Starting phenix.real_space_refine on Thu Jan 23 20:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v47_42967/01_2025/8v47_42967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v47_42967/01_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_42967/01_2025/8v47_42967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v47_42967/01_2025/8v47_42967.map" model { file = "/net/cci-nas-00/data/ceres_data/8v47_42967/01_2025/8v47_42967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v47_42967/01_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 12.66, per 1000 atoms: 0.62 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: 5.12 Conformation dependent library (CDL) restraints added in 2.4 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: 2.43 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: 7.70 Time building geometry restraints manager: 5.81 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: 5.510 Set stop_for_unknowns flag: 0.010 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: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 46.950 Find NCS groups from input model: 0.880 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.540 ------------------------------------------------------------------------------- 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= 0.385 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 *********************** 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 : 2.433 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: 0.4143 time to fit residues: 228.7030 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 : 2.681 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.045458 restraints weight = 151433.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.046237 restraints weight = 94488.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046742 restraints weight = 59943.677| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3236 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= 0.450 Angle : 0.749 11.346 28259 Z= 0.404 Chirality : 0.045 0.242 3135 Planarity : 0.005 0.052 3581 Dihedral : 8.100 82.392 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 0.003 PHE B 234 TYR 0.031 0.003 TYR C 304 ARG 0.009 0.001 ARG H 78 *********************** 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 : 2.440 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: 0.9230 (mmm) cc_final: 0.8805 (mpp) REVERT: A 154 MET cc_start: 0.9024 (ttt) cc_final: 0.8797 (ttt) REVERT: A 201 MET cc_start: 0.8678 (ppp) cc_final: 0.8357 (ppp) REVERT: A 213 ARG cc_start: 0.9239 (mtp-110) cc_final: 0.9018 (tmm160) REVERT: A 310 ASP cc_start: 0.9317 (m-30) cc_final: 0.9041 (m-30) REVERT: B 53 ASP cc_start: 0.8722 (t0) cc_final: 0.8433 (t0) REVERT: B 201 MET cc_start: 0.8575 (mpp) cc_final: 0.8219 (mpp) REVERT: D 62 MET cc_start: 0.8420 (ttp) cc_final: 0.8113 (ttt) REVERT: D 122 GLU cc_start: 0.9313 (mp0) cc_final: 0.9095 (mp0) REVERT: D 212 PHE cc_start: 0.9475 (t80) cc_final: 0.9072 (t80) REVERT: C 44 HIS cc_start: 0.8904 (m170) cc_final: 0.8674 (m90) REVERT: C 126 MET cc_start: 0.9037 (mtm) cc_final: 0.8720 (pmm) REVERT: C 129 MET cc_start: 0.9605 (mtm) cc_final: 0.9384 (mtt) REVERT: C 187 LEU cc_start: 0.9118 (mt) cc_final: 0.8848 (mt) REVERT: F 201 MET cc_start: 0.9437 (mmm) cc_final: 0.9194 (mpp) REVERT: F 304 TYR cc_start: 0.9215 (t80) cc_final: 0.8651 (t80) REVERT: F 326 MET cc_start: 0.8523 (ptp) cc_final: 0.8289 (ptm) REVERT: F 383 