Starting phenix.real_space_refine on Thu Sep 26 14:35:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_22841.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_22841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_22841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_22841.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kew_22841/09_2024/7kew_22841.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 8325 2.51 5 N 2235 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13173 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1785 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "K" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: I, H, C, B, J, L, D, F, N, Q, P, R Time building chain proxies: 6.71, per 1000 atoms: 0.51 Number of scatterers: 13173 At special positions: 0 Unit cell: (136.99, 151.41, 129.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2550 8.00 N 2235 7.00 C 8325 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG B 401 " - " ASN B 228 " " NAG C 401 " - " ASN C 228 " " NAG M 1 " - " ASN B 257 " " NAG N 1 " - " ASN A 257 " " NAG O 1 " - " ASN D 563 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 15.1% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'E' and resid 553 through 575 removed outlier: 3.511A pdb=" N THR E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'F' and resid 553 through 575 removed outlier: 3.512A pdb=" N THR F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing sheet with id=AA1, first strand: chain 'D' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 136 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 138 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 219 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 274 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER G 59 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE G 35 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 13.937A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE G 100E" --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU G 96 " --> pdb=" O PHE G 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 94 " --> pdb=" O SER G 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA6, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 601 through 602 removed outlier: 6.879A pdb=" N CYS D 601 " --> pdb=" O GLU F 611 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 610 through 611 Processing sheet with id=AB3, first strand: chain 'E' and resid 543 through 549 removed outlier: 5.538A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 136 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 138 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 219 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 274 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER H 59 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE H 35 " --> pdb=" O THR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 46 removed outlier: 4.289A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100E through 103 removed outlier: 6.929A pdb=" N PHE H 100E" --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU H 96 " --> pdb=" O PHE H 100E" (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 94 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB8, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AC2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 610 through 611 Processing sheet with id=AC4, first strand: chain 'F' and resid 543 through 549 removed outlier: 5.536A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG C 136 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 138 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN C 219 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 274 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER I 59 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU I 46 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE I 35 " --> pdb=" O THR I 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 42 through 46 removed outlier: 4.290A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 13.936A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 100E through 103 removed outlier: 6.928A pdb=" N PHE I 100E" --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU I 96 " --> pdb=" O PHE I 100E" (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG I 94 " --> pdb=" O SER I 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC9, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AD2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.842A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.28 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2227 1.31 - 1.45: 4355 1.45 - 1.59: 6747 1.59 - 1.73: 66 1.73 - 1.87: 78 Bond restraints: 13473 Sorted by residual: bond pdb=" CB ILE C 33 " pdb=" CG1 ILE C 33 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" NE1 TRP I 103 " pdb=" CE2 TRP I 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.34e+01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" CB ILE A 33 " pdb=" CG1 ILE A 33 " ideal model delta sigma weight residual 1.530 1.661 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" NE1 TRP G 103 " pdb=" CE2 TRP G 103 " ideal model delta sigma weight residual 1.370 1.298 0.072 1.10e-02 8.26e+03 4.23e+01 ... (remaining 13468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 15954 2.60 - 5.21: 1932 5.21 - 7.81: 363 7.81 - 10.42: 35 10.42 - 13.02: 16 Bond angle restraints: 18300 Sorted