Starting phenix.real_space_refine on Wed Jun 18 04:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.map" model { file = "/net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v47_42967/06_2025/8v47_42967.cif" } resolution = 4.08 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= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 13109 2.51 5 N 3449 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20580 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3320 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 4 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3218 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "C" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3301 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 10, 'TRANS': 399} Chain breaks: 4 Chain: "H" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2472 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 4 Chain: "G" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2422 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 6, 'TRANS': 298} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.80, per 1000 atoms: 0.67 Number of scatterers: 20580 At special positions: 0 Unit cell: (100.045, 163.625, 195.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 3932 8.00 N 3449 7.00 C 13109 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: 4.52 Conformation dependent library (CDL) restraints added in 2.5 seconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4876 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 21 sheets defined 55.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.677A pdb=" N ALA A 58 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.610A pdb=" N ALA A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 199 through 238 removed outlier: 3.973A pdb=" N PHE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 296 through 319 removed outlier: 3.624A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.587A pdb=" N VAL A 365 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 removed outlier: 3.793A pdb=" N ALA A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.687A pdb=" N GLU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 53 through 60 removed outlier: 3.609A pdb=" N ALA B 58 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 199 through 236 removed outlier: 3.594A pdb=" N VAL B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.550A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.617A pdb=" N SER B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 362 through 366 removed outlier: 3.539A pdb=" N VAL B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.558A pdb=" N ALA B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.128A pdb=" N ASP B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'D' and resid 7 through 18 Processing helix chain 'D' and resid 27 through 42 removed outlier: 3.599A pdb=" N PHE D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 59 through 64 removed outlier: 4.185A pdb=" N LYS D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 143 through 172 removed outlier: 4.572A pdb=" N SER D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N SER D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.739A pdb=" N ALA D 180 " --> pdb=" O GLY D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 236 through 257 removed outlier: 3.551A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 300 through 307 Processing helix chain 'C' and resid 38 through 52 Processing helix chain 'C' and resid 53 through 60 removed outlier: 3.502A pdb=" N ARG C 56 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 58 " --> pdb=" O ILE C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 125 through 138 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 199 through 234 removed outlier: 3.900A pdb=" N PHE C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.501A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 319 removed outlier: 3.628A pdb=" N ALA C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.527A pdb=" N VAL C 365 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.712A pdb=" N GLU C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU C 407 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.785A pdb=" N ALA C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'F' and resid 13 through 16 Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 53 through 60 removed outlier: 3.604A pdb=" N ALA F 58 " --> pdb=" O ILE F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.699A pdb=" N ASN F 138 " --> pdb=" O PHE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 162 Processing helix chain 'F' and resid 177 through 189 Processing helix chain 'F' and resid 199 through 235 removed outlier: 4.402A pdb=" N PHE F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 264 removed outlier: 3.944A pdb=" N LYS F 253 " --> pdb=" O GLY F 249 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 287 removed outlier: 3.727A pdb=" N VAL F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 319 Processing helix chain 'F' and resid 319 through 331 Processing helix chain 'F' and resid 362 through 366 removed outlier: 3.534A pdb=" N VAL F 365 " --> pdb=" O PRO F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 380 Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.628A pdb=" N GLU F 404 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 407 " --> pdb=" O GLN F 403 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'H' and resid 13 through 16 Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 55 through 60 removed outlier: 4.283A pdb=" N PHE H 59 " --> pdb=" O ILE H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 removed outlier: 3.760A pdb=" N GLU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 153 through 161 removed outlier: 4.656A pdb=" N ALA H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 189 Processing helix chain 'H' and resid 199 through 213 Processing helix chain 'H' and resid 320 through 331 Processing helix chain 'H' and resid 362 