc_start: 0.8791 (tp) cc_final: 0.7408 (tp) REVERT: K 90 GLN cc_start: 0.7743 (tt0) cc_final: 0.7353 (tt0) REVERT: K 97 THR cc_start: 0.7529 (t) cc_final: 0.6725 (p) REVERT: C 77 THR cc_start: 0.7675 (p) cc_final: 0.7015 (t) REVERT: C 229 MET cc_start: 0.8511 (pmm) cc_final: 0.8268 (pmm) REVERT: C 230 THR cc_start: 0.6785 (m) cc_final: 0.6452 (m) REVERT: C 235 GLN cc_start: 0.9200 (tt0) cc_final: 0.8417 (tm-30) REVERT: I 19 LYS cc_start: 0.8712 (tptt) cc_final: 0.8471 (tptp) REVERT: I 46 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7666 (mm-30) REVERT: I 48 MET cc_start: 0.9092 (mtt) cc_final: 0.8549 (mpp) REVERT: I 52 MET cc_start: 0.8112 (mmm) cc_final: 0.7843 (mmm) REVERT: I 80 MET cc_start: 0.8321 (mtp) cc_final: 0.7990 (mtp) REVERT: L 71 PHE cc_start: 0.8245 (m-10) cc_final: 0.7909 (m-10) REVERT: L 90 GLN cc_start: 0.7929 (tt0) cc_final: 0.7283 (tt0) REVERT: L 97 THR cc_start: 0.7314 (t) cc_final: 0.6430 (p) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1020 time to fit residues: 41.0032 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 : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [152, 86, 63, 30, 125, 96, 24, 99, 53, 81, 138] chunk 152 optimal weight: 0.0060 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.120159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087672 restraints weight = 34850.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.090731 restraints weight = 18176.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091920 restraints weight = 10725.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.092329 restraints weight = 9419.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092542 restraints weight = 8669.637| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13518 Z= 0.173 Angle : 0.726 11.199 18414 Z= 0.373 Chirality : 0.047 0.256 2106 Planarity : 0.005 0.050 2310 Dihedral : 5.749 29.365 1782 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.20), residues: 1614 helix: 1.42 (0.37), residues: 198 sheet: -0.76 (0.22), residues: 516 loop : -1.31 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 172 TYR 0.024 0.002 TYR E 534 PHE 0.013 0.002 PHE H 29 TRP 0.036 0.002 TRP K 35 HIS 0.013 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (13473) covalent geometry : angle 0.71252 / 0.37 (18300) SS BOND : bond 0.00435 / 0.25 ( 21) SS BOND : angle 2.12852 / 1.40 ( 42) hydrogen bonds : bond 0.04109 / 2.84 ( 461) hydrogen bonds : angle 5.80335 / 4.16 ( 1302) link_ALPHA1-3 : bond 0.00129 / 0.06 ( 3) link_ALPHA1-3 : angle 1.38672 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00218 / 0.10 ( 3) link_ALPHA1-6 : angle 1.80426 / 0.97 ( 9) link_BETA1-4 : bond 0.00205 / 0.10 ( 9) link_BETA1-4 : angle 1.97122 / 1.30 ( 27) link_NAG-ASN : bond 0.00220 / 0.10 ( 9) link_NAG-ASN : angle 1.53868 / 0.94 ( 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 284 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8045 (p) cc_final: 0.7516 (t) REVERT: A 223 ASP cc_start: 0.7801 (m-30) cc_final: 0.7243 (m-30) REVERT: A 230 THR cc_start: 0.7211 (m) cc_final: 0.6810 (m) REVERT: A 231 ASN cc_start: 0.8395 (t0) cc_final: 0.7359 (p0) REVERT: A 235 GLN cc_start: 