by residual: angle pdb=" N GLU C 71 " pdb=" CA GLU C 71 " pdb=" C GLU C 71 " ideal model delta sigma weight residual 114.62 104.18 10.44 1.14e+00 7.69e-01 8.39e+01 angle pdb=" N GLU B 71 " pdb=" CA GLU B 71 " pdb=" C GLU B 71 " ideal model delta sigma weight residual 114.62 104.26 10.36 1.14e+00 7.69e-01 8.26e+01 angle pdb=" N GLU A 71 " pdb=" CA GLU A 71 " pdb=" C GLU A 71 " ideal model delta sigma weight residual 114.62 104.27 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" N ARG C 247 " pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 114.75 104.25 10.50 1.26e+00 6.30e-01 6.95e+01 angle pdb=" N ARG A 247 " pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.86e+01 ... (remaining 18295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 8020 21.41 - 42.81: 142 42.81 - 64.22: 43 64.22 - 85.63: 27 85.63 - 107.03: 12 Dihedral angle restraints: 8244 sinusoidal: 3537 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 D 511 " pdb=" SG CYS D 511 " pdb=" SG CYS D 556 " pdb=" CB CYS D 556 " ideal model delta sinusoidal sigma weight residual 93.00 53.00 40.00 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" C VAL B 79 " pdb=" N VAL B 79 " pdb=" CA VAL B 79 " pdb=" CB VAL B 79 " ideal model delta harmonic sigma weight residual -122.00 -132.63 10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 8241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1453 0.103 - 0.207: 482 0.207 - 0.310: 128 0.310 - 0.414: 30 0.414 - 0.517: 13 Chirality restraints: 2106 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.68e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 ... (remaining 2103 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 103 " -0.065 2.00e-02 2.50e+03 3.04e-02 2.31e+01 pdb=" CG TRP H 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP H 103 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 103 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 103 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 103 " -0.065 2.00e-02 2.50e+03 3.03e-02 2.29e+01 pdb=" CG TRP I 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 103 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP I 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP I 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 103 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 103 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP I 103 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 103 " -0.065 2.00e-02 2.50e+03 3.02e-02 2.29e+01 pdb=" CG TRP G 103 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP G 103 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP G 103 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 103 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 103 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 103 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP G 103 " -0.027 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 115 2.60 - 3.18: 11520 3.18 - 3.75: 20782 3.75 - 4.33: 30261 4.33 - 4.90: 46645 Nonbonded interactions: 109323 Sorted by model distance: nonbonded pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 108 " pdb=" SG CYS C 135 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 121 " pdb=" SG CYS B 147 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 121 " pdb=" SG CYS C 147 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.034 3.760 ... (remaining 109318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 'M' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 32.180 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.136 13473 Z= 1.392 Angle : 1.882 13.024 18300 Z= 1.237 Chirality : 0.117 0.517 2106 Planarity : 0.009 0.037 2310 Dihedral : 11.742 107.032 5211 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.16 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1614 helix: -0.03 (0.30), residues: 210 sheet: -0.04 (0.25), residues: 438 loop : 0.31 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.013 TRP H 103 HIS 0.008 0.002 HIS C 238 PHE 0.031 0.007 PHE H 29 TYR 0.066 0.013 TYR D 534 ARG 0.007 0.001 ARG F 559 *********************** 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 fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6660 (tp30) REVERT: A 230 THR cc_start: 0.7277 (m) cc_final: 0.6749 (m) REVERT: A 235 GLN cc_start: 0.9171 (tt0) cc_final: 0.8890 (tm-30) REVERT: G 48 MET cc_start: 0.8819 (mtp) cc_final: 0.8369 (mtp) REVERT: J 70 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8777 (mm-30) REVERT: J 97 THR cc_start: 0.7532 (t) cc_final: 0.6244 (p) REVERT: B 156 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6768 (tp30) REVERT: B 235 GLN cc_start: 0.9153 (tt0) cc_final: 0.8672 (tm-30) REVERT: H 48 MET cc_start: 0.8772 (mtp) cc_final: 0.8325 (mtp) REVERT: H 101 ASP cc_start: 0.7210 (m-30) cc_final: 0.6877 (m-30) REVERT: K 70 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8885 (mm-30) REVERT: K 97 THR cc_start: 0.7740 (t) cc_final: 0.6526 (p) REVERT: C 156 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6595 (tp30) REVERT: C 230 THR cc_start: 0.7141 (m) cc_final: 0.6461 (m) REVERT: C 235 GLN cc_start: 0.9246 (tt0) cc_final: 0.8941 (tm-30) REVERT: I 23 ARG cc_start: 0.9050 (ttt180) cc_final: 0.8843 (tpp80) REVERT: I 48 MET cc_start: 0.8804 (mtp) cc_final: 0.8357 (mtp) REVERT: I 68 THR cc_start: 0.8376 (m) cc_final: 0.8108 (p) REVERT: I 81 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7233 (mt-10) REVERT: I 101 ASP cc_start: 0.7397 (m-30) cc_final: 0.6888 (m-30) REVERT: L 70 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8859 (mm-30) REVERT: L 97 THR cc_start: 0.7493 (t) cc_final: 0.6182 (p) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2977 time to fit residues: 206.7577 Evaluate side-chains 228 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN J 32 ASN D 602 HIS H 64 GLN K 32 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 HIS L 6 GLN L 32 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13473 Z= 0.310 Angle : 0.820 9.507 18300 Z= 0.441 Chirality : 0.050 0.242 2106 Planarity : 0.006 0.054 2310 Dihedral : 10.475 86.476 2268 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1614 helix: 0.56 (0.34), residues: 231 sheet: -0.01 (0.24), residues: 456 loop : -0.53 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 275 HIS 0.006 0.002 HIS B 238 PHE 0.049 0.003 PHE G 29 TYR 0.034 0.003 TYR D 534 ARG 0.007 0.001 ARG L 54 *********************** 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 336 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.514 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: A 120 GLU cc_start: 0.7583 (mp0) cc_final: 0.7316 (mt-10) REVERT: A 235 GLN cc_start: 0.9178 (tt0) cc_final: 0.8855 (tm-30) REVERT: G 23 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8775 (tpt-90) REVERT: G 37 VAL cc_start: 0.8538 (m) cc_final: 0.8335 (m) REVERT: G 46 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7356 (mm-30) REVERT: G 48 MET cc_start: 0.8898 (mtp) cc_final: 0.8466 (mtp) REVERT: G 52 MET cc_start: 0.8047 (mmm) cc_final: 0.7663 (mmm) REVERT: G 53 ILE cc_start: 0.8172 (tt) cc_final: 0.7863 (mm) REVERT: G 90 TYR cc_start: 0.8218 (m-80) cc_final: 0.7961 (m-80) REVERT: J 70 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9100 (mm-30) REVERT: J 89 LEU cc_start: 0.8613 (tt) cc_final: 0.8328 (tt) REVERT: J 97 THR cc_start: 0.6724 (t) cc_final: 0.5513 (p) REVERT: B 130 ARG cc_start: 0.7040 (ptt-90) cc_final: 0.6709 (ptt90) REVERT: B 156 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7075 (tp30) REVERT: B 235 GLN cc_start: 0.9208 (tt0) cc_final: 0.8676 (tm-30) REVERT: H 20 VAL cc_start: 0.8782 (t) cc_final: 0.8520 (p) REVERT: H 46 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7210 (mm-30) REVERT: K 97 THR cc_start: 0.7007 (t) cc_final: 0.6153 (p) REVERT: C 156 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7077 (tp30) REVERT: C 235 GLN cc_start: 0.9239 (tt0) cc_final: 0.8918 (tm-30) REVERT: I 20 VAL cc_start: 0.8805 (t) cc_final: 0.8547 (t) REVERT: I 46 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7275 (mm-30) REVERT: I 48 MET cc_start: 0.8890 (mtp) cc_final: 0.8567 (mtp) REVERT: L 23 CYS cc_start: 0.7780 (m) cc_final: 0.7174 (m) REVERT: L 70 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9132 (mm-30) REVERT: L 97 THR cc_start: 0.6766 (t) cc_final: 0.6511 (p) REVERT: L 103 LYS cc_start: 0.8120 (tttt) cc_final: 0.7908 (tttm) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2940 time to fit residues: 134.5818 Evaluate side-chains 221 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13473 Z= 0.355 Angle : 0.796 9.889 18300 Z= 0.420 Chirality : 0.051 0.294 2106 Planarity : 0.006 0.056 2310 Dihedral : 9.579 77.541 2268 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1614 helix: 0.53 (0.35), residues: 234 sheet: -0.25 (0.23), residues: 474 loop : -0.70 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 275 HIS 0.006 0.002 HIS A 238 PHE 0.033 0.003 PHE E 592 TYR 0.031 0.003 TYR E 534 ARG 0.010 0.001 ARG I 23 *********************** 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 308 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.8183 (pmm) cc_final: 0.7933 (pmm) REVERT: A 235 GLN cc_start: 0.9177 (tt0) cc_final: 0.8748 (tm-30) REVERT: G 19 LYS cc_start: 0.8946 (tptt) cc_final: 0.8509 (tptp) REVERT: G 23 ARG cc_start: 0.9000 (ttt180) cc_final: 0.8701 (ttm-80) REVERT: G 48 MET cc_start: 0.9031 (mtp) cc_final: 0.8702 (mtp) REVERT: J 71 PHE cc_start: 0.8280 (m-10) cc_final: 0.7271 (m-10) REVERT: J 90 GLN cc_start: 0.8487 (tt0) cc_final: 0.8057 (tt0) REVERT: J 97 THR cc_start: 0.7486 (t) cc_final: 0.7186 (p) REVERT: D 602 HIS cc_start: 0.7041 (t-90) cc_final: 0.6585 (m170) REVERT: B 229 MET cc_start: 0.8252 (pmm) cc_final: 0.7982 (pmm) REVERT: B 235 GLN cc_start: 0.9192 (tt0) cc_final: 0.8583 (tm-30) REVERT: H 19 LYS cc_start: 0.8912 (tptt) cc_final: 0.8562 (tptp) REVERT: H 20 VAL cc_start: 0.8734 (t) cc_final: 0.8308 (t) REVERT: H 35 SER cc_start: 0.8741 (t) cc_final: 0.8504 (m) REVERT: H 48 MET cc_start: 0.8412 (mtt) cc_final: 0.7863 (mtt) REVERT: K 35 TRP cc_start: 0.5895 (m-90) cc_final: 0.5530 (m-90) REVERT: K 70 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9064 (mm-30) REVERT: E 517 TYR cc_start: 0.7542 (p90) cc_final: 0.7338 (p90) REVERT: C 235 GLN cc_start: 0.9291 (tt0) cc_final: 0.8900 (tm-30) REVERT: I 23 ARG cc_start: 0.8819 (tpt170) cc_final: 0.8549 (tpm170) REVERT: I 46 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7721 (mm-30) REVERT: I 48 MET cc_start: 0.9250 (mtp) cc_final: 0.8863 (mtp) REVERT: I 64 GLN cc_start: 0.8214 (mt0) cc_final: 0.7895 (tp40) REVERT: L 70 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9072 (mm-30) REVERT: L 71 PHE cc_start: 0.8266 (m-10) cc_final: 0.7817 (m-10) REVERT: L 90 GLN cc_start: 0.7562 (tt0) cc_final: 0.7088 (tt0) REVERT: L 97 THR cc_start: 0.7163 (t) cc_final: 0.6349 (p) REVERT: F 596 ARG cc_start: 0.7397 (mpt180) cc_final: 0.6951 (tpp80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3014 time to fit residues: 126.4679 Evaluate side-chains 204 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 0.0870 chunk 75 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 overall best weight: 2.