through 366 removed outlier: 3.716A pdb=" N LEU H 366 " --> pdb=" O ILE H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 380 Processing helix chain 'H' and resid 399 through 412 removed outlier: 4.494A pdb=" N LEU H 407 " --> pdb=" O GLN H 403 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS H 408 " --> pdb=" O GLU H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 430 removed outlier: 3.766A pdb=" N ALA H 429 " --> pdb=" O SER H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 434 No H-bonds generated for 'chain 'H' and resid 432 through 434' Processing helix chain 'G' and resid 7 through 18 Processing helix chain 'G' and resid 27 through 42 removed outlier: 3.637A pdb=" N PHE G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 59 through 64 removed outlier: 4.384A pdb=" N LYS G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 120 through 126 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 143 through 172 removed outlier: 4.561A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER G 157 " --> pdb=" O GLU G 153 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE G 159 " --> pdb=" O ILE G 155 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA G 160 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 161 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 182 removed outlier: 3.911A pdb=" N ALA G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 225 Proline residue: G 221 - end of helix Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 236 through 257 removed outlier: 3.566A pdb=" N ILE G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 273 Processing helix chain 'G' and resid 275 through 291 Processing helix chain 'G' and resid 300 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 101 removed outlier: 3.712A pdb=" N GLU A 64 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N TYR A 18 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148 removed outlier: 7.425A pdb=" N ALA A 387 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE A 420 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 389 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N CYS A 422 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 391 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A 437 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 30 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE A 439 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS A 32 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.904A pdb=" N GLU B 64 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 11 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS B 66 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE B 9 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 68 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR B 18 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 removed outlier: 8.599A pdb=" N ILE B 420 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 389 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N CYS B 422 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE B 391 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE B 437 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 30 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 removed outlier: 6.204A pdb=" N LEU D 23 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 101 removed outlier: 6.652A pdb=" N GLU C 64 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C 11 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS C 66 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE C 9 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 68 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 18 " --> pdb=" O LYS C 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.925A pdb=" N ALA C 387 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE C 420 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL C 389 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS C 422 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE C 391 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE C 437 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL C 30 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 337 through 341 Processing sheet with id=AB3, first strand: chain 'F' and resid 21 through 23 Processing sheet with id=AB4, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.876A pdb=" N VAL F 389 " --> pdb=" O ILE F 420 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS F 422 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 391 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE F 437 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL F 30 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 337 through 341 removed outlier: 3.758A pdb=" N GLY F 352 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.572A pdb=" N PHE H 100 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AB9, first strand: chain 'H' and resid 389 through 392 removed outlier: 6.383A pdb=" N ASN H 29 " --> pdb=" O VAL H 421 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE H 437 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL H 30 " --> pdb=" O ILE H 437 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 337 through 340 Processing sheet with id=AC2, first strand: chain 'G' and resid 48 through 51 removed outlier: 6.119A pdb=" N LEU G 23 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG G 22 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU G 86 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 24 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 94 through 96 1122 hydrogen bonds defined for protein. 