0.9077 (tt0) cc_final: 0.8342 (tm-30) REVERT: G 19 LYS cc_start: 0.8883 (tptt) cc_final: 0.8174 (tptp) REVERT: G 90 TYR cc_start: 0.8600 (m-10) cc_final: 0.8155 (m-80) REVERT: J 71 PHE cc_start: 0.8361 (m-80) cc_final: 0.8060 (m-10) REVERT: J 90 GLN cc_start: 0.7812 (tt0) cc_final: 0.6995 (tt0) REVERT: J 97 THR cc_start: 0.7191 (p) cc_final: 0.6406 (p) REVERT: D 602 HIS cc_start: 0.6825 (t-90) cc_final: 0.6395 (m90) REVERT: B 77 THR cc_start: 0.7934 (p) cc_final: 0.7410 (t) REVERT: B 229 MET cc_start: 0.8607 (pmm) cc_final: 0.8370 (pmm) REVERT: B 230 THR cc_start: 0.6975 (m) cc_final: 0.6704 (m) REVERT: B 235 GLN cc_start: 0.9164 (tt0) cc_final: 0.8203 (tm-30) REVERT: H 19 LYS cc_start: 0.8889 (tptt) cc_final: 0.8235 (tptp) REVERT: H 20 VAL cc_start: 0.8776 (t) cc_final: 0.8303 (t) REVERT: H 32 LYS cc_start: 0.9034 (tptp) cc_final: 0.8789 (tppt) REVERT: H 35 ILE cc_start: 0.8930 (mm) cc_final: 0.8549 (tp) REVERT: H 48 MET cc_start: 0.8504 (mmp) cc_final: 0.8202 (mmm) REVERT: H 52 MET cc_start: 0.8426 (mmp) cc_final: 0.8199 (mmm) REVERT: H 80 MET cc_start: 0.8381 (mtp) cc_final: 0.8098 (mtp) REVERT: H 90 TYR cc_start: 0.8445 (m-80) cc_final: 0.8011 (m-80) REVERT: K 42 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8368 (mm110) REVERT: K 70 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8799 (mm-30) REVERT: K 90 GLN cc_start: 0.7986 (tt0) cc_final: 0.7276 (tt0) REVERT: K 97 THR cc_start: 0.7546 (t) cc_final: 0.6290 (p) REVERT: E 583 SER cc_start: 0.8021 (m) cc_final: 0.7736 (p) REVERT: C 77 THR cc_start: 0.7675 (p) cc_final: 0.7003 (t) REVERT: C 229 MET cc_start: 0.8579 (pmm) cc_final: 0.8360 (pmm) REVERT: C 235 GLN cc_start: 0.9229 (tt0) cc_final: 0.8423 (tm-30) REVERT: I 19 LYS cc_start: 0.8722 (tptt) cc_final: 0.8476 (tptp) REVERT: I 20 VAL cc_start: 0.8511 (t) cc_final: 0.7954 (t) REVERT: I 48 MET cc_start: 0.9174 (mtt) cc_final: 0.8581 (mpp) REVERT: I 52 MET cc_start: 0.8156 (mmm) cc_final: 0.7894 (mmm) REVERT: I 80 MET cc_start: 0.8506 (mtp) cc_final: 0.8148 (mtp) REVERT: L 42 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8606 (mm110) REVERT: L 71 PHE cc_start: 0.8399 (m-10) cc_final: 0.8043 (m-10) REVERT: L 90 GLN cc_start: 0.7915 (tt0) cc_final: 0.7223 (tt0) REVERT: L 97 THR cc_start: 0.7297 (t) cc_final: 0.5891 (p) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1096 time to fit residues: 45.5642 Evaluate side-chains 206 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [5, 66, 31, 114, 78, 3, 61, 141, 156, 124, 60] chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** 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 = 0.4108 r_free = 0.4108 target = 0.120034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.085505 restraints weight = 35096.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089059 restraints weight = 18355.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091394 restraints weight = 11777.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.093018 restraints weight = 8762.