Starting phenix.real_space_refine on Tue Dec 31 08:22:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.map" model { file = "/net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efv_28101/12_2024/8efv_28101.cif" } resolution = 2.97 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= 0.003 sd= 0.095 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: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 4 5.21 5 S 26 5.16 5 C 9531 2.51 5 N 2769 2.21 5 O 2909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15295 Number of models: 1 Model: "" Number of chains: 14 Chain: "D" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2324 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2355 Classifications: {'peptide': 301} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2453 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2442 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 293} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2345 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2340 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 279} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.63, per 1000 atoms: 0.63 Number of scatterers: 15295 At special positions: 0 Unit cell: (120.96, 135, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 56 15.00 Mg 4 11.99 O 2909 8.00 N 2769 7.00 C 9531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.8 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 19 sheets defined 57.3% alpha, 8.6% beta 17 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'D' and resid 17 through 34 removed outlier: 3.714A pdb=" N LYS D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 78 through 87 removed outlier: 3.681A pdb=" N ALA D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 removed outlier: 3.548A pdb=" N LEU D 102 " --> pdb=" O ILE D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 169 through 185 Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.530A pdb=" N ARG D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 222 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 266 through 275 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.561A pdb=" N LEU D 289 " --> pdb=" O HIS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'C' and resid 17 through 34 removed outlier: 3.800A pdb=" N LYS C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.920A pdb=" N ALA C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 169 through 185 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.533A pdb=" N GLU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 222 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.586A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.830A pdb=" N LEU C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'B' and resid 17 through 34 removed outlier: 3.720A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.511A pdb=" N HIS B 56 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.663A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.740A pdb=" N GLU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.962A pdb=" N GLU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.552A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 266 through 275 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.509A pdb=" N LEU B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'A' and resid 17 through 34 removed outlier: 3.598A pdb=" N LYS A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.762A pdb=" N LEU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 removed outlier: 3.601A pdb=" N LEU A 102 " --> pdb=" O ILE A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 109 through 116 removed outlier: 4.128A pdb=" N ALA A 113 " --> pdb=" O HIS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 203 through 221 removed outlier: 3.601A pdb=" N ALA A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 266 through 274 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'F' and resid 17 through 35 removed outlier: 3.821A pdb=" N LYS F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 99 through 102 removed outlier: 3.561A pdb=" N LEU F 102 " --> pdb=" O ILE F 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 102' Processing helix chain 'F' and resid 106 through 116 removed outlier: 4.000A pdb=" N TYR F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Proline residue: F 112 - end of helix Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.566A pdb=" N ILE F 151 " --> pdb=" O PRO F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.543A pdb=" N SER F 157 " --> pdb=" O PRO F 154 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 158 " --> pdb=" O LEU F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 169 through 185 Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 203 through 221 removed outlier: 3.730A pdb=" N VAL