3210 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: 6.97 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6488 1.34 - 1.46: 4096 1.46 - 1.58: 10233 1.58 - 1.69: 7 1.69 - 1.81: 137 Bond restraints: 20961 Sorted by residual: bond pdb=" O3A ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 1.592 1.527 0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 1.600 1.541 0.059 2.80e-02 1.28e+03 4.51e+00 bond pdb=" C VAL H 30 " pdb=" N ILE H 31 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.97e-02 2.58e+03 4.43e+00 bond pdb=" O3B ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 1.592 1.533 0.059 3.00e-02 1.11e+03 3.89e+00 bond pdb=" C LEU D 177 " pdb=" N PRO D 178 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.25e+00 ... (remaining 20956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 27633 2.21 - 4.41: 566 4.41 - 6.62: 50 6.62 - 8.82: 9 8.82 - 11.03: 1 Bond angle restraints: 28259 Sorted by residual: angle pdb=" C ASP A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 105.27 11.03 3.50e+00 8.16e-02 9.93e+00 angle pdb=" C PHE F 342 " pdb=" N ASP F 343 " pdb=" CA ASP F 343 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.81e+00 angle pdb=" C ASP C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 125.02 130.15 -5.13 1.76e+00 3.23e-01 8.49e+00 angle pdb=" C ASP F 83 " pdb=" N GLU F 84 " pdb=" CA GLU F 84 " ideal model delta sigma weight residual 125.02 130.08 -5.06 1.76e+00 3.23e-01 8.27e+00 ... (remaining 28254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11945 17.74 - 35.48: 621 35.48 - 53.22: 141 53.22 - 70.96: 41 70.96 - 88.70: 9 Dihedral angle restraints: 12757 sinusoidal: 5251 harmonic: 7506 Sorted by residual: dihedral pdb=" CA ASP H 23 " pdb=" C ASP H 23 " pdb=" N PHE H 24 " pdb=" CA PHE H 24 " ideal model delta harmonic sigma weight residual 180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS H 354 " pdb=" C LYS H 354 " pdb=" N PHE H 355 " pdb=" CA PHE H 355 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA SER H 427 " pdb=" C SER H 427 " pdb=" N ILE H 428 " pdb=" CA ILE H 428 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 12754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2072 0.045 - 0.089: 773 0.089 - 0.134: 249 0.134 - 0.178: 34 0.178 - 0.223: 7 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CB VAL D 255 " pdb=" CA VAL D 255 " pdb=" CG1 VAL D 255 " pdb=" CG2 VAL D 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE G 204 " pdb=" N ILE G 204 " pdb=" C ILE G 204 " pdb=" CB ILE G 204 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3132 not shown) Planarity restraints: 3581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 223 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.70e+00 pdb=" C SER B 223 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 223 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG B 224 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 312 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C GLN C 312 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN C 312 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 313 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C LEU D 196 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE D 197 " 0.014 2.00e-02 2.50e+03 ... (remaining 3578 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5558 2.80 - 3.32: 19129 3.32 - 3.85: 35012 3.85 - 4.37: 40018 4.37 - 4.90: 69232 Nonbonded interactions: 168949 Sorted by model distance: nonbonded pdb=" O LYS D 60 " pdb=" OG SER D 63 " model vdw 2.275 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR G 11 " pdb=" OD2 ASP G 50 " model vdw 2.288 3.040 nonbonded pdb=" O SER H 328 " pdb=" OG SER H 331 " model vdw 2.302 3.040 nonbonded pdb=" O PRO C 149 " pdb=" NH1 ARG C 152 " model vdw 2.316 3.120 ... (remaining 168944 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 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) selection = (chain 'B' and (resid 3 through 236 or resid 249 through 288 or resid 295 throug \ h 444)) selection = (chain 'C' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) selection = (chain 'F' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.170 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.006 0.065 20961 Z= 0.286 Angle : 0.787 11.028 28259 Z= 0.448 Chirality : 0.051 0.223 3135 Planarity : 0.006 0.053 3581 Dihedral : 12.058 88.705 7881 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.85 % Allowed : 4.81 % Favored : 92.35 % 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: -0.21 (0.16), residues: 2492 helix: 0.21 (0.13), residues: 1280 sheet: 0.26 (0.26), residues: 406 loop : -0.68 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 402 HIS 0.010 0.002 HIS D 107 PHE 0.031 0.003 PHE B 191 TYR 0.026 0.003 TYR A 69 ARG 0.009 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.15770 ( 1122) hydrogen bonds : angle 6.35523 ( 3210) covalent geometry : bond 0.00604 (20961) covalent geometry : angle 0.78670 (28259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 2.491 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 TARDY: cannot create tardy model for: "ARG B 311 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 39 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9055 (mtmm) REVERT: A 154 MET cc_start: 0.9209 (ttt) cc_final: 0.8974 (ttt) REVERT: A 213 ARG cc_start: 0.9189 (mtp-110) cc_final: 0.8979 (ttm110) REVERT: A 234 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (p90) REVERT: A 308 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 310 ASP cc_start: 0.9182 (m-30) cc_final: 0.8813 (m-30) REVERT: A 383 MET cc_start: 0.8641 (mtp) cc_final: 0.7975 (ttm) REVERT: A 436 MET cc_start: 0.8740 (mtp) cc_final: 0.8428 (mtp) REVERT: B 3 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7693 (pt) REVERT: B 53 ASP cc_start: 0.8778 (t0) cc_final: 0.7731 (p0) REVERT: B 98 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8442 (mm) REVERT: B 146 SER cc_start: 0.9377 (m) cc_final: 0.8983 (p) REVERT: B 308 LEU cc_start: 0.9650 (mt) cc_final: 0.9427 (mt) REVERT: B 392 ASP cc_start: 0.9130 (t0) cc_final: 0.8656 (t0) REVERT: D 62 MET cc_start: 0.8627 (ttp) cc_final: 0.8332 (ttt) REVERT: D 122 GLU cc_start: 0.9082 (mp0) cc_final: 0.8827 (mp0) REVERT: D 212 PHE cc_start: 0.9524 (t80) cc_final: 0.9129 (t80) REVERT: C 44 HIS cc_start: 0.9137 (m170) cc_final: 0.8885 (m90) REVERT: C 126 MET cc_start: 0.9200 (mtm) cc_final: 0.8776 (pmm) REVERT: C 187 LEU cc_start: 0.9106 (mt) cc_final: 0.8600 (mt) REVERT: C 393 GLN cc_start: 0.9146 (mt0) cc_final: 0.8728 (mp10) REVERT: F 201 MET cc_start: 0.9238 (mmm) cc_final: 0.9036 (mpp) REVERT: F 304 TYR cc_start: 0.8069 (t80) cc_final: 0.7799 (t80) REVERT: F 373 LEU cc_start: 0.8658 (mt) cc_final: 0.8375 (pp) REVERT: H 100 PHE cc_start: 0.8781 (p90) cc_final: 0.8336 (p90) REVERT: H 195 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9180 (mp) REVERT: H 326 MET cc_start: 0.9435 (mtt) cc_final: 0.9062 (ptt) REVERT: H 372 GLN cc_start: 0.8922 (mt0) cc_final: 0.8600 (mt0) REVERT: H 377 LEU cc_start: 0.9516 (mt) cc_final: 0.9288 (tp) REVERT: H 393 GLN cc_start: 0.9106 (mt0) cc_final: 0.8812 (mp10) REVERT: H 414 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8343 (mm) REVERT: G 11 TYR cc_start: 0.8163 (t80) cc_final: 0.7886 (t80) outliers start: 64 outliers final: 17 residues processed: 384 average time/residue: 0.3944 time to fit residues: 218.1021 Evaluate side-chains 192 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 215 GLN A 262 GLN A 312 GLN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS B 262 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 315 GLN C 324 ASN F 32 HIS F 262 GLN F 268 ASN F 424 HIS H 19 ASN H 324 ASN G 74 HIS G 190 ASN G 306 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.064172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.045468 restraints weight = 151435.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046266 restraints weight = 94701.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.046673 restraints weight = 60087.007| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 20961 Z= 0.340 Angle : 0.749 11.346 28259 Z= 0.404 Chirality : 0.045 0.241 3135 Planarity : 0.005 0.052 3581 Dihedral : 8.101 82.401 2914 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.53 % 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: 0.92 (0.17), residues: 2492 helix: 1.36 (0.14), residues: 1286 sheet: -0.04 (0.25), residues: 417 loop : -0.10 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 402 HIS 0.011 0.002 HIS H 32 PHE 0.046 0.002 PHE B 234 TYR 0.030 0.003 TYR C 304 ARG 0.009 0.001 ARG H 78 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 1122) hydrogen bonds : angle 5.08340 ( 3210) covalent geometry : bond 0.00699 (20961) covalent geometry : angle 0.74889 (28259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 182 time to evaluate : 2.458 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 106 MET cc_start: 0.9229 (mmm) cc_final: 0.8804 (mpp) REVERT: A 154 MET cc_start: 0.9018 (ttt) cc_final: 0.8794 (ttt) REVERT: A 201 MET cc_start: 0.8678 (ppp) cc_final: 0.8357 (ppp) REVERT: A 213 ARG cc_start: 0.9237 (mtp-110) cc_final: 0.9020 (tmm160) REVERT: A 310 ASP cc_start: 0.9316 (m-30) cc_final: 0.9039 (m-30) REVERT: B 53 ASP cc_start: 0.8720 (t0) cc_final: 0.8433 (t0) REVERT: B 201 MET cc_start: 0.8575 (mpp) cc_final: 0.8212 (mpp) REVERT: D 62 MET cc_start: 0.8428 (ttp) cc_final: 0.8121 (ttt) REVERT: D 122 GLU cc_start: 0.9311 (mp0) cc_final: 0.9095 (mp0) REVERT: D 212 PHE cc_start: 0.9472 (t80) cc_final: 0.9070 (t80) REVERT: C 44 HIS cc_start: 0.8903 (m170) cc_final: 0.8676 (m90) REVERT: C 126 MET cc_start: 0.9035 (mtm) cc_final: 0.8718 (pmm) REVERT: C 129 MET cc_start: 0.9603 (mtm) cc_final: 0.9381 (mtt) REVERT: C 187 LEU cc_start: 0.9121 (mt) cc_final: 0.8852 (mt) REVERT: F 201 MET cc_start: 0.9434 (mmm) cc_final: 0.9190 (mpp) REVERT: F 304 TYR cc_start: 0.9210 (t80) cc_final: 0.8648 (t80) REVERT: F 326 MET cc_start: 0.8526 (ptp) cc_final: 0.8290 (ptm) REVERT: F 383 MET cc_start: 0.7861 (mpp) cc_final: 0.7326 (mpp) REVERT: H 100 PHE cc_start: 0.9306 (p90) cc_final: 0.9041 (p90) REVERT: H 106 MET cc_start: 0.8644 (ppp) cc_final: 0.8374 (ppp) REVERT: H 326 MET cc_start: 0.9351 (mtt) cc_final: 0.9106 (mtp) REVERT: H 338 MET cc_start: 0.8467 (tmm) cc_final: 0.8035 (tpp) REVERT: H 340 TYR cc_start: 0.8710 (p90) cc_final: 0.8474 (p90) REVERT: H 372 GLN cc_start: 0.9106 (mt0) cc_final: 0.8649 (mt0) REVERT: H 393 GLN cc_start: 0.9025 (mt0) cc_final: 0.8707 (mp10) REVERT: G 73 ILE cc_start: 0.9832 (mm) cc_final: 0.9607 (tp) REVERT: G 191 ASP cc_start: 0.8740 (m-30) cc_final: 0.8519 (m-30) outliers start: 3 outliers final: 2 residues processed: 185 average time/residue: 0.3772 time to fit residues: 104.3257 Evaluate side-chains 121 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 89 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 228 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 393 GLN B 44 HIS D 36 GLN D 263 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN H 19 ASN G 306 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.065771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047096 restraints weight = 151024.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.048201 restraints weight = 90492.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.048600 restraints weight = 56961.604| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20961 Z= 0.126 Angle : 0.489 9.046 28259 Z= 0.269 Chirality : 0.042 0.164 3135 Planarity : 0.003 0.050 3581 Dihedral : 7.105 71.265 2914 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.04 % Allowed : 1.56 % Favored : 98.40 % 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: 1.49 (0.17), residues: 2492 helix: 1.89 (0.14), residues: 1273 sheet: 0.11 (0.26), residues: 405 loop : 0.12 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 158 HIS 0.013 0.001 HIS D 33 PHE 0.017 0.001 PHE A 234 TYR 0.015 0.001 TYR C 278 ARG 0.006 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1122) hydrogen bonds : angle 4.36270 ( 3210) covalent geometry : bond 0.00259 (20961) covalent geometry : angle 0.48867 (28259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 2.455 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 154 MET cc_start: 0.8791 (ttt) cc_final: 0.8163 (ttt) REVERT: A 201 MET cc_start: 0.8631 (ppp) cc_final: 0.8200 (ppp) REVERT: A 213 ARG cc_start: 0.9206 (mtp-110) cc_final: 0.8962 (tmm160) REVERT: A 226 PHE cc_start: 0.9214 (t80) cc_final: 0.8951 (t80) REVERT: A 310 ASP cc_start: 0.9324 (m-30) cc_final: 0.9056 (m-30) REVERT: B 154 MET cc_start: 0.9024 (ttt) cc_final: 0.6966 (ttt) REVERT: B 326 MET cc_start: 0.8470 (ttm) cc_final: 0.8079 (ttm) REVERT: D 62 MET cc_start: 0.8379 (ttp) cc_final: 0.7718 (tpt) REVERT: D 122 GLU cc_start: 0.9234 (mp0) cc_final: 0.9017 (mp0) REVERT: D 212 PHE cc_start: 0.9443 (t80) cc_final: 0.8960 (t80) REVERT: C 126 MET cc_start: 0.9062 (mtm) cc_final: 0.8766 (pmm) REVERT: C 129 MET cc_start: 0.9627 (mtm) cc_final: 0.9414 (mtt) REVERT: C 187 LEU cc_start: 0.8893 (mt) cc_final: 0.8638 (mt) REVERT: C 410 MET cc_start: 0.9011 (mtp) cc_final: 0.8736 (mtp) REVERT: F 201 MET cc_start: 0.9494 (mmm) cc_final: 0.9259 (mpp) REVERT: F 304 TYR cc_start: 0.9193 (t80) cc_final: 0.8526 (t80) REVERT: F 326 MET cc_start: 0.8573 (ptp) cc_final: 0.8330 (ptm) REVERT: F 383 MET cc_start: 0.7963 (mpp) cc_final: 0.7596 (mpp) REVERT: H 100 PHE cc_start: 0.9165 (p90) cc_final: 0.8873 (p90) REVERT: H 106 MET cc_start: 0.8669 (ppp) cc_final: 0.8367 (ppp) REVERT: H 340 TYR cc_start: 0.8638 (p90) cc_final: 0.8430 (p90) REVERT: H 372 GLN cc_start: 0.9075 (mt0) cc_final: 0.8575 (mt0) REVERT: H 393 GLN cc_start: 0.8940 (mt0) cc_final: 0.8652 (mp10) REVERT: G 23 LEU cc_start: 0.9369 (tp) cc_final: 0.9124 (tp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.3573 time to fit residues: 98.2872 Evaluate side-chains 124 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 232 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 0.0370 chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 HIS D 36 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN H 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.065205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046089 restraints weight = 149792.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047167 restraints weight = 94163.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047393 restraints weight = 59602.926| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20961 Z= 0.171 Angle : 0.513 8.053 28259 Z= 0.284 Chirality : 0.042 0.154 3135 Planarity : 0.003 0.051 3581 Dihedral : 6.891 69.393 2914 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.09 % Allowed : 2.54 % Favored : 97.37 % 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: 1.55 (0.17), residues: 2492 helix: 1.93 (0.14), residues: 1282 sheet: 0.01 (0.25), residues: 415 loop : 0.25 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 158 HIS 0.011 0.001 HIS D 33 PHE 0.048 0.001 PHE B 234 TYR 0.016 0.002 TYR B 304 ARG 0.006 0.000 ARG G 236 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 1122) hydrogen bonds : angle 4.37772 ( 3210) covalent geometry : bond 0.00359 (20961) covalent geometry : angle 0.51304 (28259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9219 (mmm) cc_final: 0.8677 (mpp) REVERT: A 154 MET cc_start: 0.8892 (ttt) cc_final: 0.8131 (ttt) REVERT: A 201 MET cc_start: 0.8635 (ppp) cc_final: 0.8289 (ppp) REVERT: A 213 ARG cc_start: 0.9273 (mtp-110) cc_final: 0.9006 (tmm160) REVERT: A 304 TYR cc_start: 0.9158 (t80) cc_final: 0.8957 (t80) REVERT: A 310 ASP cc_start: 0.9350 (m-30) cc_final: 0.9143 (m-30) REVERT: B 154 MET cc_start: 0.9005 (ttt) cc_final: 0.6921 (ttt) REVERT: D 62 MET cc_start: 0.8326 (ttp) cc_final: 0.8033 (ttt) REVERT: D 122 GLU cc_start: 0.9227 (mp0) cc_final: 0.9018 (mp0) REVERT: C 44 HIS cc_start: 0.9078 (m90) cc_final: 0.8684 (m90) REVERT: C 126 MET cc_start: 0.9052 (mtm) cc_final: 0.8767 (pmm) REVERT: C 129 MET cc_start: 0.9622 (mtm) cc_final: 0.9410 (mtt) REVERT: C 187 LEU cc_start: 0.8879 (mt) cc_final: 0.8405 (mt) REVERT: C 436 MET cc_start: 0.9018 (mpp) cc_final: 0.8748 (mpp) REVERT: F 201 MET cc_start: 0.9478 (mmm) cc_final: 0.9206 (mpp) REVERT: F 304 TYR cc_start: 0.9165 (t80) cc_final: 0.8513 (t80) REVERT: F 383 MET cc_start: 0.7913 (mpp) cc_final: 0.7566 (mpp) REVERT: H 100 PHE cc_start: 0.9142 (p90) cc_final: 0.8785 (p90) REVERT: H 106 MET cc_start: 0.8639 (ppp) cc_final: 0.8330 (ppp) REVERT: H 130 ASP cc_start: 0.9316 (t0) cc_final: 0.8931 (m-30) REVERT: H 372 GLN cc_start: 0.8977 (mt0) cc_final: 0.8554 (mt0) REVERT: H 393 GLN cc_start: 0.9057 (mt0) cc_final: 0.8728 (mp10) REVERT: G 23 LEU cc_start: 0.9342 (tp) cc_final: 0.9125 (tp) REVERT: G 31 ARG cc_start: 0.9406 (mtm110) cc_final: 0.9146 (ttp-110) REVERT: G 33 HIS cc_start: 0.9561 (m-70) cc_final: 0.9220 (m-70) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.3446 time to fit residues: 85.0174 Evaluate side-chains 116 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 63 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 217 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 44 HIS D 306 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN F 315 GLN H 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.063491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044763 restraints weight = 154620.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.045308 restraints weight = 96165.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.045804 restraints weight = 62495.164| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20961 Z= 0.294 Angle : 0.663 9.959 28259 Z= 0.361 Chirality : 0.044 0.168 3135 Planarity : 0.005 0.052 3581 Dihedral : 7.335 74.515 2914 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % 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: 0.99 (0.17), residues: 2492 helix: 1.48 (0.14), residues: 1276 sheet: -0.36 (0.24), residues: 424 loop : 0.05 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 402 HIS 0.006 0.002 HIS D 74 PHE 0.038 0.002 PHE B 234 TYR 0.021 0.002 TYR D 35 ARG 0.007 0.001 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 1122) hydrogen bonds : angle 4.94478 ( 3210) covalent geometry : bond 0.00612 (20961) covalent geometry : angle 0.66254 (28259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 2.487 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 106 MET cc_start: 0.9231 (mmm) cc_final: 0.8707 (mpp) REVERT: A 154 