Starting phenix.real_space_refine on Wed Aug 7 19:29:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_42967.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_42967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_42967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_42967.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v47_42967/08_2024/8v47_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 Residue "A TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 11.63, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 8.88 Conformation dependent library (CDL) restraints added in 3.8 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: 2.61 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: 7.10 Time building geometry restraints manager: 9.45 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: 98.63 - 106.82: 448 106.82 - 115.01: 12534 115.01 - 123.20: 14187 123.20 - 131.38: 1052 131.38 - 139.57: 38 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: 6.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 57.130 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.150 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 64 poor density : 329 time to evaluate : 3.135 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: 0.3863 time to fit residues: 212.8486 Evaluate side-chains 192 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 fitting. rotamer outliers: 3 poor density : 182 time to evaluate : 2.731 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: 0.9282 (mmm) cc_final: 0.8846 (mpp) REVERT: A 154 MET cc_start: 0.9318 (ttt) cc_final: 0.8979 (ttt) REVERT: A 201 MET cc_start: 0.8944 (ppp) cc_final: 0.8589 (ppp) REVERT: A 213 ARG cc_start: 0.9271 (mtp-110) cc_final: 0.9055 (tmm160) REVERT: A 310 ASP cc_start: 0.9245 (m-30) cc_final: 0.8963 (m-30) REVERT: A 383 MET cc_start: 0.8846 (mtp) cc_final: 0.8524 (ttm) REVERT: A 436 MET cc_start: 0.8861 (mtp) cc_final: 0.8617 (mtp) REVERT: B 53 ASP cc_start: 0.8798 (t0) cc_final: 0.8285 (t0) REVERT: B 201 MET cc_start: 0.9051 (mpp) cc_final: 0.8489 (mpp) REVERT: D 62 MET cc_start: 0.8609 (ttp) cc_final: 0.8305 (ttt) REVERT: D 122 GLU cc_start: 0.9334 (mp0) cc_final: 0.9074 (mp0) REVERT: D 212 PHE cc_start: 0.9503 (t80) cc_final: 0.9069 (t80) REVERT: C 44 HIS cc_start: 0.9063 (m170) cc_final: 0.8832 (m90) REVERT: C 126 MET cc_start: 0.9193 (mtm) cc_final: 0.8851 (pmm) REVERT: C 129 MET cc_start: 0.9674 (mtm) cc_final: 0.9469 (mtt) REVERT: C 187 LEU cc_start: 0.9208 (mt) cc_final: 0.8912 (mt) REVERT: C 393 GLN cc_start: 0.9262 (mt0) cc_final: 0.8987 (mp10) REVERT: F 201 MET cc_start: 0.9184 (mmm) cc_final: 0.8878 (mpp) REVERT: F 304 TYR cc_start: 0.8188 (t80) cc_final: 0.7926 (t80) REVERT: F 326 MET cc_start: 0.8583 (ptp) cc_final: 0.8255 (ptm) REVERT: F 383 MET cc_start: 0.7380 (mpp) cc_final: 0.6913 (mpp) REVERT: H 100 PHE cc_start: 0.9025 (p90) cc_final: 0.8724 (p90) REVERT: H 106 MET cc_start: 0.8634 (ppp) cc_final: 0.8334 (ppp) REVERT: H 326 MET cc_start: 0.9279 (mtt) cc_final: 0.9016 (mtp) REVERT: H 338 MET cc_start: 0.8312 (tmm) cc_final: 0.7956 (tpp) REVERT: H 372 GLN cc_start: 0.9012 (mt0) cc_final: 0.8536 (mt0) REVERT: H 393 GLN cc_start: 0.8981 (mt0) cc_final: 0.8703 (mp10) REVERT: G 73 ILE cc_start: 0.9554 (mm) cc_final: 0.9286 (tp) REVERT: G 191 ASP cc_start: 0.8399 (m-30) cc_final: 0.8179 (m-30) outliers start: 3 outliers final: 2 residues processed: 185 average time/residue: 0.3742 time to fit residues: 103.6407 Evaluate side-chains 121 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN B 44 HIS D 263 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN H 19 ASN ** H 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20961 Z= 0.249 Angle : 0.545 9.734 28259 Z= 0.299 Chirality : 0.042 0.156 3135 Planarity : 0.004 0.064 3581 Dihedral : 7.400 72.509 2914 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.26 % 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: 1.27 (0.17), residues: 2492 helix: 1.70 (0.14), residues: 1284 sheet: -0.07 (0.25), residues: 417 loop : 0.06 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 402 HIS 0.013 0.001 HIS D 33 PHE 0.017 0.001 PHE A 234 TYR 0.018 0.002 TYR C 304 ARG 0.008 0.001 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 164 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9152 (ttt) cc_final: 0.8556 (ttt) REVERT: A 201 MET cc_start: 0.8909 (ppp) cc_final: 0.8525 (ppp) REVERT: A 213 ARG cc_start: 0.9287 (mtp-110) cc_final: 0.9047 (tmm160) REVERT: A 226 PHE cc_start: 0.9096 (t80) cc_final: 0.8702 (t80) REVERT: A 310 ASP cc_start: 0.9272 (m-30) cc_final: 0.9063 (m-30) REVERT: A 383 MET cc_start: 0.8768 (mtp) cc_final: 0.8380 (ttm) REVERT: A 436 MET cc_start: 0.8817 (mtp) cc_final: 0.8579 (mtp) REVERT: B 154 MET cc_start: 0.9238 (ttt) cc_final: 0.7149 (ttt) REVERT: D 62 MET cc_start: 0.8579 (ttp) cc_final: 0.7736 (tpt) REVERT: D 122 GLU cc_start: 0.9292 (mp0) cc_final: 0.9032 (mp0) REVERT: C 44 HIS cc_start: 0.9040 (m170) cc_final: 0.8800 (m90) REVERT: C 126 MET cc_start: 0.9225 (mtm) cc_final: 0.8909 (pmm) REVERT: C 187 LEU cc_start: 0.8926 (mt) cc_final: 0.8317 (mt) REVERT: C 393 GLN cc_start: 0.9185 (mt0) cc_final: 0.8851 (mp10) REVERT: C 410 MET cc_start: 0.9120 (mtp) cc_final: 0.8816 (mtp) REVERT: F 201 MET cc_start: 0.9210 (mmm) cc_final: 0.8877 (mpp) REVERT: F 304 TYR cc_start: 0.8108 (t80) cc_final: 0.7784 (t80) REVERT: F 326 MET cc_start: 0.8613 (ptp) cc_final: 0.8289 (ptm) REVERT: F 383 MET cc_start: 0.7443 (mpp) cc_final: 0.6974 (mpp) REVERT: H 106 MET cc_start: 0.8652 (ppp) cc_final: 0.8315 (ppp) REVERT: H 372 GLN cc_start: 0.8955 (mt0) cc_final: 0.8399 (mt0) REVERT: H 393 GLN cc_start: 0.8934 (mt0) cc_final: 0.8679 (mp10) REVERT: G 23 LEU cc_start: 0.8375 (tp) cc_final: 0.8009 (tp) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3509 time to fit residues: 87.5877 Evaluate side-chains 115 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 230 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN D 33 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN H 403 GLN