F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 221 " --> pdb=" O PHE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 246 through 261 removed outlier: 3.871A pdb=" N ARG F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 4.376A pdb=" N ALA F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 285 through 292 Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 78 through 86 removed outlier: 3.671A pdb=" N ASN E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 109 through 115 removed outlier: 3.725A pdb=" N ALA E 113 " --> pdb=" O HIS E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.604A pdb=" N ILE E 151 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 169 through 185 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.635A pdb=" N GLU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 222 Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 268 through 274 removed outlier: 3.581A pdb=" N THR E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.857A pdb=" N LEU E 289 " --> pdb=" O HIS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.819A pdb=" N ARG E 310 " --> pdb=" O GLU E 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.063A pdb=" N ARG D 67 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP D 97 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR D 69 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP D 92 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE D 142 " --> pdb=" O ASP D 92 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 94 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 144 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE D 96 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 42 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 187 through 188 removed outlier: 7.270A pdb=" N ARG D 187 " --> pdb=" O ILE D 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 296 through 298 Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.362A pdb=" N LEU C 42 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 187 through 188 removed outlier: 7.281A pdb=" N ARG C 187 " --> pdb=" O ILE C 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 296 through 298 Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.353A pdb=" N ARG B 67 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP B 97 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 69 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 42 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'B' and resid 295 through 298 Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.302A pdb=" N LEU A 42 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.668A pdb=" N ALA F 144 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'F' and resid 187 through 188 removed outlier: 7.325A pdb=" N ARG F 187 " --> pdb=" O ILE F 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 295 through 297 Processing sheet with id=AB8, first strand: chain 'E' and resid 69 through 70 removed outlier: 7.217A pdb=" N THR E 69 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 41 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N THR E 145 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU E 43 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU E 42 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 187 through 188 removed outlier: 7.233A pdb=" N ARG E 187 " --> pdb=" O ILE E 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 296 through 298 692 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5217 1.36 - 1.51: 4047 1.51 - 1.66: 6332 1.66 - 1.80: 42 1.80 - 1.95: 7 Bond restraints: 15645 Sorted by residual: bond pdb=" CA ARG E 104 " pdb=" C ARG E 104 " ideal model delta sigma weight residual 1.522 1.546 -0.024 1.72e-02 3.38e+03 1.91e+00 bond pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" C4 ADP A 400 " pdb=" C5 ADP A 400 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C4 ADP E 400 " pdb=" C5 ADP E 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C4 ADP F 400 " pdb=" C5 ADP F 400 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 ... (remaining 15640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 20834 1.50 - 3.00: 398 3.00 - 4.50: 104 4.50 - 6.00: 29 6.00 - 7.50: 9 Bond angle restraints: 21374 Sorted by residual: angle pdb=" N GLY A 16 " pdb=" CA GLY A 16 " pdb=" C GLY A 16 " ideal model delta sigma weight residual 113.18 120.68 -7.50 2.37e+00 1.78e-01 1.00e+01 angle pdb=" N GLY C 16 " pdb=" CA GLY C 16 " pdb=" C GLY C 16 " ideal model delta sigma weight residual 113.18 120.43 -7.25 2.37e+00 1.78e-01 9.36e+00 angle pdb=" N GLY D 16 " pdb=" CA GLY D 16 " pdb=" C GLY D 16 " ideal model delta sigma weight residual 113.18 120.02 -6.84 2.37e+00 1.78e-01 8.32e+00 angle pdb=" N GLY F 16 " pdb=" CA GLY F 16 " pdb=" C GLY F 16 " ideal model delta sigma weight residual 113.18 119.61 -6.43 2.37e+00 1.78e-01 7.37e+00 angle