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** J 37 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13473 Z= 0.311 Angle : 0.752 8.646 18300 Z= 0.397 Chirality : 0.050 0.245 2106 Planarity : 0.006 0.068 2310 Dihedral : 8.883 69.652 2268 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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 : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1614 helix: 0.33 (0.35), residues: 234 sheet: -0.54 (0.23), residues: 495 loop : -0.86 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 597 HIS 0.006 0.002 HIS H 100C PHE 0.021 0.002 PHE D 592 TYR 0.020 0.002 TYR E 534 ARG 0.013 0.001 ARG H 94 *********************** 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 298 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.7290 (m-30) cc_final: 0.7079 (m-30) REVERT: A 77 THR cc_start: 0.7642 (p) cc_final: 0.6994 (t) REVERT: A 229 MET cc_start: 0.8334 (pmm) cc_final: 0.8098 (pmm) REVERT: A 235 GLN cc_start: 0.9185 (tt0) cc_final: 0.8511 (tm-30) REVERT: A 236 VAL cc_start: 0.7845 (t) cc_final: 0.7290 (t) REVERT: G 23 ARG cc_start: 0.9015 (ttt180) cc_final: 0.8747 (ttm-80) REVERT: G 48 MET cc_start: 0.9105 (mtp) cc_final: 0.8803 (mtp) REVERT: G 81 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7294 (tp30) REVERT: G 90 TYR cc_start: 0.8603 (m-80) cc_final: 0.8018 (m-80) REVERT: G 94 ARG cc_start: 0.6721 (mtp85) cc_final: 0.6373 (mtt90) REVERT: J 3 VAL cc_start: 0.5556 (t) cc_final: 0.5348 (t) REVERT: J 33 LEU cc_start: 0.8979 (tp) cc_final: 0.8314 (tp) REVERT: J 71 PHE cc_start: 0.8398 (m-80) cc_final: 0.7272 (m-10) REVERT: J 90 GLN cc_start: 0.8102 (tt0) cc_final: 0.7561 (tt0) REVERT: J 97 THR cc_start: 0.7430 (t) cc_final: 0.6630 (p) REVERT: D 602 HIS cc_start: 0.6897 (t-90) cc_final: 0.6306 (m170) REVERT: B 44 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5989 (tm-30) REVERT: B 124 GLU cc_start: 0.8654 (tp30) cc_final: 0.8439 (tp30) REVERT: B 130 ARG cc_start: 0.7657 (ptt90) cc_final: 0.6697 (ptt-90) REVERT: B 229 MET cc_start: 0.8372 (pmm) cc_final: 0.8107 (pmm) REVERT: B 230 THR cc_start: 0.7235 (m) cc_final: 0.7028 (m) REVERT: B 235 GLN cc_start: 0.9195 (tt0) cc_final: 0.8550 (tm-30) REVERT: B 236 VAL cc_start: 0.7645 (t) cc_final: 0.7187 (t) REVERT: H 19 LYS cc_start: 0.8934 (tptt) cc_final: 0.8545 (tptp) REVERT: H 20 VAL cc_start: 0.8708 (t) cc_final: 0.8147 (t) REVERT: H 46 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7141 (mp0) REVERT: H 48 MET cc_start: 0.8437 (mtt) cc_final: 0.7818 (mtt) REVERT: K 27 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7205 (tm-30) REVERT: K 35 TRP cc_start: 0.5932 (m-90) cc_final: 0.5570 (m-90) REVERT: K 48 ILE cc_start: 0.7504 (mm) cc_final: 0.7177 (mm) REVERT: K 70 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9099 (mm-30) REVERT: C 229 MET cc_start: 0.8397 (pmm) cc_final: 0.8094 (pmm) REVERT: C 230 THR cc_start: 0.7022 (m) cc_final: 0.6808 (m) REVERT: C 235 GLN cc_start: 0.9298 (tt0) cc_final: 0.8551 (tm-30) REVERT: I 19 LYS cc_start: 0.8845 (tppt) cc_final: 0.8423 (tptp) REVERT: I 23 ARG cc_start: 0.8845 (tpt170) cc_final: 0.8579 (tpp-160) REVERT: I 46 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7732 (mm-30) REVERT: I 48 MET cc_start: 0.9281 (mtp) cc_final: 0.8925 (mtp) REVERT: I 52 MET cc_start: 0.8256 (mpp) cc_final: 0.7902 (mpp) REVERT: I 64 GLN cc_start: 0.8310 (mt0) cc_final: 0.8104 (tp40) REVERT: I 81 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7725 (tp30) REVERT: L 27 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7312 (tm-30) REVERT: L 70 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9063 (mm-30) REVERT: L 71 PHE cc_start: 0.8373 (m-10) cc_final: 0.8073 (m-10) REVERT: L 90 GLN cc_start: 0.7682 (tt0) cc_final: 0.7133 (tt0) REVERT: L 97 THR cc_start: 0.7542 (t) cc_final: 0.6718 (p) REVERT: F 545 GLU cc_start: 0.7710 (pm20) cc_final: 0.7457 (mt-10) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2929 time to fit residues: 121.1904 Evaluate side-chains 218 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 114 optimal weight: 0.0020 chunk 63 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13473 Z= 0.212 Angle : 0.684 8.456 18300 Z= 0.356 Chirality : 0.048 0.280 2106 Planarity : 0.006 0.096 2310 Dihedral : 8.156 63.106 2268 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1614 helix: 1.66 (0.38), residues: 198 sheet: -0.45 (0.23), residues: 495 loop : -1.07 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS C 238 PHE 0.017 0.002 PHE E 592 TYR 0.034 0.002 TYR D 534 ARG 0.008 0.001 ARG F 587 *********************** 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 284 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 1.707 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: A 77 THR cc_start: 0.7714 (p) cc_final: 0.7071 (t) REVERT: A 122 LEU cc_start: 0.9372 (mm) cc_final: 0.9075 (mm) REVERT: A 229 MET cc_start: 0.8331 (pmm) cc_final: 0.8123 (pmm) REVERT: A 235 GLN cc_start: 0.9143 (tt0) cc_final: 0.8472 (tm-30) REVERT: G 23 ARG cc_start: 0.9001 (ttt180) cc_final: 0.8752 (ttm-80) REVERT: G 48 MET cc_start: 0.9057 (mtp) cc_final: 0.8795 (mtp) REVERT: G 90 TYR cc_start: 0.8658 (m-80) cc_final: 0.8036 (m-80) REVERT: J 90 GLN