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093943 restraints weight = 7180.658| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13518 Z= 0.169 Angle : 0.720 11.704 18414 Z= 0.371 Chirality : 0.047 0.272 2106 Planarity : 0.005 0.065 2310 Dihedral : 5.682 28.613 1782 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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 : 0.00 % 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: -1.20 (0.20), residues: 1614 helix: 1.53 (0.37), residues: 198 sheet: -0.79 (0.22), residues: 507 loop : -1.34 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG K 18 TYR 0.037 0.002 TYR K 91 PHE 0.019 0.002 PHE H 100E TRP 0.038 0.003 TRP G 103 HIS 0.014 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13473) covalent geometry : angle 0.70650 / 0.37 (18300) SS BOND : bond 0.00464 / 0.26 ( 21) SS BOND : angle 2.15847 / 1.45 ( 42) hydrogen bonds : bond 0.04141 / 2.92 ( 461) hydrogen bonds : angle 5.72477 / 4.12 ( 1302) link_ALPHA1-3 : bond 0.00261 / 0.12 ( 3) link_ALPHA1-3 : angle 1.45650 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00213 / 0.10 ( 3) link_ALPHA1-6 : angle 1.74145 / 0.94 ( 9) link_BETA1-4 : bond 0.00244 / 0.15 ( 9) link_BETA1-4 : angle 1.95346 / 1.30 ( 27) link_NAG-ASN : bond 0.00210 / 0.10 ( 9) link_NAG-ASN : angle 1.53500 / 0.95 ( 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 275 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.460 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: 0.8049 (p) cc_final: 0.7528 (t) REVERT: A 223 ASP cc_start: 0.7954 (m-30) cc_final: 0.7423 (m-30) REVERT: A 229 MET cc_start: 0.8367 (pmm) cc_final: 0.8099 (pmm) REVERT: A 230 THR cc_start: 0.7360 (m) cc_final: 0.7004 (m) REVERT: A 231 ASN cc_start: 0.8482 (t0) cc_final: 0.7460 (p0) REVERT: A 235 GLN cc_start: 0.9106 (tt0) cc_final: 0.8388 (tm-30) REVERT: G 19 LYS cc_start: 0.8861 (tptt) cc_final: 0.8121 (tptp) REVERT: G 90 TYR cc_start: 0.8562 (m-10) cc_final: 0.8103 (m-80) REVERT: J 42 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8569 (mp-120) REVERT: J 71 PHE cc_start: 0.8586 (m-80) cc_final: 0.8233 (m-10) REVERT: J 90 GLN cc_start: 0.7882 (tt0) cc_final: 0.7265 (tt0) REVERT: J 97 THR cc_start: 0.6829 (p) cc_final: 0.6412 (p) REVERT: D 602 HIS cc_start: 0.6827 (t-90) cc_final: 0.6337 (m90) REVERT: B 77 THR cc_start: 0.8035 (p) cc_final: 0.7505 (t) REVERT: B 130 ARG cc_start: 0.7632 (ptt-90) cc_final: 0.6698 (ptt-90) REVERT: B 229 MET cc_start: 0.8514 (pmm) cc_final: 0.8297 (pmm) REVERT: B 230 THR cc_start: 0.7149 (m) cc_final: 0.6878 (m) REVERT: B 235 GLN cc_start: 0.9145 (tt0) cc_final: 0.8129 (tm-30) REVERT: H 19 LYS cc_start: 0.8881 (tptt) cc_final: 0.8215 (tptp) REVERT: H 20 VAL cc_start: 0.8638 (t) cc_final: 0.8079 (t) REVERT: H 32 LYS cc_start: 0.9062 (tptp) cc_final: 0.8819 (tppt) REVERT: H 35 ILE cc_start: 0.8893 (mm) cc_final: 0.8453 (tp) REVERT: H 48 MET cc_start: 0.8398 (mmp) cc_final: 0.8058 (mmm) REVERT: H 80 MET cc_start: 0.8358 (mtp) cc_final: 0.7853 (mtp) REVERT: H 90 TYR cc_start: 0.8436 (m-80) cc_final: 0.7973 (m-80) REVERT: K 42 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8550 (mp-120) REVERT: K 48 ILE cc_start: 0.8071 (tp) cc_final: 0.7730 (tp) REVERT: K 90 GLN cc_start: 0.8042 (tt0) cc_final: 0.7678 (tt0) REVERT: K 97 THR cc_start: 0.7301 (t) cc_final: 0.6737 (p) REVERT: E 