pdb=" N GLY B 16 " pdb=" CA GLY B 16 " pdb=" C GLY B 16 " ideal model delta sigma weight residual 113.18 119.59 -6.41 2.37e+00 1.78e-01 7.32e+00 ... (remaining 21369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 9086 34.01 - 68.03: 357 68.03 - 102.04: 19 102.04 - 136.05: 5 136.05 - 170.07: 2 Dihedral angle restraints: 9469 sinusoidal: 4295 harmonic: 5174 Sorted by residual: dihedral pdb=" O2A ADP A 400 " pdb=" O3A ADP A 400 " pdb=" PA ADP A 400 " pdb=" PB ADP A 400 " ideal model delta sinusoidal sigma weight residual 300.00 167.74 132.26 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" O1B ADP E 400 " pdb=" O3A ADP E 400 " pdb=" PB ADP E 400 " pdb=" PA ADP E 400 " ideal model delta sinusoidal sigma weight residual 300.00 178.00 122.00 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP F 400 " pdb=" O3A ADP F 400 " pdb=" PB ADP F 400 " pdb=" PA ADP F 400 " ideal model delta sinusoidal sigma weight residual -60.00 61.76 -121.77 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 9466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1625 0.030 - 0.060: 549 0.060 - 0.090: 152 0.090 - 0.121: 126 0.121 - 0.151: 5 Chirality restraints: 2457 Sorted by residual: chirality pdb=" CA ILE D 290 " pdb=" N ILE D 290 " pdb=" C ILE D 290 " pdb=" CB ILE D 290 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" P DT G 4 " pdb=" OP1 DT G 4 " pdb=" OP2 DT G 4 " pdb=" O5' DT G 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.47 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 2454 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 298 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO D 299 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 169 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO F 170 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 170 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 170 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 169 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 170 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.026 5.00e-02 4.00e+02 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 117 2.59 - 3.17: 11696 3.17 - 3.75: 23411 3.75 - 4.32: 32956 4.32 - 4.90: 55338 Nonbonded interactions: 123518 Sorted by model distance: nonbonded pdb=" OD1 ASP A 97 " pdb="MG MG A 401 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR F 52 " pdb=" O2B ADP F 400 " model vdw 2.177 3.040 nonbonded pdb=" O GLY D 293 " pdb=" OG1 THR D 305 " model vdw 2.191 3.040 nonbonded pdb=" ND1 HIS B 100 " pdb=" OG1 THR B 145 " model vdw 2.276 3.120 nonbonded pdb=" O LEU D 49 " pdb=" OH TYR D 168 " model vdw 2.280 3.040 ... (remaining 123513 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' and (resid 7 through 74 or resid 77 through 118 or (resid 119 and (na \ me N or name CA or name C or name O or name CB )) or resid 133 through 137 or (r \ esid 138 and (name N or name CA or name C or name O )) or resid 139 through 317) \ ) selection = (chain 'B' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'C' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 317)) selection = (chain 'D' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'E' and (resid 7 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB )) or resid 133 through 137 or (resid 138 and (name N or \ name CA or name C or name O )) or resid 139 through 317)) selection = (chain 'F' and (resid 7 through 119 or resid 133 through 137 or (resid 138 and ( \ name N or name CA or name C or name O )) or resid 139 through 317)) } 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 individual isotropic 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: 0.710 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: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.760 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.003 0.037 15645 Z= 0.182 Angle : 0.576 7.501 21374 Z= 0.280 Chirality : 0.039 0.151 2457 Planarity : 0.005 0.047 2607 Dihedral : 17.042 170.067 6149 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.20), residues: 1791 helix: 1.00 (0.17), residues: 955 sheet: 0.26 (0.37), residues: 216 loop : -0.01 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 40 PHE 0.010 0.001 PHE A 211 TYR 0.008 0.001 TYR C 111 ARG 0.003 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.682 Fit side-chains REVERT: C 216 ASP cc_start: 0.8420 (m-30) cc_final: 0.8145 (m-30) REVERT: B 65 ASN cc_start: 0.8098 (m110) cc_final: 0.7794 (m-40) REVERT: B 191 GLU cc_start: 0.7989 (mp0) cc_final: 0.7777 (mp0) REVERT: B 310 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7966 (mtm-85) REVERT: A 204 MET cc_start: 0.8848 (tpp) cc_final: 0.8181 (tpt) REVERT: F 243 LEU cc_start: 0.7966 (mt) cc_final: 0.7757 (mt) REVERT: E 198 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7257 (mtt-85) outliers start: 0 outliers final: 1 residues processed: 220 average