cc_start: 0.8303 (tt0) cc_final: 0.7778 (tt0) REVERT: J 97 THR cc_start: 0.7508 (t) cc_final: 0.6791 (p) REVERT: D 602 HIS cc_start: 0.6915 (t-90) cc_final: 0.6396 (m170) REVERT: B 77 THR cc_start: 0.7713 (p) cc_final: 0.7255 (t) REVERT: B 99 TYR cc_start: 0.8025 (p90) cc_final: 0.7798 (p90) REVERT: B 229 MET cc_start: 0.8339 (pmm) cc_final: 0.8094 (pmm) REVERT: B 235 GLN cc_start: 0.9174 (tt0) cc_final: 0.8351 (tm-30) REVERT: H 19 LYS cc_start: 0.8949 (tptt) cc_final: 0.8438 (tptp) REVERT: H 20 VAL cc_start: 0.8707 (t) cc_final: 0.8111 (t) REVERT: H 46 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7287 (mm-30) REVERT: H 48 MET cc_start: 0.8285 (mtt) cc_final: 0.7696 (mtt) REVERT: K 70 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9110 (mm-30) REVERT: K 73 LEU cc_start: 0.8783 (tp) cc_final: 0.7504 (tp) REVERT: C 77 THR cc_start: 0.7561 (p) cc_final: 0.7024 (t) REVERT: C 229 MET cc_start: 0.8354 (pmm) cc_final: 0.8052 (pmm) REVERT: C 230 THR cc_start: 0.6993 (m) cc_final: 0.6766 (m) REVERT: C 235 GLN cc_start: 0.9241 (tt0) cc_final: 0.8532 (tm-30) REVERT: C 236 VAL cc_start: 0.7822 (t) cc_final: 0.7345 (t) REVERT: I 19 LYS cc_start: 0.8788 (tppt) cc_final: 0.8561 (tptp) REVERT: I 23 ARG cc_start: 0.8814 (tpt170) cc_final: 0.8524 (tpp-160) REVERT: I 46 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7721 (mm-30) REVERT: I 48 MET cc_start: 0.9318 (mtp) cc_final: 0.9037 (mtp) REVERT: I 80 MET cc_start: 0.8733 (pmm) cc_final: 0.8140 (pmm) REVERT: I 81 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7769 (tp30) REVERT: L 33 LEU cc_start: 0.8843 (tp) cc_final: 0.8529 (tp) REVERT: L 53 THR cc_start: 0.8835 (m) cc_final: 0.8622 (p) REVERT: L 70 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9114 (mm-30) REVERT: L 71 PHE cc_start: 0.8277 (m-10) cc_final: 0.7879 (m-10) REVERT: L 90 GLN cc_start: 0.7722 (tt0) cc_final: 0.7252 (tt0) REVERT: L 97 THR cc_start: 0.7536 (t) cc_final: 0.6715 (p) REVERT: F 596 ARG cc_start: 0.7449 (mmt-90) cc_final: 0.7041 (mmm160) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3035 time to fit residues: 120.3633 Evaluate side-chains 210 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS B 235 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13473 Z= 0.344 Angle : 0.763 8.518 18300 Z= 0.394 Chirality : 0.050 0.254 2106 Planarity : 0.006 0.087 2310 Dihedral : 8.128 59.027 2268 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1614 helix: 1.36 (0.37), residues: 198 sheet: -0.61 (0.22), residues: 513 loop : -1.21 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP K 35 HIS 0.012 0.002 HIS H 100C PHE 0.013 0.002 PHE B 232 TYR 0.028 0.002 TYR E 534 ARG 0.014 0.001 ARG G 94 *********************** 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 fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.581 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: 0.8024 (p) cc_final: 0.7433 (t) REVERT: A 223 ASP cc_start: 0.7567 (m-30) cc_final: 0.7359 (m-30) REVERT: A 229 MET cc_start: 0.8478 (pmm) cc_final: 0.8256 (pmm) REVERT: A 230 THR cc_start: 0.7252 (m) cc_final: 0.6978 (m) REVERT: A 231 ASN cc_start: 0.8465 (t0) cc_final: 0.7589 (p0) REVERT: A 235 GLN cc_start: 0.9164 (tt0) cc_final: 0.8490 (tm-30) REVERT: A 236 VAL cc_start: 0.7560 (t) cc_final: 0.7259 (t) REVERT: G 23 ARG cc_start: 0.8960 (ttt180) cc_final: 0.8738 (ttm-80) REVERT: G 29 PHE cc_start: 0.6496 (m-10) cc_final: 0.6135 (m-80) REVERT: J 90 GLN cc_start: 0.8165 (tt0) cc_final: 0.7526 (tt0) REVERT: J 97 THR cc_start: 0.7719 (t) cc_final: 0.6965 (p) REVERT: D 545 GLU cc_start: 0.8141 (mp0) cc_final: 0.7505 (mt-10) REVERT: B 44 GLN cc_start: 0.6380 (tm-30) cc_final: 0.5906 (tm-30) REVERT: B 77 THR cc_start: 0.7862 (p) cc_final: 0.7388 (t) REVERT: B 229 MET cc_start: 0.8530 (pmm) cc_final: 0.8301 (pmm) REVERT: B 230 THR cc_start: 0.7344 (m) cc_final: 0.7138 (m) REVERT: B 235 GLN cc_start: 0.9190 (tt0) cc_final: 0.8343 (tm-30) REVERT: B 236 VAL cc_start: 0.7506 (t) cc_final: 0.7040 (t) REVERT: H 19 LYS cc_start: 0.8628 (tptt) cc_final: 0.8397 (tptp) REVERT: H 20 VAL cc_start: 0.8794 (t) cc_final: 0.8180 (t) REVERT: H 32 LYS cc_start: 0.9011 (tptp) cc_final: 0.8746 (ttpt) REVERT: H 46 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7272 (mp0) REVERT: K 27 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6935 (tm-30) REVERT: K 48 ILE cc_start: 0.8052 (tt) cc_final: 0.5150 (tt) REVERT: K 70 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9101 (mm-30) REVERT: C 77 THR cc_start: 0.7848 (p) cc_final: 0.7289 (t) REVERT: C 229 MET cc_start: 0.8542 (pmm) cc_final: 0.8288 (pmm) REVERT: C 230 THR cc_start: 0.7195 (m) cc_final: 0.6898 (m) REVERT: C 235 GLN cc_start: 0.9249 (tt0) cc_final: 0.8462 (tm-30) REVERT: I 20 VAL cc_start: 0.8470 (t) cc_final: 0.8265 (t) REVERT: I 23 ARG cc_start: 0.8830 (tpt170) cc_final: 0.8587 (tpp-160) REVERT: I 46 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7652 (mm-30) REVERT: I 48 MET cc_start: 0.9400 (mtp) cc_final: 0.9131 (mtp) REVERT: I 56 LEU cc_start: 0.7479 (tp) cc_final: 0.7257 (mt) REVERT: I 80 MET cc_start: 0.8686 (pmm) cc_final: 0.8281 (pmm) REVERT: I 81 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7591 (tp30) REVERT: L 70 GLU cc_start: 0.9393 (mt-10) cc_final: 0.9096 (mm-30) REVERT: L 73 LEU cc_start: 0.8867 (tp) cc_final: 0.7189 (tp) REVERT: L 90 GLN cc_start: 0.7751 (tt0) cc_final: 0.7313 (tt0) REVERT: L 97 THR cc_start: 0.7719 (t) cc_final: 0.6755 (p) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2727 