MET cc_start: 0.8948 (ttt) cc_final: 0.8173 (ttm) REVERT: A 201 MET cc_start: 0.8758 (ppp) cc_final: 0.8396 (ppp) REVERT: A 436 MET cc_start: 0.7933 (mtt) cc_final: 0.7731 (mtt) REVERT: B 129 MET cc_start: 0.8773 (mpp) cc_final: 0.8348 (mpp) REVERT: B 154 MET cc_start: 0.9022 (ttt) cc_final: 0.7701 (ttt) REVERT: D 62 MET cc_start: 0.8498 (ttp) cc_final: 0.8160 (ttt) REVERT: D 122 GLU cc_start: 0.9229 (mp0) cc_final: 0.8984 (mp0) REVERT: C 44 HIS cc_start: 0.9039 (m90) cc_final: 0.8592 (m90) REVERT: C 126 MET cc_start: 0.9102 (mtm) cc_final: 0.8784 (pmm) REVERT: C 187 LEU cc_start: 0.9081 (mt) cc_final: 0.8775 (mt) REVERT: F 304 TYR cc_start: 0.9282 (t80) cc_final: 0.8539 (t80) REVERT: F 383 MET cc_start: 0.7835 (mpp) cc_final: 0.7306 (mpp) REVERT: F 436 MET cc_start: 0.6995 (tpt) cc_final: 0.6780 (tpt) REVERT: H 100 PHE cc_start: 0.9325 (p90) cc_final: 0.8999 (p90) REVERT: H 186 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8350 (tm-30) REVERT: H 326 MET cc_start: 0.9441 (mtt) cc_final: 0.8909 (ptp) REVERT: H 372 GLN cc_start: 0.9064 (mt0) cc_final: 0.8704 (mt0) REVERT: H 393 GLN cc_start: 0.9103 (mt0) cc_final: 0.8762 (mp10) REVERT: G 23 LEU cc_start: 0.9339 (tp) cc_final: 0.9126 (tp) REVERT: G 33 HIS cc_start: 0.9516 (m-70) cc_final: 0.9291 (m90) REVERT: G 53 GLN cc_start: 0.8949 (tt0) cc_final: 0.8743 (pt0) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3381 time to fit residues: 78.2570 Evaluate side-chains 110 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS C 35 ASN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN G 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.046020 restraints weight = 151846.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047224 restraints weight = 82731.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.047959 restraints weight = 56077.439| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20961 Z= 0.111 Angle : 0.479 9.585 28259 Z= 0.263 Chirality : 0.042 0.205 3135 Planarity : 0.003 0.043 3581 Dihedral : 6.592 71.799 2914 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.13 % Allowed : 1.11 % Favored : 98.75 % 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: 1.50 (0.17), residues: 2492 helix: 1.91 (0.14), residues: 1283 sheet: -0.20 (0.25), residues: 413 loop : 0.31 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 158 HIS 0.004 0.001 HIS G 119 PHE 0.026 0.001 PHE B 234 TYR 0.014 0.001 TYR C 278 ARG 0.011 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 1122) hydrogen bonds : angle 4.31193 ( 3210) covalent geometry : bond 0.00235 (20961) covalent geometry : angle 0.47859 (28259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 2.279 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 106 MET cc_start: 0.9119 (mmm) cc_final: 0.8644 (mpp) REVERT: A 154 MET cc_start: 0.8894 (ttt) cc_final: 0.8663 (ttt) REVERT: A 201 MET cc_start: 0.8694 (ppp) cc_final: 0.8319 (ppp) REVERT: A 373 LEU cc_start: 0.9680 (mt) cc_final: 0.9465 (tp) REVERT: B 129 MET cc_start: 0.8678 (mpp) cc_final: 0.8263 (mpp) REVERT: D 62 MET cc_start: 0.8338 (ttp) cc_final: 0.8030 (ttt) REVERT: C 44 HIS cc_start: 0.8985 (m90) cc_final: 0.8584 (m90) REVERT: C 126 MET cc_start: 0.8917 (mtm) cc_final: 0.8675 (pmm) REVERT: C 129 MET cc_start: 0.9545 (mtm) cc_final: 0.9343 (mtt) REVERT: C 187 LEU cc_start: 0.8875 (mt) cc_final: 0.8456 (mt) REVERT: F 201 MET cc_start: 0.9377 (mmp) cc_final: 0.9122 (mmm) REVERT: F 304 TYR cc_start: 0.9131 (t80) cc_final: 0.8280 (t80) REVERT: F 383 MET cc_start: 0.7919 (mpp) cc_final: 0.7597 (mpp) REVERT: F 436 MET cc_start: 0.6915 (tpt) cc_final: 0.6686 (mmm) REVERT: H 100 PHE cc_start: 0.8953 (p90) cc_final: 0.8747 (p90) REVERT: H 106 MET cc_start: 0.8248 (ppp) cc_final: 0.7998 (ppp) REVERT: H 209 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8985 (pm20) REVERT: H 326 MET cc_start: 0.9295 (mtt) cc_final: 0.8857 (ptp) REVERT: H 372 GLN cc_start: 0.8957 (mt0) cc_final: 0.8645 (mt0) REVERT: H 393 GLN cc_start: 0.8955 (mt0) cc_final: 0.8630 (mp10) REVERT: G 23 LEU cc_start: 0.9298 (tp) cc_final: 0.9081 (tp) REVERT: G 31 ARG cc_start: 0.9370 (mtm110) cc_final: 0.9164 (ttm110) REVERT: G 33 HIS cc_start: 0.9471 (m-70) cc_final: 0.9234 (m-70) REVERT: G 53 GLN cc_start: 0.9001 (tt0) cc_final: 0.8782 (pt0) outliers start: 3 outliers final: 0 residues processed: 159 average time/residue: 0.3341 time to fit residues: 82.1944 Evaluate side-chains 119 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 158 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN G 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.063928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045115 restraints weight = 152376.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.045945 restraints weight = 95630.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046129 restraints weight = 61335.470| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20961 Z= 0.256 Angle : 0.604 9.308 28259 Z= 0.330 Chirality : 0.043 0.201 3135 Planarity : 0.004 0.045 3581 Dihedral : 7.021 76.089 2914 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.04 % Allowed : 1.51 % Favored : 98.44 % 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 (0.17), residues: 2492 helix: 1.64 (0.14), residues: 1285 sheet: -0.47 (0.24), residues: 427 loop : 0.07 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 402 HIS 0.006 0.002 HIS D 238 PHE 0.066 0.002 PHE B 234 TYR 0.020 0.002 TYR B 304 ARG 0.009 0.001 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 1122) hydrogen bonds : angle 4.71621 ( 3210) covalent geometry : bond 0.00537 (20961) covalent geometry : angle 0.60436 (28259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 2.287 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 106 MET cc_start: 0.9208 (mmm) cc_final: 0.8726 (mpp) REVERT: A 154 MET cc_start: 0.8922 (ttt) cc_final: 0.8058 (ttt) REVERT: A 201 MET cc_start: 0.8741 (ppp) cc_final: 0.8377 (ppp) REVERT: A 304 TYR cc_start: 0.9161 (t80) cc_final: 0.8930 (t80) REVERT: A 326 MET cc_start: 0.8581 (mmm) cc_final: 0.8194 (mmm) REVERT: A 