MET cc_start: 0.7866 (mpp) cc_final: 0.7331 (mpp) REVERT: H 100 PHE cc_start: 0.9312 (p90) cc_final: 0.9049 (p90) REVERT: H 106 MET cc_start: 0.8643 (ppp) cc_final: 0.8375 (ppp) REVERT: H 326 MET cc_start: 0.9351 (mtt) cc_final: 0.9110 (mtp) REVERT: H 338 MET cc_start: 0.8463 (tmm) cc_final: 0.8031 (tpp) REVERT: H 340 TYR cc_start: 0.8714 (p90) cc_final: 0.8476 (p90) REVERT: H 372 GLN cc_start: 0.9106 (mt0) cc_final: 0.8650 (mt0) REVERT: H 393 GLN cc_start: 0.9025 (mt0) cc_final: 0.8706 (mp10) REVERT: G 73 ILE cc_start: 0.9831 (mm) cc_final: 0.9605 (tp) REVERT: G 191 ASP cc_start: 0.8745 (m-30) cc_final: 0.8525 (m-30) outliers start: 3 outliers final: 2 residues processed: 185 average time/residue: 0.3802 time to fit residues: 104.9404 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 : 2.389 ------------------------------------------------------------------------------- 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: 0.4980 chunk 215 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 226 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 F 315 GLN H 19 ASN G 306 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.066118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047435 restraints weight = 149913.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048690 restraints weight = 89108.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049052 restraints weight = 52708.415| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20961 Z= 0.142 Angle : 0.482 9.638 28259 Z= 0.265 Chirality : 0.042 0.165 3135 Planarity : 0.003 0.053 3581 Dihedral : 7.085 71.475 2914 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.04 % Allowed : 1.47 % Favored : 98.49 % 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: 1.48 (0.17), residues: 2492 helix: 1.93 (0.14), residues: 1257 sheet: 0.16 (0.26), residues: 391 loop : 0.06 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 158 HIS 0.013 0.001 HIS D 33 PHE 0.017 0.001 PHE A 234 TYR 0.014 0.001 TYR C 278 ARG 0.007 0.000 ARG B 144 *********************** 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 189 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 2.609 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: 0.8771 (ttt) cc_final: 0.8167 (ttt) REVERT: A 201 MET cc_start: 0.8597 (ppp) cc_final: 0.8181 (ppp) REVERT: A 213 ARG cc_start: 0.9200 (mtp-110) cc_final: 0.8967 (tmm160) REVERT: A 226 PHE cc_start: 0.9209 (t80) cc_final: 0.8944 (t80) REVERT: A 310 ASP cc_start: 0.9311 (m-30) cc_final: 0.9044 (m-30) REVERT: B 154 MET cc_start: 0.9014 (ttt) cc_final: 0.7018 (ttt) REVERT: D 62 MET cc_start: 0.8329 (ttp) cc_final: 0.8036 (ttt) REVERT: D 122 GLU cc_start: 0.9196 (mp0) cc_final: 0.8985 (mp0) REVERT: D 212 PHE cc_start: 0.9411 (t80) cc_final: 0.8924 (t80) REVERT: C 126 MET cc_start: 0.9028 (mtm) cc_final: 0.8710 (pmm) REVERT: C 129 MET cc_start: 0.9605 (mtm) cc_final: 0.9383 (mtt) REVERT: C 187 LEU cc_start: 0.8874 (mt) cc_final: 0.8250 (mt) REVERT: C 410 MET cc_start: 0.9013 (mtp) cc_final: 0.8782 (mtp) REVERT: F 201 MET cc_start: 0.9485 (mmm) cc_final: 0.9258 (mpp) REVERT: F 304 TYR cc_start: 0.9136 (t80) cc_final: 0.8470 (t80) REVERT: F 326 MET cc_start: 0.8596 (ptp) cc_final: 0.8342 (ptm) REVERT: F 383 MET cc_start: 0.7896 (mpp) cc_final: 0.7536 (mpp) REVERT: H 100 PHE cc_start: 0.9100 (p90) cc_final: 0.8805 (p90) REVERT: H 106 MET cc_start: 0.8653 (ppp) cc_final: 0.8341 (ppp) REVERT: H 372 GLN cc_start: 0.9050 (mt0) cc_final: 0.8567 (mt0) REVERT: H 393 GLN cc_start: 0.8916 (mt0) cc_final: 0.8635 (mp10) REVERT: G 23 LEU cc_start: 0.9343 (tp) cc_final: 0.9084 (tp) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.3674 time to fit residues: 105.7893 Evaluate side-chains 121 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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: 5.9990 chunk 146 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS D 33 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.063990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045207 restraints weight = 153822.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.045978 restraints weight = 96643.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.046188 restraints weight = 61149.387| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4017 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= 0.365 Angle : 0.634 8.772 28259 Z= 0.346 Chirality : 0.043 0.172 3135 Planarity : 0.004 0.052 3581 Dihedral : 7.302 73.981 2914 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % 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: 1.22 (0.17), residues: 2492 helix: 1.63 (0.14), residues: 1280 sheet: -0.15 (0.25), residues: 420 loop : 0.18 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 402 HIS 0.012 0.002 HIS D 33 PHE 0.056 0.002 PHE B 234 TYR 0.021 0.002 TYR B 270 ARG 0.009 0.001 ARG C 224 *********************** 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 143 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 2.480 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: 0.9225 (mmm) cc_final: 0.8719 (mpp) REVERT: A 154 MET cc_start: 0.8903 (ttt) cc_final: 0.8103 (ttm) REVERT: A 201 MET cc_start: 0.8694 (ppp) cc_final: 0.8340 (ppp) REVERT: B 154 MET cc_start: 0.9034 (ttt) cc_final: 0.7706 (ttt) REVERT: D 122 GLU cc_start: 0.9273 (mp0) cc_final: 0.9054 (mp0) REVERT: C 44 HIS cc_start: 0.9072 (m90) cc_final: 0.8678 (m-70) REVERT: C 126 MET cc_start: 0.9126 (mtm) cc_final: 0.8826 (pmm) REVERT: C 187 LEU cc_start: 0.9024 (mt) cc_final: 0.8532 (mt) REVERT: C 436 MET cc_start: 0.8999 (mpp) cc_final: 0.8789 (mpp) REVERT: F 201 MET cc_start: 0.9501 (mmm) cc_final: 0.9203 (mpp) REVERT: F 304 TYR cc_start: 0.9214 (t80) cc_final: 0.8582 (t80) REVERT: F 383 MET cc_start: 0.7922 (mpp) cc_final: 0.7360 (mpp) REVERT: H 100 PHE cc_start: 0.9284 (p90) cc_final: 0.9012 (p90) REVERT: H 372 GLN cc_start: 0.9050 (mt0) cc_final: 0.8632 (mt0) REVERT: H 393 GLN cc_start: 0.9129 (mt0) cc_final: 0.8789 (mp10) REVERT: G 53 GLN cc_start: 0.8961 (tt0) cc_final: 0.8732 (pt0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.3646 time to fit residues: 81.1732 Evaluate side-chains 107 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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: 8.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 166 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN H 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.065144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046416 restraints weight = 152357.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047249 restraints weight = 93803.