519 THR cc_start: 0.8263 (t) cc_final: 0.8008 (p) REVERT: E 520 THR cc_start: 0.8363 (m) cc_final: 0.8136 (m) REVERT: E 583 SER cc_start: 0.8013 (m) cc_final: 0.7726 (p) REVERT: C 55 ASP cc_start: 0.7887 (m-30) cc_final: 0.7666 (m-30) REVERT: C 77 THR cc_start: 0.7703 (p) cc_final: 0.7110 (t) REVERT: C 148 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: C 229 MET cc_start: 0.8452 (pmm) cc_final: 0.8246 (pmm) REVERT: C 235 GLN cc_start: 0.9200 (tt0) cc_final: 0.8328 (tm-30) REVERT: I 19 LYS cc_start: 0.8720 (tptt) cc_final: 0.8454 (tptp) REVERT: I 20 VAL cc_start: 0.8460 (t) cc_final: 0.7883 (t) REVERT: I 46 GLU cc_start: 0.8160 (tp30) cc_final: 0.7736 (mm-30) REVERT: I 48 MET cc_start: 0.9251 (mtt) cc_final: 0.8566 (mpp) REVERT: I 52 MET cc_start: 0.8201 (mmm) cc_final: 0.7881 (mmm) REVERT: I 80 MET cc_start: 0.8377 (mtp) cc_final: 0.7909 (mtp) REVERT: L 42 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8682 (mm110) REVERT: L 71 PHE cc_start: 0.8520 (m-10) cc_final: 0.8149 (m-10) REVERT: L 90 GLN cc_start: 0.8367 (tt0) cc_final: 0.7601 (tt0) REVERT: L 97 THR cc_start: 0.7086 (t) cc_final: 0.5805 (p) REVERT: F 583 SER cc_start: 0.7731 (m) cc_final: 0.7376 (p) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1053 time to fit residues: 42.4388 Evaluate side-chains 200 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [141, 21, 137, 15, 89, 114, 75, 87, 31, 18, 44] chunk 141 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 75 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081834 restraints weight = 35764.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.084887 restraints weight = 20013.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.087569 restraints weight = 11589.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087837 restraints weight = 8613.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.088127 restraints weight = 8172.859| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13518 Z= 0.248 Angle : 0.814 11.372 18414 Z= 0.416 Chirality : 0.050 0.263 2106 Planarity : 0.006 0.083 2310 Dihedral : 6.089 30.042 1782 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1614 helix: 1.13 (0.37), residues: 198 sheet: -1.09 (0.22), residues: 525 loop : -1.38 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 172 TYR 0.049 0.003 TYR I 33 PHE 0.017 0.002 PHE D 592 TRP 0.042 0.003 TRP I 103 HIS 0.028 0.003 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (13473) covalent geometry : angle 0.80143 / 0.41 (18300) SS BOND : bond 0.00440 / 0.29 ( 21) SS BOND : angle 2.25881 / 1.59 ( 42) hydrogen bonds : bond 0.04738 / 3.32 ( 461) hydrogen bonds : angle 6.02835 / 4.33 ( 1302) link_ALPHA1-3 : bond 0.00107 / 0.05 ( 3) link_ALPHA1-3 : angle 1.62306 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00020 / 0.01 ( 3) link_ALPHA1-6 : angle 1.99823 / 1.08 ( 9) link_BETA1-4 : bond 0.00307 / 0.15 ( 9) link_BETA1-4 : angle 2.04560 / 1.34 ( 27) link_NAG-ASN : bond 0.00323 / 0.16 ( 9) link_NAG-ASN : angle 1.54759 / 0.93 ( 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 255 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.510 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: 