G 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20961 Z= 0.187 Angle : 0.487 7.615 28259 Z= 0.269 Chirality : 0.041 0.161 3135 Planarity : 0.003 0.044 3581 Dihedral : 6.868 68.433 2914 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.20 % 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: 1.94 (0.14), residues: 1281 sheet: 0.02 (0.25), residues: 415 loop : 0.25 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 158 HIS 0.010 0.001 HIS D 33 PHE 0.043 0.001 PHE B 234 TYR 0.019 0.001 TYR H 176 ARG 0.011 0.000 ARG G 22 *********************** 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 165 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 2.530 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: 0.9138 (ttt) cc_final: 0.8409 (ttt) REVERT: A 201 MET cc_start: 0.8878 (ppp) cc_final: 0.8508 (ppp) REVERT: A 213 ARG cc_start: 0.9283 (mtp-110) cc_final: 0.9017 (tmm160) REVERT: A 310 ASP cc_start: 0.9289 (m-30) cc_final: 0.9086 (m-30) REVERT: A 383 MET cc_start: 0.8718 (mtp) cc_final: 0.8420 (ttm) REVERT: A 436 MET cc_start: 0.8795 (mtp) cc_final: 0.8575 (mtp) REVERT: B 154 MET cc_start: 0.9219 (ttt) cc_final: 0.7569 (ttt) REVERT: D 62 MET cc_start: 0.8519 (ttp) cc_final: 0.8221 (ttt) REVERT: D 122 GLU cc_start: 0.9223 (mp0) cc_final: 0.8987 (mp0) REVERT: C 44 HIS cc_start: 0.9042 (m170) cc_final: 0.8795 (m90) REVERT: C 126 MET cc_start: 0.9197 (mtm) cc_final: 0.8845 (pmm) REVERT: C 187 LEU cc_start: 0.8946 (mt) cc_final: 0.8431 (mt) REVERT: C 393 GLN cc_start: 0.9172 (mt0) cc_final: 0.8827 (mp10) REVERT: C 436 MET cc_start: 0.9129 (mpp) cc_final: 0.8839 (mpp) REVERT: F 201 MET cc_start: 0.9211 (mmm) cc_final: 0.8888 (mpp) REVERT: F 304 TYR cc_start: 0.8171 (t80) cc_final: 0.7850 (t80) REVERT: F 326 MET cc_start: 0.8651 (ptp) cc_final: 0.8393 (ptm) REVERT: F 383 MET cc_start: 0.7432 (mpp) cc_final: 0.7159 (mpp) REVERT: H 100 PHE cc_start: 0.8788 (p90) cc_final: 0.8566 (p90) REVERT: H 106 MET cc_start: 0.8621 (ppp) cc_final: 0.8286 (ppp) REVERT: H 130 ASP cc_start: 0.9190 (t0) cc_final: 0.8896 (m-30) REVERT: H 372 GLN cc_start: 0.8940 (mt0) cc_final: 0.8414 (mt0) REVERT: H 393 GLN cc_start: 0.8938 (mt0) cc_final: 0.8702 (mp10) REVERT: G 23 LEU cc_start: 0.8261 (tp) cc_final: 0.7961 (tp) REVERT: G 33 HIS cc_start: 0.9060 (m-70) cc_final: 0.8562 (m-70) REVERT: G 36 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: G 283 LEU cc_start: 0.9545 (mm) cc_final: 0.9324 (mt) outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.3288 time to fit residues: 84.9016 Evaluate side-chains 117 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 124 optimal weight: 0.3980 chunk 219 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4042 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= 0.184 Angle : 0.487 10.017 28259 Z= 0.268 Chirality : 0.041 0.169 3135 Planarity : 0.003 0.051 3581 Dihedral : 6.668 68.033 2914 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.04 % Allowed : 1.29 % Favored : 98.66 % 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: 