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047828 restraints weight = 57680.149| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20961 Z= 0.206 Angle : 0.505 10.146 28259 Z= 0.279 Chirality : 0.042 0.169 3135 Planarity : 0.004 0.066 3581 Dihedral : 6.825 68.489 2914 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 1.44 (0.17), residues: 2492 helix: 1.86 (0.14), residues: 1274 sheet: -0.15 (0.25), residues: 413 loop : 0.24 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 158 HIS 0.005 0.001 HIS H 32 PHE 0.033 0.001 PHE B 234 TYR 0.015 0.001 TYR C 278 ARG 0.010 0.000 ARG A 213 *********************** 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 162 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.399 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: 0.9203 (mmm) cc_final: 0.8674 (mpp) REVERT: A 154 MET cc_start: 0.8901 (ttt) cc_final: 0.7998 (ttt) REVERT: A 201 MET cc_start: 0.8635 (ppp) cc_final: 0.8270 (ppp) REVERT: B 106 MET cc_start: 0.9194 (mtm) cc_final: 0.8949 (ptp) REVERT: B 129 MET cc_start: 0.8745 (mpp) cc_final: 0.8332 (mpp) REVERT: B 154 MET cc_start: 0.8991 (ttt) cc_final: 0.6931 (ttt) REVERT: D 62 MET cc_start: 0.8340 (ttp) cc_final: 0.7616 (tpp) REVERT: C 44 HIS cc_start: 0.9018 (m90) cc_final: 0.8633 (m90) REVERT: C 126 MET cc_start: 0.9026 (mtm) cc_final: 0.8719 (pmm) REVERT: C 129 MET cc_start: 0.9626 (mtm) cc_final: 0.9419 (mtt) REVERT: C 187 LEU cc_start: 0.9061 (mt) cc_final: 0.8729 (mt) REVERT: F 201 MET cc_start: 0.9456 (mmm) cc_final: 0.9021 (mpp) REVERT: F 304 TYR cc_start: 0.9274 (t80) cc_final: 0.8461 (t80) REVERT: F 383 MET cc_start: 0.7888 (mpp) cc_final: 0.7575 (mpp) REVERT: H 100 PHE cc_start: 0.9198 (p90) cc_final: 0.8970 (p90) REVERT: H 106 MET cc_start: 0.8268 (ppp) cc_final: 0.8052 (ppp) REVERT: H 372 GLN cc_start: 0.8987 (mt0) cc_final: 0.8539 (mt0) REVERT: H 393 GLN cc_start: 0.9016 (mt0) cc_final: 0.8733 (mp10) REVERT: G 23 LEU cc_start: 0.9316 (tp) cc_final: 0.9030 (tp) REVERT: G 33 HIS cc_start: 0.9558 (m-70) cc_final: 0.9329 (m-70) REVERT: G 53 GLN cc_start: 0.8974 (tt0) cc_final: 0.8767 (pt0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.3605 time to fit residues: 91.4966 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 : 2.515 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN D 36 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.065717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.046407 restraints weight = 152767.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047602 restraints weight = 83475.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.048360 restraints weight = 56535.859| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20961 Z= 0.145 Angle : 0.474 9.540 28259 Z= 0.260 Chirality : 0.041 0.193 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.492 68.482 2914 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.09 % Allowed : 0.98 % Favored : 98.93 % 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: 1.63 (0.17), residues: 2492 helix: 2.00 (0.14), residues: 1281 sheet: 0.03 (0.26), residues: 407 loop : 0.28 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 158 HIS 0.006 0.001 HIS D 238 PHE 0.025 0.001 PHE B 234 TYR 0.013 0.001 TYR C 278 ARG 0.007 0.000 ARG A 213 *********************** 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 162 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 2.453 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: 0.8662 (mpp) REVERT: A 154 MET cc_start: 0.8925 (ttt) cc_final: 0.8690 (ttt) REVERT: A 201 MET cc_start: 0.8665 (ppp) cc_final: 0.8298 (ppp) REVERT: B 106 MET cc_start: 0.9140 (mtm) cc_final: 0.8915 (ptp) REVERT: B 129 MET cc_start: 0.8705 (mpp) cc_final: 0.8288 (mpp) REVERT: D 62 MET cc_start: 0.8326 (ttp) cc_final: 0.7623 (tpp) REVERT: D 212 PHE cc_start: 0.9016 (t80) cc_final: 0.8736 (t80) REVERT: C 44 HIS cc_start: 0.8972 (m90) cc_final: 0.8578 (m90) REVERT: C 126 MET cc_start: 0.8897 (mtm) cc_final: 0.8669 (pmm) REVERT: C 129 MET cc_start: 0.9531 (mtm) cc_final: 0.9324 (mtt) REVERT: C 410 MET cc_start: 0.8981 (mtp) cc_final: 0.8731 (mtp) REVERT: C 436 MET cc_start: 0.9088 (mpp) cc_final: 0.8819 (mpp) REVERT: F 201 MET cc_start: 0.9500 (mmm) cc_final: 0.9097 (mpp) REVERT: F 304 TYR cc_start: 0.9142 (t80) cc_final: 0.8276 (t80) REVERT: F 376 MET cc_start: 0.7195 (mmp) cc_final: 0.6988 (mmt) REVERT: F 383 MET cc_start: 0.7930 (mpp) cc_final: 0.7613 (mpp) REVERT: H 106 MET cc_start: 0.8303 (ppp) cc_final: 0.8034 (ppp) REVERT: H 129 MET cc_start: 0.8370 (ptp) cc_final: 0.8141 (mpp) REVERT: H 209 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.9020 (pm20) REVERT: H 372 GLN cc_start: 0.8987 (mt0) cc_final: 0.8618 (mt0) REVERT: H 393 GLN cc_start: 0.9004 (mt0) cc_final: 0.8703 (mp10) REVERT: G 23 LEU cc_start: 0.9312 (tp) cc_final: 0.9029 (tp) REVERT: G 31 ARG cc_start: 0.9339 (mtm110) cc_final: 0.9095 (ttp-110) REVERT: G 33 HIS cc_start: 0.9517 (m-70) cc_final: 0.9278 (m-70) REVERT: G 53 GLN cc_start: 0.9017 (tt0) cc_final: 0.8803 (pt0) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3368 time to fit residues: 85.1696 Evaluate side-chains 115 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.064142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045424 restraints weight = 152232.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.046091 restraints weight = 95395.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.046664 restraints weight = 61683.172| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20961 Z= 0.318 Angle : 0.589 8.702 28259 Z= 0.324 Chirality : 0.043 0.189 3135 Planarity : 0.004 0.044 3581 Dihedral : 6.956 74.880 2914 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.04 % Allowed : 1.02 % Favored : 98.93 % 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: 1.21 (0.17), residues: 2492 helix: 1.68 (0.14), residues: 1297 sheet: -0.30 (0.25), residues: 430 loop : 0.11 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 402 HIS 0.005 0.001 HIS B 32 PHE 0.057 0.002 PHE B 234 TYR 0.020 0.002 TYR D 35 ARG 0.007 0.001 ARG C 305 *********************** 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 144 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 2.561 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: 0.9197 (mmm) cc_final: 0.8737 (mpp) REVERT: A 154 MET cc_start: 0.8916 (ttt) cc_final: 0.8080 (ttt) REVERT: A 201 MET cc_start: 0.8700 (ppp) cc_final: 0.8349 (ppp) REVERT: A 304 TYR cc_start: 0.9138 (t80) cc_final: 0.8924 (t80) REVERT: A 436 MET cc_start: 0.7933 (mtt) cc_final: 0.7719 (mtt) REVERT: B 106 MET cc_start: 0.9217 (mtm) cc_final: 0.8998 (ptp) REVERT: B 154 MET cc_start: 0.8982 (ttt) cc_final: 0.7276 (ttt) REVERT: B 232 LYS cc_start: 0.9438 (mttp) cc_final: 0.9035 (mttm) REVERT: D 62 MET cc_start: 0.8462 (ttp) cc_final: 0.8044 (ttt) REVERT: C 44 HIS cc_start: 0.8960 (m90) cc_final: 0.8630 (m90) REVERT: C 126 MET cc_start: 0.9018 (mtm) cc_final: 0.8727 (pmm) REVERT: F 201 MET cc_start: 0.9420 (mmm) cc_final: 0.9003 (mpp) REVERT: F 304 TYR cc_start: 0.9185 (t80) cc_final: 0.8383 (t80) REVERT: F 383 MET cc_start: 0.7911 (mpp) cc_final: 0.7433 (mpp) REVERT: H 106 MET cc_start: 0.8383 (ppp) cc_final: 0.8123 (ppp) REVERT: H 372 GLN cc_start: 