0.8263 (p) cc_final: 0.7804 (t) REVERT: A 148 PRO cc_start: 0.8441 (Cg_exo) cc_final: 0.8208 (Cg_endo) REVERT: A 223 ASP cc_start: 0.8200 (m-30) cc_final: 0.7713 (m-30) REVERT: A 230 THR cc_start: 0.7478 (m) cc_final: 0.7195 (m) REVERT: A 231 ASN cc_start: 0.8588 (t0) cc_final: 0.7600 (p0) REVERT: A 235 GLN cc_start: 0.9091 (tt0) cc_final: 0.8288 (tm-30) REVERT: G 19 LYS cc_start: 0.8816 (tptt) cc_final: 0.8083 (tptp) REVERT: G 48 MET cc_start: 0.9030 (mtt) cc_final: 0.8544 (mpp) REVERT: G 90 TYR cc_start: 0.8632 (m-10) cc_final: 0.8383 (m-80) REVERT: J 90 GLN cc_start: 0.8101 (tt0) cc_final: 0.7376 (tt0) REVERT: J 97 THR cc_start: 0.7007 (p) cc_final: 0.6679 (p) REVERT: D 517 TYR cc_start: 0.8076 (p90) cc_final: 0.7831 (p90) REVERT: D 602 HIS cc_start: 0.7104 (t70) cc_final: 0.6116 (m90) REVERT: B 77 THR cc_start: 0.8239 (p) cc_final: 0.7797 (t) REVERT: B 130 ARG cc_start: 0.7572 (ptt-90) cc_final: 0.6618 (ptt-90) REVERT: B 229 MET cc_start: 0.8703 (pmm) cc_final: 0.8452 (pmm) REVERT: B 230 THR cc_start: 0.7359 (m) cc_final: 0.7066 (m) REVERT: B 235 GLN cc_start: 0.9116 (tt0) cc_final: 0.8213 (tm-30) REVERT: B 236 VAL cc_start: 0.6999 (t) cc_final: 0.6643 (t) REVERT: H 19 LYS cc_start: 0.8887 (tptt) cc_final: 0.8209 (tptp) REVERT: H 20 VAL cc_start: 0.8639 (t) cc_final: 0.8174 (t) REVERT: H 35 ILE cc_start: 0.8757 (mm) cc_final: 0.8449 (tp) REVERT: H 48 MET cc_start: 0.8484 (mmp) cc_final: 0.8275 (mmm) REVERT: H 80 MET cc_start: 0.8323 (mtp) cc_final: 0.7766 (mtp) REVERT: H 90 TYR cc_start: 0.8506 (m-80) cc_final: 0.8147 (m-80) REVERT: K 42 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8527 (mm110) REVERT: K 48 ILE cc_start: 0.8164 (tp) cc_final: 0.7932 (tp) REVERT: K 90 GLN cc_start: 0.8158 (tt0) cc_final: 0.7564 (tt0) REVERT: K 97 THR cc_start: 0.7521 (t) cc_final: 0.6889 (p) REVERT: E 583 SER cc_start: 0.8152 (m) cc_final: 0.7864 (p) REVERT: C 77 THR cc_start: 0.7949 (p) cc_final: 0.7435 (t) REVERT: C 231 ASN cc_start: 0.8733 (t0) cc_final: 0.7675 (p0) REVERT: C 235 GLN cc_start: 0.9218 (tt0) cc_final: 0.8419 (tm-30) REVERT: I 19 LYS cc_start: 0.8742 (tptt) cc_final: 0.8418 (tptp) REVERT: I 20 VAL cc_start: 0.8481 (t) cc_final: 0.8012 (t) REVERT: I 48 MET cc_start: 0.9261 (mtt) cc_final: 0.8583 (mpp) REVERT: I 52 MET cc_start: 0.8295 (mmm) cc_final: 0.8086 (mmm) REVERT: I 80 MET cc_start: 0.8396 (mtp) cc_final: 0.7873 (mtp) REVERT: L 42 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8675 (mm110) REVERT: L 71 PHE cc_start: 0.8804 (m-10) cc_final: 0.8502 (m-10) REVERT: L 90 GLN cc_start: 0.8445 (tt0) cc_final: 0.7675 (tt0) REVERT: L 97 THR cc_start: 0.7252 (t) cc_final: 0.6042 (p) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1039 time to fit residues: 39.6770 Evaluate side-chains 184 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [56, 134, 31, 57, 90, 39, 123, 64, 98, 50, 38] chunk 56 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 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 = 0.4083 r_free = 0.4083 target = 0.118200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083309 restraints weight = 35640.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.086726 restraints weight = 18918.