time to fit residues: 106.2433 Evaluate side-chains 215 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 112 optimal weight: 0.2980 chunk 129 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN I 3 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 13473 Z= 0.493 Angle : 0.919 12.419 18300 Z= 0.471 Chirality : 0.054 0.245 2106 Planarity : 0.007 0.065 2310 Dihedral : 8.796 56.535 2268 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1614 helix: 0.73 (0.37), residues: 180 sheet: -0.89 (0.22), residues: 507 loop : -1.26 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP L 35 HIS 0.014 0.003 HIS H 100C PHE 0.042 0.004 PHE K 71 TYR 0.026 0.003 TYR I 33 ARG 0.006 0.001 ARG A 266 *********************** 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 269 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.512 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: 0.8323 (p) cc_final: 0.7936 (t) REVERT: A 223 ASP cc_start: 0.8186 (m-30) cc_final: 0.7904 (m-30) REVERT: A 229 MET cc_start: 0.8680 (pmm) cc_final: 0.8423 (pmm) REVERT: A 230 THR cc_start: 0.7624 (m) cc_final: 0.7362 (m) REVERT: A 231 ASN cc_start: 0.8704 (t0) cc_final: 0.7984 (p0) REVERT: A 235 GLN cc_start: 0.9222 (tt0) cc_final: 0.8549 (tm-30) REVERT: J 13 VAL cc_start: 0.7001 (t) cc_final: 0.6313 (t) REVERT: J 18 ARG cc_start: 0.8476 (tmm-80) cc_final: 0.8253 (tmm-80) REVERT: J 90 GLN cc_start: 0.8483 (tt0) cc_final: 0.7848 (tt0) REVERT: J 97 THR cc_start: 0.7957 (t) cc_final: 0.7219 (p) REVERT: D 517 TYR cc_start: 0.8237 (p90) cc_final: 0.7974 (p90) REVERT: B 77 THR cc_start: 0.8369 (p) cc_final: 0.7969 (t) REVERT: B 130 ARG cc_start: 0.7938 (ptt-90) cc_final: 0.6905 (ptt-90) REVERT: B 229 MET cc_start: 0.8735 (pmm) cc_final: 0.8503 (pmm) REVERT: B 230 THR cc_start: 0.7552 (m) cc_final: 0.7249 (m) REVERT: B 231 ASN cc_start: 0.8898 (t0) cc_final: 0.7956 (p0) REVERT: B 235 GLN cc_start: 0.9158 (tt0) cc_final: 0.8512 (tm-30) REVERT: H 19 LYS cc_start: 0.8642 (tptt) cc_final: 0.8306 (tptp) REVERT: H 46 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7272 (mp0) REVERT: K 42 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8486 (mp10) REVERT: K 70 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9109 (mm-30) REVERT: K 91 TYR cc_start: 0.7679 (p90) cc_final: 0.6877 (p90) REVERT: E 517 TYR cc_start: 0.8272 (p90) cc_final: 0.7931 (p90) REVERT: C 77 THR cc_start: 0.8320 (p) cc_final: 0.7898 (t) REVERT: C 122 LEU cc_start: 0.9311 (mm) cc_final: 0.8959 (mm) REVERT: C 229 MET cc_start: 0.8685 (pmm) cc_final: 0.8450 (pmm) REVERT: C 231 ASN cc_start: 0.8837 (t0) cc_final: 0.7849 (p0) REVERT: C 235 GLN cc_start: 0.9286 (tt0) cc_final: 0.8630 (tm-30) REVERT: I 19 LYS cc_start: 0.8924 (tptt) cc_final: 0.8623 (tptp) REVERT: I 23 ARG cc_start: 0.8798 (tpt170) cc_final: 0.8567 (tpp-160) REVERT: I 29 PHE cc_start: 0.6981 (m-10) cc_final: 0.6224 (m-80) REVERT: I 33 TYR cc_start: 0.7757 (m-10) cc_final: 0.7304 (m-10) REVERT: I 48 MET cc_start: 0.9455 (mtp) cc_final: 0.9220 (mtp) REVERT: I 80 MET cc_start: 0.8614 (pmm) cc_final: 0.7900 (pmm) REVERT: I 97 ILE cc_start: 0.8590 (tp) cc_final: 0.8202 (tp) REVERT: L 42 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8522 (mm110) REVERT: L 53 THR cc_start: 0.8885 (m) cc_final: 0.8649 (p) REVERT: L 70 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9146 (mm-30) REVERT: L 90 GLN cc_start: 0.8087 (tt0) cc_final: 0.7437 (tt0) REVERT: L 97 THR cc_start: 0.8029 (t) cc_final: 0.6767 (p) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2636 time to fit residues: 100.0321 Evaluate side-chains 202 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS E 521 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 521 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13473 Z= 0.205 Angle : 0.755 12.444 18300 Z= 0.383 Chirality : 0.049 0.234 2106 Planarity : 0.006 0.090 2310 Dihedral : 7.759 48.441 2268 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.07 % Allowed : 0.64 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.21), residues: 1614 helix: 1.37 (0.38), residues: 195 sheet: -0.77 (0.23), residues: 492 loop : -1.25 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP L 35 HIS 0.010 0.002 HIS H 100C PHE 0.024 0.002 PHE E 592 TYR 0.034 0.002 TYR G 33 ARG 0.012 0.001 ARG H 94 *********************** 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 279 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 1.760 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: 0.8166 (p) cc_final: 0.7700 (t) REVERT: A 148 PRO cc_start: 0.8692 (Cg_exo) cc_final: 0.8489 (Cg_endo) REVERT: A 223 ASP cc_start: 0.8215 (m-30) cc_final: 0.7858 (m-30) REVERT: A 229 MET cc_start: 0.8573 (pmm) cc_final: 0.8368 (pmm) REVERT: A 230 THR cc_start: 0.7456 (m) cc_final: 0.7218 (m) REVERT: A 231 ASN cc_start: 0.8687 (t0) cc_final: 0.7809 (p0) REVERT: A 235 GLN cc_start: 0.9129 (tt0) cc_final: 0.8488 (tm-30) REVERT: G 35 ILE cc_start: 0.8919 (mm) cc_final: 0.8541 (tp) REVERT: G 48 MET cc_start: 0.9025 (mtt) cc_final: 0.8742 (mpp) REVERT: G 53 ILE cc_start: 0.8473 (tt) cc_final: 0.7971 (pt) REVERT: J 18 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.8127 (tmm-80) REVERT: J 90 GLN cc_start: 0.8616 (tt0) cc_final: 0.8065 (tt0) REVERT: J 97 THR cc_start: 0.7803 (t) cc_final: 0.7178 (p) REVERT: D 517 TYR cc_start: 0.7864 (p90) cc_final: 0.7623 (p90) REVERT: D 583 SER cc_start: 0.7953 (m) cc_final: 0.7679 (p) REVERT: B 77 THR cc_start: 0.8259 (p) cc_final: 0.7846 (t) REVERT: B 130 ARG cc_start: 0.7975 (ptt-90) cc_final: 0.7095 (ptt-90) REVERT: B 229 MET cc_start: 0.8623 (pmm) cc_final: 0.8373 (pmm) REVERT: B 230 THR cc_start: 0.7305 (m) cc_final: 0.6984 (m) REVERT: B 231 ASN cc_start: 0.8892 (t0) cc_final: 0.7942 (p0) REVERT: B 235 GLN cc_start: 0.9211 (tt0) cc_final: 0.8258 (tm-30) REVERT: H 20 VAL cc_start: 0.8671 (t) cc_final: 0.8308 (t) REVERT: H 32 LYS cc_start: 0.8947 (tptp) cc_final: 0.8589 (ttpt) REVERT: H 46 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7269 (mp0) REVERT: H 47 TRP cc_start: 0.8463 (t60) cc_final: 0.8205 (t60) REVERT: H 52 MET cc_start: 0.8401 (mmm) cc_final: 0.8020 (mmm) REVERT: H 64 GLN cc_start: 0.8756 (mt0) cc_final: 0.8451 (mt0) REVERT: K 27 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6747 (tm-30) REVERT: K 42 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8496 (mm110) REVERT: K 70 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9136 (mm-30) REVERT: K 71 PHE cc_start: 0.8240 (m-80) cc_final: 0.8013 (m-10) REVERT: K 91 TYR cc_start: 0.7180 (p90) cc_final: 0.6639 (p90) REVERT: E 517 TYR cc_start: 0.7737 (p90) cc_final: 0.7478 (p90) REVERT: E 583 SER cc_start: 0.8048 (m) cc_final: 0.7775 (p) REVERT: E 600 THR cc_start: 0.6769 (t) cc_final: 0.6016 (m) REVERT: C 55 ASP cc_start: 0.7715 (m-30) cc_final: 0.7514 (m-30) REVERT: C 77 THR cc_start: 0.8078 (p) cc_final: 0.7620 (t) REVERT: C 229 MET cc_start: 0.8574 (pmm) cc_final: 0.8360 (pmm) REVERT: C 231 ASN cc_start: 0.8874 (t0) cc_final: 0.7853 (p0) REVERT: C 235 GLN cc_start: 0.9270 (tt0) cc_final: 0.8488 (tm-30) REVERT: I 19 LYS cc_start: 0.9093 (tptt) cc_final: 0.8559 (tptp) REVERT: I 23 ARG cc_start: 0.8794 (tpt170) cc_final: 0.8581 (tpp-160) REVERT: I 46 GLU cc_start: 0.8410 (tp30) cc_final: 0.7632 (mm-30) REVERT: I 80 MET cc_start: 0.8709 (pmm) cc_final: 0.7994 (pmm) REVERT: L 33 LEU cc_start: 0.8764 (tp) cc_final: 0.8524 (pt) REVERT: L 42 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8536 (mm110) REVERT: L 70 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9140 (mm-30) REVERT: L 90 GLN cc_start: 0.7891 (tt0) cc_final: 0.7329 (tt0) REVERT: L 97 THR cc_start: 0.7905 (t) cc_final: 0.6786 (p) REVERT: F 583 SER cc_start: 0.7977 (m) cc_final: 0.7528 (p) REVERT: F 600 THR cc_start: 0.6665 (t) cc_final: 0.5796 (m) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.2572 time to fit residues: 102.4362 Evaluate side-chains 201 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 50.0000 chunk 151 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13473 Z= 0.299 Angle : 0.762 12.121 18300 Z= 0.392 Chirality : 0.048 0.209 2106 Planarity : 0.006 0.086 2310 Dihedral : 7.708 53.369 2268 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1614 helix: 1.22 (0.37), residues: 195 sheet: -1.07 (0.22), residues: 519 loop : -1.23 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP L 35 HIS 0.013 0.002 HIS H 100C PHE 0.040 0.002 PHE I 29 TYR 0.037 0.002 TYR I 33 ARG 0.008 0.001 ARG C 172 *********************** 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 266 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.541 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: 0.8278 (p) cc_final: 0.7856 (t) REVERT: A 223 ASP cc_start: 0.8234 (m-30) cc_final: 0.7889 (m-30) REVERT: A 229 MET cc_start: 0.8634 (pmm) cc_final: 0.8409 (pmm) REVERT: A 230 THR cc_start: 0.7531 (m) cc_final: 0.7274 (m) REVERT: A 231 ASN cc_start: 0.8719 (t0) cc_final: 0.7890 (p0) REVERT: A 235 GLN cc_start: 0.9163 (tt0) cc_final: 0.8483 (tm-30) REVERT: G 19 LYS cc_start: 0.8785 (tptt) cc_final: 0.8252 (tptp) REVERT: G 35 ILE cc_start: 0.8863 (mm) cc_final: 0.8471 (tp) REVERT: G 48 MET cc_start: 0.9152 (mtt) cc_final: 0.8668 (mpp) REVERT: G 100 PHE cc_start: 0.6337 (p90) cc_final: 0.5900 (p90) REVERT: J 18 ARG cc_start: 0.8408 (tmm-80) cc_final: 0.7860 (tmm-80) REVERT: J 39 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8695 (mmpt) REVERT: J 42 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8529 (mm110) REVERT: J 78 LEU cc_start: 0.8516 (pp) cc_final: 0.7997 (tt) REVERT: J 90 GLN cc_start: 0.8553 (tt0) cc_final: 0.7988 (tt0) REVERT: J 97 THR cc_start: 0.7887 (t) cc_final: 0.7108 (p) REVERT: D 517 TYR cc_start: 0.8150 (p90) cc_final: 0.7858 (p90) REVERT: B 77 THR cc_start: 0.8351 (p) cc_final: 0.7957 (t) REVERT: B 130 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7348 (ptt-90) REVERT: B 229 MET cc_start: 0.8664 (pmm) cc_final: 0.8435 (pmm) REVERT: B 230 THR cc_start: 0.7538 (m) cc_final: 0.7231 (m) REVERT: B 231 ASN cc_start: 0.8869 (t0) cc_final: 0.8014 (p0) REVERT: B 235 GLN cc_start: 0.9191 (tt0) cc_final: 0.8318 (tm-30) REVERT: B 236 VAL cc_start: 0.7215 (t) cc_final: 0.6818 (t) REVERT: H 46 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7240 (mp0) REVERT: H 47 TRP cc_start: 0.8545 (t60) cc_final: 0.7987 (t60) REVERT: H 52 MET cc_start: 0.8453 (mmm) cc_final: 0.8081 (mmm) REVERT: K 27 GLN cc_start: 0.7168 (tm-30) cc_final: 0.6890 (tm-30) REVERT: K 42 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8494 (mm110) REVERT: K 70 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9161 (mm-30) REVERT: E 517 TYR cc_start: 0.8168 (p90) cc_final: 0.7927 (p90) REVERT: E 583 SER cc_start: 0.8200 (m) cc_final: 0.7900 (p) REVERT: C 55 ASP cc_start: 0.7717 (m-30) cc_final: 0.7446 (m-30) REVERT: C 77 THR cc_start: 0.8146 (p) cc_final: 0.7693 (t) REVERT: C 231 ASN cc_start: 0.8663 (t0) cc_final: 0.7915 (p0) REVERT: C 235 GLN cc_start: 0.9277 (tt0) cc_final: 0.8440 (tm-30) REVERT: I 19 LYS cc_start: 0.8933 (tptt) cc_final: 0.8698 (tptp) REVERT: I 23 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8580 (tpp-160) REVERT: I 48 MET cc_start: 0.9223 (mtt) cc_final: 0.8789 (mpp) REVERT: I 80 MET cc_start: 0.8533 (pmm) cc_final: 0.8043 (pmm) REVERT: I 81 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7529 (tp30) REVERT: L 42 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8551 (mm110) REVERT: L 70 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9159 (mm-30) REVERT: L 90 GLN cc_start: 0.8121 (tt0) cc_final: 0.7655 (tt0) REVERT: L 97 THR cc_start: 0.8015 (t) cc_final: 0.7381 (p) REVERT: F 600 THR cc_start: 0.7179 (t) cc_final: 0.6673 (m) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.2513 time to fit residues: 96.4980 Evaluate side-chains 186 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS F 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.8190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13473 Z= 0.237 Angle : 0.739 12.326 18300 Z= 0.379 Chirality : 0.048 0.225 2106 Planarity : 0.006 0.069 2310 Dihedral : 7.067 51.296 2268 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1614 helix: 1.36 (0.37), residues: 195 sheet: -0.96 (0.23), residues: 507 loop : -1.27 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP L 35 HIS 0.013 0.002 HIS H 100C PHE 0.021 0.002 PHE K 71 TYR 0.025 0.002 TYR L 36 ARG 0.010 0.001 ARG C 172 ********************** 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 261 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.623 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: 0.8201 (p) cc_final: 0.7779 (t) REVERT: A 223 ASP cc_start: 0.8291 (m-30) cc_final: 0.7959 (m-30) REVERT: A 230 THR cc_start: 0.7555 (m) cc_final: 0.7311 (m) REVERT: A 231 ASN cc_start: 0.8724 (t0) cc_final: 0.7891 (p0) REVERT: A 235 GLN cc_start: 0.9154 (tt0) cc_final: 0.8520 (tm-30) REVERT: G 19 LYS cc_start: 0.8755 (tptt) cc_final: 0.8334 (tptp) REVERT: G 35 ILE cc_start: 0.8894 (mm) cc_final: 0.8673 (tp) REVERT: G 48 MET cc_start: 0.9142 (mtt) cc_final: 0.8629 (mpp) REVERT: G 100 PHE cc_start: 0.6438 (p90) cc_final: 0.5735 (p90) REVERT: J 18 ARG cc_start: 0.8398 (tmm-80) cc_final: 0.7862 (tmm-80) REVERT: J 42 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8526 (mm110) REVERT: J 78 LEU cc_start: 0.8593 (pp) cc_final: 0.7891 (tt) REVERT: J 90 GLN cc_start: 0.8777 (tt0) cc_final: 0.8206 (tt0) REVERT: J 97 THR cc_start: 0.7869 (t) cc_final: 0.7258 (p) REVERT: D 517 TYR cc_start: 0.8035 (p90) cc_final: 0.7774 (p90) REVERT: D 583 SER cc_start: 0.8070 (m) cc_final: 0.7809 (p) REVERT: B 77 THR cc_start: 0.8334 (p) cc_final: 0.7948 (t) REVERT: B 130 ARG cc_start: 0.8049 (ptt-90) cc_final: 0.7572 (ptt-90) REVERT: B 229 MET cc_start: 0.8696 (pmm) cc_final: 0.8475 (pmm) REVERT: B 230 THR cc_start: 0.7564 (m) cc_final: 0.7280 (m) REVERT: B 231 ASN cc_start: 0.8701 (t0) cc_final: 0.8045 (p0) REVERT: B 235 GLN cc_start: 0.9248 (tt0) cc_final: 0.8328 (tm-30) REVERT: H 19 LYS cc_start: 0.8842 (tptt) cc_final: 0.8474 (tptp) REVERT: H 46 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7243 (mp0) REVERT: H 47 TRP cc_start: 0.8466 (t60) cc_final: 0.8098 (t60) REVERT: K 70 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9195 (mm-30) REVERT: K 91 TYR cc_start: 0.6605 (p90) cc_final: 0.5908 (p90) REVERT: E 600 THR cc_start: 0.6740 (t) cc_final: 0.6033 (m) REVERT: C 55 ASP cc_start: 0.7657 (m-30) cc_final: 0.7380 (m-30) REVERT: C 77 THR cc_start: 0.8091 (p) cc_final: 0.7645 (t) REVERT: C 229 MET cc_start: 0.8444 (pmm) cc_final: 0.8202 (pmm) REVERT: C 231 ASN cc_start: 0.8821 (t0) cc_final: 0.7910 (p0) REVERT: C 235 GLN cc_start: 0.9282 (tt0) cc_final: 0.8399 (tm-30) REVERT: I 23 ARG cc_start: 0.8719 (tpt170) cc_final: 0.8502 (tpp-160) REVERT: I 46 GLU cc_start: 0.8347 (tp30) cc_final: 0.7750 (mm-30) REVERT: I 48 MET cc_start: 0.9244 (mtt) cc_final: 0.8729 (mpp) REVERT: I 80 MET cc_start: 0.8234 (pmm) cc_final: 0.7714 (pmm) REVERT: I 81 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7701 (tp30) REVERT: I 97 ILE cc_start: 0.7840 (tp) cc_final: 0.7579 (mm) REVERT: L 70 GLU cc_start: 0.9531 (mt-10) cc_final: 0.9181 (mm-30) REVERT: L 90 GLN cc_start: 0.8003 (tt0) cc_final: 0.7629 (tt0) REVERT: L 97 THR cc_start: 0.7918 (t) cc_final: 0.6769 (t) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2629 time to fit residues: 100.2634 Evaluate side-chains 196 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 100CHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.116444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081157 restraints weight = 35815.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084250 restraints weight = 20054.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086353 restraints weight = 13572.883| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.8342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13473 Z= 0.255 Angle : 0.730 11.711 18300 Z= 0.376 Chirality : 0.047 0.191 2106 Planarity : 0.006 0.059 2310 Dihedral : 6.493 58.258 2268 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1614 helix: 1.38 (0.38), residues: 195 sheet: -0.95 (0.23), residues: 507 loop : -1.28 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP L 35 HIS 0.009 0.002 HIS H 100C PHE 0.020 0.002 PHE K 71 TYR 0.036 0.002 TYR F 534 ARG 0.009 0.001 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.28 seconds wall clock time: 54 minutes 33.27 seconds (3273.27 seconds total)