0.9031 (mt0) cc_final: 0.8659 (mt0) REVERT: H 393 GLN cc_start: 0.9071 (mt0) cc_final: 0.8747 (mp10) REVERT: G 23 LEU cc_start: 0.9285 (tp) cc_final: 0.8994 (tp) REVERT: G 53 GLN cc_start: 0.9025 (tt0) cc_final: 0.8768 (pt0) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.3429 time to fit residues: 76.8389 Evaluate side-chains 111 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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: 0.9990 chunk 114 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** ** C 413 GLN ** 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 = 0.065399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047122 restraints weight = 152544.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.048212 restraints weight = 88311.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048596 restraints weight = 53390.158| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20961 Z= 0.151 Angle : 0.478 9.418 28259 Z= 0.263 Chirality : 0.042 0.218 3135 Planarity : 0.003 0.041 3581 Dihedral : 6.510 77.660 2914 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.04 % Allowed : 0.67 % Favored : 99.29 % 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: 1.57 (0.17), residues: 2492 helix: 1.97 (0.14), residues: 1296 sheet: -0.13 (0.26), residues: 410 loop : 0.28 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 158 HIS 0.023 0.001 HIS G 33 PHE 0.040 0.001 PHE B 234 TYR 0.014 0.001 TYR C 278 ARG 0.005 0.000 ARG A 213 *********************** 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 154 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 2.266 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: 0.9212 (mmm) cc_final: 0.8723 (mpp) REVERT: A 154 MET cc_start: 0.8738 (ttt) cc_final: 0.8033 (ttt) REVERT: A 201 MET cc_start: 0.8652 (ppp) cc_final: 0.8271 (ppp) REVERT: A 326 MET cc_start: 0.8676 (mmm) cc_final: 0.8183 (mmm) REVERT: B 129 MET cc_start: 0.8708 (mpp) cc_final: 0.8417 (mpp) REVERT: B 154 MET cc_start: 0.9000 (ttt) cc_final: 0.6935 (ttt) REVERT: D 62 MET cc_start: 0.8367 (ttp) cc_final: 0.7689 (tpp) REVERT: D 212 PHE cc_start: 0.9261 (t80) cc_final: 0.8973 (t80) REVERT: C 44 HIS cc_start: 0.8955 (m90) cc_final: 0.8631 (m90) REVERT: C 126 MET cc_start: 0.9025 (mtm) cc_final: 0.8737 (pmm) REVERT: C 129 MET cc_start: 0.9623 (mtm) cc_final: 0.9413 (mtt) REVERT: C 187 LEU cc_start: 0.9148 (mt) cc_final: 0.8879 (mt) REVERT: C 338 MET cc_start: 0.8941 (ttp) cc_final: 0.8474 (tmm) REVERT: F 201 MET cc_start: 0.9454 (mmm) cc_final: 0.9052 (mpp) REVERT: F 304 TYR cc_start: 0.9185 (t80) cc_final: 0.8304 (t80) REVERT: F 383 MET cc_start: 0.7972 (mpp) cc_final: 0.7485 (mpp) REVERT: H 106 MET cc_start: 0.8368 (ppp) cc_final: 0.8140 (ppp) REVERT: H 130 ASP cc_start: 0.9308 (t0) cc_final: 0.9049 (m-30) REVERT: H 372 GLN cc_start: 0.8890 (mt0) cc_final: 0.8521 (mt0) REVERT: H 393 GLN cc_start: 0.8900 (mt0) cc_final: 0.8565 (mp10) REVERT: G 23 LEU cc_start: 0.9265 (tp) cc_final: 0.8942 (tp) REVERT: G 33 HIS cc_start: 0.9568 (m-70) cc_final: 0.9196 (m90) REVERT: G 53 GLN cc_start: 0.9014 (tt0) cc_final: 0.8801 (pt0) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.3477 time to fit residues: 82.4480 Evaluate side-chains 115 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.064012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.045308 restraints weight = 152885.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046068 restraints weight = 95693.