time/residue: 1.9056 time to fit residues: 448.9498 Evaluate side-chains 183 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9980 chunk 138 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.165 Angle : 0.585 8.112 21374 Z= 0.283 Chirality : 0.038 0.137 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.984 170.457 2593 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.82 % Allowed : 8.36 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1791 helix: 1.38 (0.17), residues: 953 sheet: 0.25 (0.36), residues: 225 loop : 0.20 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.008 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.685 Fit side-chains REVERT: C 216 ASP cc_start: 0.8433 (m-30) cc_final: 0.8164 (m-30) REVERT: B 65 ASN cc_start: 0.8149 (m110) cc_final: 0.7856 (m-40) REVERT: A 312 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7850 (mp) REVERT: F 243 LEU cc_start: 0.7929 (mt) cc_final: 0.7714 (mt) REVERT: F 248 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7345 (mmm160) REVERT: E 119 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6370 (ttt) outliers start: 12 outliers final: 2 residues processed: 191 average time/residue: 1.9053 time to fit residues: 390.7223 Evaluate side-chains 167 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain E residue 119 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 166 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15645 Z= 0.237 Angle : 0.611 9.108 21374 Z= 0.290 Chirality : 0.040 0.153 2457 Planarity : 0.005 0.061 2607 Dihedral : 16.936 171.958 2591 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.29 % Allowed : 10.88 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.20), residues: 1791 helix: 1.38 (0.17), residues: 954 sheet: 0.17 (0.35), residues: 225 loop : 0.09 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.012 0.001 PHE B 117 TYR 0.013 0.001 TYR C 111 ARG 0.008 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.935 Fit side-chains REVERT: C 216 ASP cc_start: 0.8489 (m-30) cc_final: 0.8144 (m-30) REVERT: C 280 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8869 (t) REVERT: C 283 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: C 296 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8062 (ttmt) REVERT: B 65 ASN cc_start: 0.8199 (m110) cc_final: 0.7901 (m-40) REVERT: A 312 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7776 (mp) REVERT: F 243 LEU cc_start: 0.7867 (mt) cc_final: 0.7640 (mt) REVERT: F 248 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7340 (mmm160) REVERT: E 119 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6465 (ttt) outliers start: 19 outliers final: 5 residues processed: 180 average time/residue: 1.9184 time to fit residues: 371.0348 Evaluate side-chains 169 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.173 Angle : 0.571 10.741 21374 Z= 0.272 Chirality : 0.038 0.142 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.708 170.178 2591 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.36 % Allowed : 12.92 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.20), residues: 1791 helix: 1.52 (0.17), residues: 953 sheet: 0.14 (0.35), residues: 225 loop : 0.14 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.009 0.001 PHE A 44 TYR 0.010 0.001 TYR C 111 ARG 0.007 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.698 Fit side-chains REVERT: C 216 ASP cc_start: 0.8384 (m-30) cc_final: 0.8071 (m-30) REVERT: C 280 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8864 (t) REVERT: C 283 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 65 ASN cc_start: 0.8214 (m110) cc_final: 0.7917 (m-40) REVERT: A 283 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 312 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7692 (mp) REVERT: F 199 ARG cc_start: 0.8297 (mpt90) cc_final: 0.7857 (mmt-90) REVERT: F 248 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7346 (mmm160) outliers start: 20 outliers final: 8 residues processed: 180 average time/residue: 1.9444 time to fit residues: 375.2504 Evaluate side-chains 174 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 150 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.180 Angle : 0.571 10.700 21374 Z= 0.273 Chirality : 0.038 0.143 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.616 170.975 2591 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.56 % Allowed : 13.32 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.20), residues: 1791 helix: 1.56 (0.17), residues: 952 sheet: 0.12 (0.35), residues: 225 loop : 0.20 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.010 0.001 PHE A 44 TYR 0.010 0.001 TYR C 111 ARG 0.008 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.828 Fit side-chains REVERT: D 32 LYS cc_start: 0.7609 (mmpt) cc_final: 0.7155 (mttp) REVERT: C 216 ASP cc_start: 0.8357 (m-30) cc_final: 0.8155 (m-30) REVERT: C 280 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8851 (t) REVERT: C 283 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 65 ASN cc_start: 0.8216 (m110) cc_final: 0.7907 (m-40) REVERT: A 147 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: A 283 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: A 312 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7657 (mp) REVERT: F 199 ARG cc_start: 0.8275 (mpt90) cc_final: 0.7818 (mmt-90) REVERT: F 248 ARG cc_start: 0.7622 (mtt90) cc_final: 0.7342 (mmm160) outliers start: 23 outliers final: 9 residues processed: 185 average time/residue: 1.9179 time to fit residues: 380.9359 Evaluate side-chains 172 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 HIS F 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.211 Angle : 0.591 11.221 21374 Z= 0.281 Chirality : 0.039 0.148 2457 Planarity : 0.005 0.063 2607 Dihedral : 16.639 171.115 2591 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.84 % Allowed : 14.07 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.20), residues: 1791 helix: 1.53 (0.17), residues: 955 sheet: 0.11 (0.35), residues: 225 loop : 0.15 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 40 PHE 0.011 0.001 PHE B 117 TYR 0.012 0.001 TYR C 111 ARG 0.008 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.741 Fit side-chains REVERT: D 32 LYS cc_start: 0.7714 (mmpt) cc_final: 0.7196 (mttp) REVERT: C 283 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: C 296 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8059 (ttmt) REVERT: B 65 ASN cc_start: 0.8185 (m110) cc_final: 0.7880 (m-40) REVERT: A 9 LYS cc_start: 0.8246 (ptpp) cc_final: 0.8018 (ptpt) REVERT: A 147 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7793 (mtp85) REVERT: A 312 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7676 (mp) REVERT: F 199 ARG cc_start: 0.8258 (mpt90) cc_final: 0.7805 (mmt-90) REVERT: F 243 LEU cc_start: 0.8164 (mm) cc_final: 0.7900 (mt) REVERT: F 248 ARG cc_start: 0.7652 (mtt90) cc_final: 0.7373 (mmm160) outliers start: 27 outliers final: 10 residues processed: 182 average time/residue: 1.8372 time to fit residues: 359.5815 Evaluate side-chains 173 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 176 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.167 Angle : 0.571 11.879 21374 Z= 0.274 Chirality : 0.038 0.140 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.483 170.241 2591 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.43 % Allowed : 15.57 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.20), residues: 1791 helix: 1.65 (0.17), residues: 951 sheet: 0.04 (0.35), residues: 227 loop : 0.27 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.009 0.001 PHE A 44 TYR 0.009 0.001 TYR C 111 ARG 0.009 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.786 Fit side-chains REVERT: D 32 LYS cc_start: 0.7691 (mmpt) cc_final: 0.7203 (mttp) REVERT: D 230 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7854 (tpp-160) REVERT: C 283 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: B 65 ASN cc_start: 0.8145 (m110) cc_final: 0.7833 (m-40) REVERT: B 259 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7275 (ttt-90) REVERT: A 9 LYS cc_start: 0.8237 (ptpp) cc_final: 0.7997 (ptpt) REVERT: A 147 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7780 (mtp85) REVERT: F 199 ARG cc_start: 0.8242 (mpt90) cc_final: 0.7781 (mmt-90) REVERT: F 248 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7372 (mmm160) outliers start: 21 outliers final: 6 residues processed: 181 average time/residue: 1.8885 time to fit residues: 366.4699 Evaluate side-chains 173 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 0.0770 chunk 120 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15645 Z= 0.183 Angle : 0.579 12.246 21374 Z= 0.276 Chirality : 0.038 0.143 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.414 170.949 2591 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.09 % Allowed : 16.59 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.20), residues: 1791 helix: 1.62 (0.17), residues: 952 sheet: 0.04 (0.35), residues: 227 loop : 0.27 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 40 PHE 0.009 0.001 PHE A 44 TYR 0.010 0.001 TYR C 111 ARG 0.011 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.780 Fit side-chains REVERT: D 32 LYS cc_start: 0.7697 (mmpt) cc_final: 0.7211 (mttp) REVERT: D 230 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7876 (tpp-160) REVERT: C 283 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: B 65 ASN cc_start: 0.8172 (m110) cc_final: 0.7857 (m-40) REVERT: B 259 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7261 (ttt-90) REVERT: A 9 LYS cc_start: 0.8252 (ptpp) cc_final: 0.8015 (ptpt) REVERT: A 89 GLU cc_start: 0.7700 (tt0) cc_final: 0.7484 (tt0) REVERT: A 147 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7797 (mtp85) REVERT: A 312 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7629 (mp) REVERT: F 199 ARG cc_start: 0.8259 (mpt90) cc_final: 0.7831 (mmt-90) REVERT: F 243 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7921 (mm) REVERT: F 248 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7371 (mmm160) outliers start: 16 outliers final: 9 residues processed: 179 average time/residue: 1.8885 time to fit residues: 363.0880 Evaluate side-chains 179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15645 Z= 0.194 Angle : 0.588 12.491 21374 Z= 0.281 Chirality : 0.039 0.145 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.411 170.961 2591 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.16 % Allowed : 16.79 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.20), residues: 1791 helix: 1.62 (0.17), residues: 952 sheet: 0.05 (0.35), residues: 227 loop : 0.27 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 40 PHE 0.010 0.001 PHE B 117 TYR 0.011 0.001 TYR C 111 ARG 0.012 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.746 Fit side-chains REVERT: D 32 LYS cc_start: 0.7689 (mmpt) cc_final: 0.7221 (mttp) REVERT: C 283 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 296 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8055 (ttmt) REVERT: B 65 ASN cc_start: 0.8170 (m110) cc_final: 0.7902 (m-40) REVERT: A 9 LYS cc_start: 0.8252 (ptpp) cc_final: 0.8011 (ptpt) REVERT: A 89 GLU cc_start: 0.7695 (tt0) cc_final: 0.7479 (tt0) REVERT: A 147 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7808 (mtp85) REVERT: A 312 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7617 (mp) REVERT: F 199 ARG cc_start: 0.8253 (mpt90) cc_final: 0.7789 (mmt-90) REVERT: F 243 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7917 (mm) REVERT: F 248 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7399 (mmm160) REVERT: E 36 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6787 (pm20) outliers start: 17 outliers final: 7 residues processed: 181 average time/residue: 1.8860 time to fit residues: 366.6268 Evaluate side-chains 179 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15645 Z= 0.210 Angle : 0.599 12.682 21374 Z= 0.285 Chirality : 0.039 0.147 2457 Planarity : 0.005 0.062 2607 Dihedral : 16.434 171.127 2591 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.09 % Allowed : 17.00 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.20), residues: 1791 helix: 1.57 (0.17), residues: 955 sheet: 0.05 (0.35), residues: 227 loop : 0.24 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 40 PHE 0.010 0.001 PHE B 117 TYR 0.012 0.001 TYR C 111 ARG 0.012 0.000 ARG A 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.738 Fit side-chains REVERT: D 32 LYS cc_start: 0.7713 (mmpt) cc_final: 0.7238 (mttp) REVERT: D 230 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7963 (tpp-160) REVERT: C 283 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: C 296 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8063 (ttmt) REVERT: B 65 ASN cc_start: 0.8172 (m110) cc_final: 0.7908 (m-40) REVERT: B 92 ASP cc_start: 0.8258 (p0) cc_final: 0.7981 (m-30) REVERT: A 9 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7979 (ptpt) REVERT: A 147 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7953 (mtp85) REVERT: A 312 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7611 (mp) REVERT: F 178 MET cc_start: 0.7641 (mtp) cc_final: 0.7298 (mmm) REVERT: F 199 ARG cc_start: 0.8264 (mpt90) cc_final: 0.7802 (mmt-90) REVERT: F 204 MET cc_start: 0.8409 (tpt) cc_final: 0.8136 (mmt) REVERT: F 238 LEU cc_start: 0.8758 (mp) cc_final: 0.8483 (mt) REVERT: F 248 ARG cc_start: 0.7695 (mtt90) cc_final: 0.7400 (mmm160) outliers start: 16 outliers final: 10 residues processed: 179 average time/residue: 1.8906 time to fit residues: 363.6350 Evaluate side-chains 184 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain E residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 145 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.185414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.145949 restraints weight = 15486.244| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.48 r_work: 0.3297 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15645 Z= 0.206 Angle : 0.598 12.499 21374 Z= 0.286 Chirality : 0.039 0.146 2457 Planarity : 0.005 0.071 2607 Dihedral : 16.419 170.761 2591 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.02 % Allowed : 17.13 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.20), residues: 1791 helix: 1.54 (0.17), residues: 961 sheet: 0.05 (0.35), residues: 227 loop : 0.27 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 40 PHE 0.011 0.001 PHE B 117 TYR 0.012 0.001 TYR C 111 ARG 0.014 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.65 seconds wall clock time: 104 minutes 18.51 seconds (6258.51 seconds total)