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.089037 restraints weight = 12295.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090577 restraints weight = 9185.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091595 restraints weight = 7586.448| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13518 Z= 0.170 Angle : 0.730 11.638 18414 Z= 0.374 Chirality : 0.048 0.261 2106 Planarity : 0.006 0.077 2310 Dihedral : 5.851 29.639 1782 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: -1.45 (0.20), residues: 1614 helix: 1.26 (0.37), residues: 198 sheet: -1.21 (0.21), residues: 552 loop : -1.29 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 94 TYR 0.044 0.002 TYR H 33 PHE 0.026 0.002 PHE E 592 TRP 0.028 0.002 TRP I 103 HIS 0.019 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13473) covalent geometry : angle 0.71690 / 0.37 (18300) SS BOND : bond 0.00426 / 0.28 ( 21) SS BOND : angle 2.14867 / 1.47 ( 42) hydrogen bonds : bond 0.04233 / 2.98 ( 461) hydrogen bonds : angle 5.81351 / 4.15 ( 1302) link_ALPHA1-3 : bond 0.00151 / 0.07 ( 3) link_ALPHA1-3 : angle 1.46024 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00173 / 0.08 ( 3) link_ALPHA1-6 : angle 1.70718 / 0.93 ( 9) link_BETA1-4 : bond 0.00262 / 0.16 ( 9) link_BETA1-4 : angle 1.90177 / 1.27 ( 27) link_NAG-ASN : bond 0.00250 / 0.12 ( 9) link_NAG-ASN : angle 1.64218 / 1.02 ( 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 257 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.500 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: 0.8172 (p) cc_final: 0.7673 (t) REVERT: A 148 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8099 (Cg_endo) REVERT: A 230 THR cc_start: 0.7431 (m) cc_final: 0.7128 (m) REVERT: A 235 GLN cc_start: 0.9062 (tt0) cc_final: 0.8372 (tm-30) REVERT: G 19 LYS cc_start: 0.8879 (tptt) cc_final: 0.8121 (tptp) REVERT: G 48 MET cc_start: 0.9098 (mtt) cc_final: 0.8532 (mpp) REVERT: G 90 TYR cc_start: 0.8582 (m-10) cc_final: 0.8261 (m-80) REVERT: J 90 GLN cc_start: 0.8075 (tt0) cc_final: 0.7581 (tt0) REVERT: J 97 THR cc_start: 0.6943 (p) cc_final: 0.6638 (p) REVERT: D 583 SER cc_start: 0.7916 (m) cc_final: 0.7700 (p) REVERT: D 602 HIS cc_start: 0.7146 (t70) cc_final: 0.6195 (m-70) REVERT: B 77 THR cc_start: 0.8264 (p) cc_final: 0.7831 (t) REVERT: B 130 ARG cc_start: 0.7701 (ptt-90) cc_final: 0.6765 (ptt-90) REVERT: B 229 MET cc_start: 0.8602 (pmm) cc_final: 0.8394 (pmm) REVERT: B 230 THR cc_start: 0.7359 (m) cc_final: 0.7096 (m) REVERT: B 235 GLN cc_start: 0.9181 (tt0) cc_final: 0.8179 (tm-30) REVERT: H 19 LYS cc_start: 0.8895 (tptt) cc_final: 0.8222 (tptp) REVERT: H 20 VAL cc_start: 0.8686 (t) cc_final: 0.8244 (t) REVERT: H 35 ILE cc_start: 0.8830 (mm) cc_final: 0.8596 (tp) REVERT: H 80 MET cc_start: 0.8269 (mtp) cc_final: 0.7713 (mtp) REVERT: H 90 TYR cc_start: 0.8518 (m-80) cc_final: 0.8102 (m-80) REVERT: K 48 ILE cc_start: 0.8141 (tp) cc_final: 0.7935 (tp) REVERT: K 90 GLN cc_start: 0.8191 (tt0) cc_final: 0.7483 (tt0) REVERT: K 97 THR cc_start: 0.7495 (t) cc_final: 0.6355 (p) REVERT: E 583 SER cc_start: 0.8027 (m) cc_final: 0.7767 (p) REVERT: C 77 THR cc_start: 0.7866 (p) cc_final: 0.7363 (t) REVERT: C 122 LEU cc_start: 0.9248 (mm) cc_final: 0.8669 (mm) REVERT: C 148 PRO cc_start: 0.8257 (Cg_exo) cc_final: 0.7929 (Cg_endo) REVERT: C 223 ASP cc_start: 0.7392 (m-30) cc_final: 0.6917 (m-30) REVERT: C 229 MET cc_start: 0.8370 (pmm) cc_final: 0.8152 (pmm) REVERT: C 231 ASN cc_start: 0.8581 (t0) cc_final: 0.7758 (p0) REVERT: C 235 GLN cc_start: 0.9201 (tt0) cc_final: 0.8243 (tm-30) REVERT: C 236 VAL cc_start: 0.7769 (t) cc_final: 0.7358 (t) REVERT: I 19 LYS cc_start: 0.8733 (tptt) cc_final: 0.8418 (tptp) REVERT: I 20 VAL cc_start: 0.8490 (t) cc_final: 0.8014 (t) REVERT: I 48 MET cc_start: 0.9305 (mtt) cc_final: 0.8530 (mpp) REVERT: I 52 MET cc_start: 0.8290 (mmm) cc_final: 0.8033 (mmm) REVERT: I 80 MET cc_start: 0.8342 (mtp) cc_final: 0.7761 (mtp) REVERT: L 42 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8643 (mm110) REVERT: L 71 PHE cc_start: 0.8618 (m-10) cc_final: 0.8353 (m-10) REVERT: L 90 GLN cc_start: 0.8470 (tt0) cc_final: 0.7738 (tt0) REVERT: L 97 THR cc_start: 0.7333 (t) cc_final: 0.6179 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1035 time to fit residues: 39.4228 Evaluate side-chains 176 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: [92, 16, 21, 113, 77, 39, 4, 48, 139, 66, 65] chunk 92 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 3 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.118055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.085811 restraints weight = 33539.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.088151 restraints weight = 18716.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089564 restraints weight = 11294.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090017 restraints weight = 9840.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.090418 restraints weight = 8924.042| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.8111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13518 Z= 0.182 Angle : 0.752 11.816 18414 Z= 0.381 Chirality : 0.048 0.256 2106 Planarity : 0.006 0.063 2310 Dihedral : 5.876 30.325 1782 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 : 0.13 % 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: 1.24 (0.37), residues: 198 sheet: -1.26 (0.21), residues: 555 loop : -1.34 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 172 TYR 0.043 0.002 TYR H 33 PHE 0.014 0.002 PHE J 83 TRP 0.042 0.003 TRP I 103 HIS 0.014 0.002 HIS H 100C Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13473) covalent geometry : angle 0.73796 / 0.38 (18300) SS BOND : bond 0.00416 / 0.22 ( 21) SS BOND : angle 2.35245 / 1.66 ( 42) hydrogen bonds : bond 0.04187 / 2.94 ( 461) hydrogen bonds : angle 5.79150 / 4.14 ( 1302) link_ALPHA1-3 : bond 0.00107 / 0.05 ( 3) link_ALPHA1-3 : angle 1.47444 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00108 / 0.05 ( 3) link_ALPHA1-6 : angle 1.75336 / 0.95 ( 9) link_BETA1-4 : bond 0.00217 / 0.13 ( 9) link_BETA1-4 : angle 1.91852 / 1.28 ( 27) link_NAG-ASN : bond 0.00242 / 0.11 ( 9) link_NAG-ASN : angle 1.51421 / 0.93 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.21 seconds wall clock time: 39 minutes 36.09 seconds (2376.09 seconds total)