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046229 restraints weight = 63654.604| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20961 Z= 0.319 Angle : 0.596 8.264 28259 Z= 0.328 Chirality : 0.044 0.222 3135 Planarity : 0.004 0.044 3581 Dihedral : 6.930 82.496 2914 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % 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: 1.16 (0.17), residues: 2492 helix: 1.66 (0.14), residues: 1305 sheet: -0.40 (0.25), residues: 418 loop : 0.06 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 402 HIS 0.014 0.001 HIS G 33 PHE 0.044 0.002 PHE B 234 TYR 0.038 0.002 TYR G 35 ARG 0.004 0.001 ARG G 31 *********************** 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 : 2.598 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: 0.9244 (mmm) cc_final: 0.8740 (mpp) REVERT: A 154 MET cc_start: 0.8822 (ttt) cc_final: 0.8041 (ttm) REVERT: A 201 MET cc_start: 0.8728 (ppp) cc_final: 0.8378 (ppp) REVERT: A 304 TYR cc_start: 0.9146 (t80) cc_final: 0.8924 (t80) REVERT: A 436 MET cc_start: 0.7924 (mtt) cc_final: 0.7672 (mtt) REVERT: B 129 MET cc_start: 0.8739 (mpp) cc_final: 0.8359 (mpp) REVERT: B 154 MET cc_start: 0.9009 (ttt) cc_final: 0.7709 (ttt) REVERT: B 232 LYS cc_start: 0.9482 (mttp) cc_final: 0.9184 (mttm) REVERT: D 62 MET cc_start: 0.8591 (ttp) cc_final: 0.8203 (ttt) REVERT: C 44 HIS cc_start: 0.9010 (m90) cc_final: 0.8659 (m90) REVERT: C 126 MET cc_start: 0.9088 (mtm) cc_final: 0.8773 (pmm) REVERT: C 187 LEU cc_start: 0.9108 (mt) cc_final: 0.8828 (mt) REVERT: C 338 MET cc_start: 0.8879 (ttp) cc_final: 0.8499 (tmm) REVERT: F 201 MET cc_start: 0.9452 (mmm) cc_final: 0.9076 (mpp) REVERT: F 304 TYR cc_start: 0.9269 (t80) cc_final: 0.8427 (t80) REVERT: F 383 MET cc_start: 0.7957 (mpp) cc_final: 0.7471 (mpp) REVERT: F 436 MET cc_start: 0.7548 (mmm) cc_final: 0.7326 (mmm) REVERT: H 106 MET cc_start: 0.8344 (ppp) cc_final: 0.8133 (ppp) REVERT: H 130 ASP cc_start: 0.9377 (t0) cc_final: 0.9073 (m-30) REVERT: H 186 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8325 (tm-30) REVERT: H 372 GLN cc_start: 0.9011 (mt0) cc_final: 0.8691 (mt0) REVERT: H 393 GLN cc_start: 0.9017 (mt0) cc_final: 0.8656 (mp10) REVERT: G 23 LEU cc_start: 0.9332 (tp) cc_final: 0.9099 (tp) REVERT: G 53 GLN cc_start: 0.9019 (tt0) cc_final: 0.8770 (pt0) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3518 time to fit residues: 79.7746 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 : 2.496 ------------------------------------------------------------------------------- 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: 7.9990 chunk 155 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 222 optimal weight: 0.7980 chunk 90 optimal weight: 0.0050 overall best weight: 1.8998 ------------------------------------------------------------------------------- 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** C 413 GLN H 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046300 restraints weight = 152539.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047286 restraints weight = 94129.