436 MET cc_start: 0.7945 (mtt) cc_final: 0.7702 (mtt) REVERT: B 154 MET cc_start: 0.9024 (ttt) cc_final: 0.7299 (ttt) REVERT: B 232 LYS cc_start: 0.9488 (mttp) cc_final: 0.9069 (mttm) REVERT: D 62 MET cc_start: 0.8502 (ttp) cc_final: 0.8160 (ttt) REVERT: C 44 HIS cc_start: 0.8974 (m90) cc_final: 0.8620 (m90) REVERT: C 126 MET cc_start: 0.9067 (mtm) cc_final: 0.8756 (pmm) REVERT: C 187 LEU cc_start: 0.9079 (mt) cc_final: 0.8643 (mt) REVERT: C 436 MET cc_start: 0.9115 (mpp) cc_final: 0.8915 (mpp) REVERT: F 201 MET cc_start: 0.9381 (mmp) cc_final: 0.9139 (mmm) REVERT: F 304 TYR cc_start: 0.9248 (t80) cc_final: 0.8444 (t80) REVERT: F 383 MET cc_start: 0.7903 (mpp) cc_final: 0.7418 (mpp) REVERT: H 106 MET cc_start: 0.8289 (ppp) cc_final: 0.8065 (ppp) REVERT: H 326 MET cc_start: 0.9391 (mtt) cc_final: 0.8955 (ptp) REVERT: H 372 GLN cc_start: 0.9057 (mt0) cc_final: 0.8698 (mt0) REVERT: H 393 GLN cc_start: 0.9096 (mt0) cc_final: 0.8769 (mp10) REVERT: G 33 HIS cc_start: 0.9533 (m-70) cc_final: 0.9297 (m90) REVERT: G 53 GLN cc_start: 0.9007 (tt0) cc_final: 0.8760 (pt0) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.3386 time to fit residues: 77.6724 Evaluate side-chains 113 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN G 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.065573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046096 restraints weight = 150781.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047249 restraints weight = 81822.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048003 restraints weight = 55613.789| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20961 Z= 0.111 Angle : 0.478 9.398 28259 Z= 0.261 Chirality : 0.042 0.236 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.536 78.990 2914 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.04 % Allowed : 0.58 % Favored : 99.38 % 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: 1.47 (0.17), residues: 2492 helix: 1.90 (0.14), residues: 1298 sheet: -0.31 (0.25), residues: 420 loop : 0.29 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 158 HIS 0.004 0.001 HIS G 33 PHE 0.045 0.001 PHE B 234 TYR 0.016 0.001 TYR C 304 ARG 0.007 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 1122) hydrogen bonds : angle 4.27293 ( 3210) covalent geometry : bond 0.00240 (20961) covalent geometry : angle 0.47769 (28259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 2.195 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 106 MET cc_start: 0.9146 (mmm) cc_final: 0.8713 (mpp) REVERT: A 154 MET cc_start: 0.8886 (ttt) cc_final: 0.7994 (ttt) REVERT: A 201 MET cc_start: 0.8733 (ppp) cc_final: 0.8349 (ppp) REVERT: A 326 MET cc_start: 0.8668 (mmm) cc_final: 0.8307 (mmm) REVERT: A 338 MET cc_start: 0.9024 (ttm) cc_final: 0.8631 (ttp) REVERT: A 436 MET cc_start: 0.7956 (mtt) cc_final: 0.7634 (mtt) REVERT: B 106 MET cc_start: 0.9185 (ptt) cc_final: 0.8976 (ptm) REVERT: B 129 MET cc_start: 0.8661 (mpp) cc_final: 0.8340 (mpp) REVERT: B 154 MET cc_start: 0.8992 (ttt) cc_final: 0.7004 (ttt) REVERT: D 62 MET cc_start: 0.8371 (ttp) cc_final: 0.8070 (ttt) REVERT: C 44 HIS cc_start: 0.8903 (m90) cc_final: 0.8538 (m90) REVERT: C 126 MET cc_start: 0.8933 (mtm) cc_final: 0.8692 (pmm) REVERT: C 129 MET cc_start: 0.9543 (mtm) cc_final: 0.9332 (mtt) REVERT: C 187 LEU cc_start: 0.9070 (mt) cc_final: 0.8663 (mt) REVERT: C 383 MET cc_start: 0.8456 (mpp) cc_final: 0.8229 (mpp) REVERT: F 201 MET cc_start: 0.9451 (mmp) cc_final: 0.9196 (mmm) REVERT: F 209 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8832 (tm-30) REVERT: F 304 TYR cc_start: 0.9135 (t80) cc_final: 0.8237 (t80) REVERT: F 383 MET cc_start: 0.7932 (mpp) cc_final: 0.7613 (mpp) REVERT: H 100 PHE cc_start: 0.8916 (p90) cc_final: 0.8477 (p90) REVERT: H 106 MET cc_start: 0.8219 (ppp) cc_final: 0.7990 (ppp) REVERT: H 130 ASP cc_start: 0.9178 (t0) cc_final: 0.8895 (m-30) REVERT: H 326 MET cc_start: 0.9247 (mtt) cc_final: 0.8845 (ptp) REVERT: H 372 GLN cc_start: 0.8873 (mt0) cc_final: 0.8524 (mt0) REVERT: H 393 GLN cc_start: 0.8921 (mt0) cc_final: 0.8631 (mp10) REVERT: G 23 LEU cc_start: 0.9315 (tp) cc_final: 0.9032 (tp) REVERT: G 33 HIS cc_start: 0.9463 (m-70) cc_final: 0.9212 (m-70) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.3234 time to fit residues: 77.7432 Evaluate side-chains 117 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 144 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN G 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.045923 restraints weight = 151390.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.046706 restraints weight = 93154.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047083 restraints weight = 55859.511| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20961 Z= 0.191 Angle : 0.550 8.713 28259 Z= 0.300 Chirality : 0.043 0.229 3135 Planarity : 0.004 0.042 3581 Dihedral : 6.772 82.268 2914 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.64 % 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: 1.33 (0.17), residues: 2492 helix: 1.80 (0.14), residues: 1306 sheet: -0.34 (0.25), residues: 429 loop : 0.18 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 158 HIS 0.004 0.001 HIS D 29 PHE 0.048 0.001 PHE B 234 TYR 0.027 0.002 TYR D 35 ARG 0.007 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1122) hydrogen bonds : angle 4.48656 ( 3210) covalent geometry : bond 0.00407 (20961) covalent geometry : angle 0.54978 (28259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 2.391 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 106 MET cc_start: 0.9184 (mmm) cc_final: 0.8705 (mpp) REVERT: A 154 MET cc_start: 0.8945 (ttt) cc_final: 0.8053 (ttt) REVERT: A 201 MET cc_start: 0.8670 (ppp) cc_final: 0.8319 (ppp) REVERT: A 304 TYR cc_start: 0.9123 (t80) cc_final: 0.8896 (t80) REVERT: A 326 MET cc_start: 0.8646 (mmm) cc_final: 0.8351 (mmm) REVERT: A 338 MET cc_start: 0.8992 (ttm) cc_final: 0.8759 (ttp) REVERT: A 436 MET cc_start: 0.7992 (mtt) cc_final: 0.7744 (mtt) REVERT: B 129 MET cc_start: 0.8796 (mpp) cc_final: 0.8414 (mpp) REVERT: B 154 