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047442 restraints weight = 57964.894| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20961 Z= 0.194 Angle : 0.514 8.725 28259 Z= 0.284 Chirality : 0.042 0.213 3135 Planarity : 0.003 0.041 3581 Dihedral : 6.628 85.934 2914 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.73 % 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: 1.81 (0.14), residues: 1303 sheet: -0.32 (0.25), residues: 404 loop : 0.19 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 158 HIS 0.004 0.001 HIS G 33 PHE 0.037 0.001 PHE B 234 TYR 0.022 0.001 TYR G 35 ARG 0.006 0.000 ARG B 56 ********************** 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 148 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 2.413 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: 0.9199 (mmm) cc_final: 0.8733 (mpp) REVERT: A 154 MET cc_start: 0.8893 (ttt) cc_final: 0.7988 (ttm) REVERT: A 201 MET cc_start: 0.8698 (ppp) cc_final: 0.8328 (ppp) REVERT: A 304 TYR cc_start: 0.9110 (t80) cc_final: 0.8899 (t80) REVERT: B 129 MET cc_start: 0.8802 (mpp) cc_final: 0.8437 (mpp) REVERT: B 154 MET cc_start: 0.9024 (ttt) cc_final: 0.7134 (ttt) REVERT: B 232 LYS cc_start: 0.9450 (mttp) cc_final: 0.9139 (mttm) REVERT: D 62 MET cc_start: 0.8461 (ttp) cc_final: 0.7779 (tpp) REVERT: C 44 HIS cc_start: 0.9003 (m90) cc_final: 0.8606 (m90) REVERT: C 126 MET cc_start: 0.9051 (mtm) cc_final: 0.8769 (pmm) REVERT: C 129 MET cc_start: 0.9628 (mtm) cc_final: 0.9422 (mtt) REVERT: C 154 MET cc_start: 0.8799 (ttm) cc_final: 0.8505 (ttm) REVERT: C 326 MET cc_start: 0.9024 (mtm) cc_final: 0.8781 (ptp) REVERT: C 338 MET cc_start: 0.8944 (ttp) cc_final: 0.8445 (tmm) REVERT: F 201 MET cc_start: 0.9457 (mmm) cc_final: 0.9054 (mpp) REVERT: F 209 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8865 (tm-30) REVERT: F 304 TYR cc_start: 0.9196 (t80) cc_final: 0.8302 (t80) REVERT: F 383 MET cc_start: 0.8031 (mpp) cc_final: 0.7522 (mpp) REVERT: F 436 MET cc_start: 0.7522 (mmm) cc_final: 0.7309 (mmm) REVERT: H 106 MET cc_start: 0.8272 (ppp) cc_final: 0.8047 (ppp) REVERT: H 130 ASP cc_start: 0.9336 (t0) cc_final: 0.9056 (m-30) REVERT: H 186 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8333 (tm-30) REVERT: H 372 GLN cc_start: 0.9019 (mt0) cc_final: 0.8652 (mt0) REVERT: H 393 GLN cc_start: 0.8931 (mt0) cc_final: 0.8620 (mp10) REVERT: G 23 LEU cc_start: 0.9310 (tp) cc_final: 0.9062 (tp) REVERT: G 53 GLN cc_start: 0.9008 (tt0) cc_final: 0.8798 (pt0) REVERT: G 245 GLN cc_start: 0.8954 (tt0) cc_final: 0.8624 (tp40) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3521 time to fit residues: 80.5045 Evaluate side-chains 118 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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: 0.9990 chunk 190 optimal weight: 40.0000 chunk 150 optimal weight: 0.4980 chunk 214 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.064451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046002 restraints weight = 153288.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047052 restraints weight = 94309.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047361 restraints weight = 56271.503| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20961 Z= 0.215 Angle : 0.524 8.222 28259 Z= 0.289 Chirality : 0.042 0.224 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.639 87.584 2914 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % 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: 1.81 (0.14), residues: 1303 sheet: -0.33 (0.26), residues: 404 loop : 0.19 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 158 HIS 0.004 0.001 HIS G 119 PHE 0.042 0.001 PHE B 234 TYR 0.023 0.001 TYR G 35 ARG 0.006 0.000 ARG B 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6091.46 seconds wall clock time: 111 minutes 2.60 seconds (6662.60 seconds total)