MET cc_start: 0.8934 (ttt) cc_final: 0.7056 (ttt) REVERT: D 62 MET cc_start: 0.8397 (ttp) cc_final: 0.8089 (ttt) REVERT: C 44 HIS cc_start: 0.8978 (m90) cc_final: 0.8593 (m90) REVERT: C 126 MET cc_start: 0.9063 (mtm) cc_final: 0.8770 (pmm) REVERT: C 187 LEU cc_start: 0.9070 (mt) cc_final: 0.8703 (mt) REVERT: C 338 MET cc_start: 0.8801 (ttp) cc_final: 0.8483 (tmm) REVERT: C 383 MET cc_start: 0.8563 (mpp) cc_final: 0.8318 (mpp) REVERT: F 201 MET cc_start: 0.9483 (mmp) cc_final: 0.9226 (mmm) REVERT: F 209 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8807 (tm-30) REVERT: F 304 TYR cc_start: 0.9254 (t80) cc_final: 0.8375 (t80) REVERT: F 383 MET cc_start: 0.7965 (mpp) cc_final: 0.7452 (mpp) REVERT: H 106 MET cc_start: 0.8273 (ppp) cc_final: 0.8052 (ppp) REVERT: H 130 ASP cc_start: 0.9346 (t0) cc_final: 0.8997 (m-30) REVERT: H 326 MET cc_start: 0.9293 (mtt) cc_final: 0.8741 (ptp) REVERT: H 372 GLN cc_start: 0.9070 (mt0) cc_final: 0.8707 (mt0) REVERT: H 393 GLN cc_start: 0.9052 (mt0) cc_final: 0.8724 (mp10) REVERT: G 23 LEU cc_start: 0.9273 (tp) cc_final: 0.8929 (tp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3302 time to fit residues: 74.8887 Evaluate side-chains 113 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.064757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046306 restraints weight = 151386.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047286 restraints weight = 94334.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047438 restraints weight = 57496.608| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20961 Z= 0.163 Angle : 0.529 9.450 28259 Z= 0.290 Chirality : 0.042 0.206 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.669 83.423 2914 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.64 % 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: 1.36 (0.17), residues: 2492 helix: 1.82 (0.14), residues: 1303 sheet: -0.40 (0.25), residues: 414 loop : 0.24 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 287 HIS 0.004 0.001 HIS G 119 PHE 0.043 0.001 PHE B 234 TYR 0.021 0.001 TYR C 304 ARG 0.006 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1122) hydrogen bonds : angle 4.46180 ( 3210) covalent geometry : bond 0.00351 (20961) covalent geometry : angle 0.52880 (28259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 2.470 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 106 MET cc_start: 0.9206 (mmm) cc_final: 0.8710 (mpp) REVERT: A 154 MET cc_start: 0.8958 (ttt) cc_final: 0.8082 (ttm) REVERT: A 201 MET cc_start: 0.8709 (ppp) cc_final: 0.8356 (ppp) REVERT: A 304 TYR cc_start: 0.9129 (t80) cc_final: 0.8915 (t80) REVERT: A 326 MET cc_start: 0.8617 (mmm) cc_final: 0.8329 (mmm) REVERT: A 338 MET cc_start: 0.9016 (ttm) cc_final: 0.8782 (ttp) REVERT: A 436 MET cc_start: 0.7948 (mtt) cc_final: 0.7568 (mtt) REVERT: B 106 MET cc_start: 0.9210 (ptt) cc_final: 0.9004 (ptm) REVERT: B 129 MET cc_start: 0.8840 (mpp) cc_final: 0.8481 (mpp) REVERT: B 154 MET cc_start: 0.8959 (ttt) cc_final: 0.7204 (ttt) REVERT: B 232 LYS cc_start: 0.9481 (mttp) cc_final: 0.9178 (mttm) REVERT: D 62 MET cc_start: 0.8414 (ttp) cc_final: 0.8106 (ttt) REVERT: D 212 PHE cc_start: 0.9342 (t80) cc_final: 0.9047 (t80) REVERT: C 44 HIS cc_start: 0.9031 (m90) cc_final: 0.8596 (m90) REVERT: C 126 MET cc_start: 0.9067 (mtm) cc_final: 0.8777 (pmm) REVERT: C 129 MET cc_start: 0.9661 (mtm) cc_final: 0.9455 (mtt) REVERT: C 187 LEU cc_start: 0.9022 (mt) cc_final: 0.8634 (mt) REVERT: C 338 MET cc_start: 0.8823 (ttp) cc_final: 0.8450 (tmm) REVERT: C 383 MET cc_start: 0.8566 (mpp) cc_final: 0.8312 (mpp) REVERT: F 201 MET cc_start: 0.9473 (mmp) cc_final: 0.9221 (mmm) REVERT: F 209 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8793 (tm-30) REVERT: F 304 TYR cc_start: 0.9229 (t80) cc_final: 0.8329 (t80) REVERT: F 383 MET cc_start: 0.7964 (mpp) cc_final: 0.7440 (mpp) REVERT: F 436 MET cc_start: 0.7561 (mmm) cc_final: 0.7312 (mmm) REVERT: H 106 MET cc_start: 0.8279 (ppp) cc_final: 0.8054 (ppp) REVERT: H 130 ASP cc_start: 0.9378 (t0) cc_final: 0.9075 (m-30) REVERT: H 326 MET cc_start: 0.9306 (mtt) cc_final: 0.8901 (ptp) REVERT: H 372 GLN cc_start: 0.9076 (mt0) cc_final: 0.8710 (mt0) REVERT: H 393 GLN cc_start: 0.8997 (mt0) cc_final: 0.8692 (mp10) REVERT: G 23 LEU cc_start: 0.9264 (tp) cc_final: 0.8924 (tp) REVERT: G 31 ARG cc_start: 0.9477 (mtm110) cc_final: 0.9259 (mtm110) REVERT: G 53 GLN cc_start: 0.9062 (tt0) cc_final: 0.8836 (pt0) REVERT: G 245 GLN cc_start: 0.8875 (tt0) cc_final: 0.8523 (tp40) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3618 time to fit residues: 80.6518 Evaluate side-chains 116 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 74 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 150 optimal weight: 0.0770 chunk 214 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 413 GLN H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.064246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.045659 restraints weight = 153747.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.046712 restraints weight = 94388.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046865 restraints weight = 58262.129| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20961 Z= 0.191 Angle : 0.552 9.345 28259 Z= 0.301 Chirality : 0.043 0.227 3135 Planarity : 0.004 0.042 3581 Dihedral : 6.816 85.182 2914 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.04 % Allowed : 0.13 % Favored : 99.82 % 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: 1.24 (0.17), residues: 2492 helix: 1.70 (0.14), residues: 1316 sheet: -0.41 (0.25), residues: 427 loop : 0.17 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 287 HIS 0.004 0.001 HIS B 32 PHE 0.043 0.001 PHE B 234 TYR 0.019 0.002 TYR B 304 ARG 0.006 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1122) hydrogen bonds : angle 4.55780 ( 3210) covalent geometry : bond 0.00407 (20961) covalent geometry : angle 0.55221 (28259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7052.33 seconds wall clock time: 123 minutes 53.08 seconds (7433.08 seconds total)