1.69 (0.17), residues: 2492 helix: 2.04 (0.14), residues: 1271 sheet: 0.05 (0.25), residues: 414 loop : 0.36 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 158 HIS 0.006 0.001 HIS G 33 PHE 0.033 0.001 PHE B 234 TYR 0.014 0.001 TYR C 278 ARG 0.010 0.000 ARG G 31 *********************** 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 fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9142 (ttt) cc_final: 0.8396 (ttt) REVERT: A 201 MET cc_start: 0.8859 (ppp) cc_final: 0.8493 (ppp) REVERT: A 213 ARG cc_start: 0.9306 (mtp-110) cc_final: 0.9054 (tmm160) REVERT: A 226 PHE cc_start: 0.8857 (t80) cc_final: 0.8478 (t80) REVERT: A 304 TYR cc_start: 0.7990 (t80) cc_final: 0.7757 (t80) REVERT: A 383 MET cc_start: 0.8745 (mtp) cc_final: 0.8420 (ttm) REVERT: A 436 MET cc_start: 0.8790 (mtp) cc_final: 0.8567 (mtp) REVERT: B 129 MET cc_start: 0.8740 (mpp) cc_final: 0.8367 (mpp) REVERT: B 154 MET cc_start: 0.9213 (ttt) cc_final: 0.7569 (ttt) REVERT: D 62 MET cc_start: 0.8498 (ttp) cc_final: 0.8192 (ttt) REVERT: D 122 GLU cc_start: 0.9189 (mp0) cc_final: 0.8979 (mp0) REVERT: C 44 HIS cc_start: 0.9058 (m170) cc_final: 0.8812 (m90) REVERT: C 126 MET cc_start: 0.9191 (mtm) cc_final: 0.8869 (pmm) REVERT: C 187 LEU cc_start: 0.8993 (mt) cc_final: 0.8750 (mt) REVERT: C 393 GLN cc_start: 0.9203 (mt0) cc_final: 0.8864 (mp10) REVERT: F 201 MET cc_start: 0.9219 (mmm) cc_final: 0.8760 (mpp) REVERT: F 304 TYR cc_start: 0.8200 (t80) cc_final: 0.7656 (t80) REVERT: F 383 MET cc_start: 0.7427 (mpp) cc_final: 0.7158 (mpp) REVERT: F 436 MET cc_start: 0.6576 (tpt) cc_final: 0.6354 (mmm) REVERT: H 106 MET cc_start: 0.8585 (ppp) cc_final: 0.8232 (ppp) REVERT: H 129 MET cc_start: 0.8419 (ptp) cc_final: 0.8155 (mpp) REVERT: H 326 MET cc_start: 0.9358 (mtt) cc_final: 0.8883 (ptp) REVERT: H 372 GLN cc_start: 0.8871 (mt0) cc_final: 0.8393 (mt0) REVERT: H 393 GLN cc_start: 0.8925 (mt0) cc_final: 0.8690 (mp10) REVERT: G 23 LEU cc_start: 0.8224 (tp) cc_final: 0.7919 (tp) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.3232 time to fit residues: 82.5698 Evaluate side-chains 119 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** C 35 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** F 268 ASN F 315 GLN H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20961 Z= 0.243 Angle : 0.522 9.562 28259 Z= 0.285 Chirality : 0.042 0.185 3135 Planarity : 0.003 0.047 3581 Dihedral : 6.738 70.640 2914 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.13 % Allowed : 1.38 % 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: 1.54 (0.17), residues: 2492 helix: 1.97 (0.14), residues: 1274 sheet: -0.09 (0.25), residues: 428 loop : 0.24 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 158 HIS 0.005 0.001 HIS G 33 PHE 0.026 0.001 PHE B 234 TYR 0.017 0.002 TYR B 304 ARG 0.006 0.000 ARG G 31 *********************** 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 153 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9188 (ttt) cc_final: 0.8451 (ttt) REVERT: A 201 MET cc_start: 0.8902 (ppp) cc_final: 0.8531 (ppp) REVERT: A 213 ARG cc_start: 0.9338 (mtp-110) cc_final: 0.9082 (tmm160) REVERT: A 226 PHE cc_start: 0.8950 (t80) cc_final: 0.8575 (t80) REVERT: A 436 MET cc_start: 0.8796 (mtp) cc_final: 0.8538 (mtp) REVERT: B 129 MET cc_start: 0.8777 (mpp) cc_final: 0.8405 (mpp) REVERT: B 154 MET cc_start: 0.9240 (ttt) cc_final: 0.7933 (ttt) REVERT: D 62 MET cc_start: 0.8554 (ttp) cc_final: 0.8244 (ttt) REVERT: D 122 GLU cc_start: 0.9181 (mp0) cc_final: 0.8964 (mp0) REVERT: C 44 HIS cc_start: 0.9036 (m170) cc_final: 0.8778 (m90) REVERT: C 126 MET cc_start: 0.9190 (mtm) cc_final: 0.8872 (pmm) REVERT: C 154 MET cc_start: 0.8688 (ttm) cc_final: 0.8317 (ttm) REVERT: C 393 GLN cc_start: 0.9252 (mt0) cc_final: 0.8897 (mp10) REVERT: F 201 MET cc_start: 0.9196 (mmm) cc_final: 0.8705 (mpp) REVERT: F 304 TYR cc_start: 0.8172 (t80) cc_final: 0.7694 (t80) REVERT: F 383 MET cc_start: 0.7493 (mpp) cc_final: 0.7198 (mpp) REVERT: F 436 MET cc_start: 0.6727 (tpt) cc_final: 0.6495 (mmm) REVERT: H 130 ASP cc_start: 0.9149 (t0) cc_final: 0.8894 (m-30) REVERT: H 209 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.9005 (pm20) REVERT: H 326 MET cc_start: 0.9326 (mtt) cc_final: 0.8776 (ptp) REVERT: H 372 GLN cc_start: 0.8868 (mt0) cc_final: 0.8343 (mt0) REVERT: H 393 GLN cc_start: 0.8957 (mt0) cc_final: 0.8717 (mp10) REVERT: G 23 LEU cc_start: 0.8329 (tp) cc_final: 0.8037 (tp) outliers start: 3 outliers final: 0 residues processed: 152 average time/residue: 0.3285 time to fit residues: 78.5546 Evaluate side-chains 115 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 243 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20961 Z= 0.228 Angle : 0.514 8.503 28259 Z= 0.283 Chirality : 0.042 0.207 3135 Planarity : 0.003 0.046 3581 Dihedral : 6.695 74.643 2914 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2492 helix: 1.92 (0.14), residues: 1286 sheet: -0.21 (0.24), residues: 430 loop : 0.27 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 158 HIS 0.004 0.001 HIS H 32 PHE 0.022 0.001 PHE B 234 TYR 0.015 0.001 TYR C 278 ARG 0.004 0.000 ARG G 31 *********************** 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 154 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.472 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: 0.9169 (ttt) cc_final: 0.8454 (ttt) REVERT: A 201 MET cc_start: 0.8925 (ppp) cc_final: 0.8545 (ppp) REVERT: A 213 ARG cc_start: 0.9356 (mtp-110) cc_final: 0.9099 (tmm160) REVERT: A 226 PHE cc_start: 0.8969 (t80) cc_final: 0.8631 (t80) REVERT: A 304 TYR cc_start: 0.8010 (t80) cc_final: 0.7770 (t80) REVERT: A 326 MET cc_start: 0.8916 (mmm) cc_final: 0.8357 (mmm) REVERT: A 436 MET cc_start: 0.8782 (mtp) cc_final: 0.8543 (mtp) REVERT: B 154 MET cc_start: 0.9229 (ttt) cc_final: 0.7831 (ttt) REVERT: D 62 MET cc_start: 0.8544 (ttp) cc_final: 0.8235 (ttt) REVERT: D 122 GLU cc_start: 0.9187 (mp0) cc_final: 0.8981 (mp0) REVERT: D 212 PHE cc_start: 0.9245 (t80) cc_final: 0.8912 (t80) REVERT: C 44 HIS cc_start: 0.9046 (m170) cc_final: 0.8778 (m90) REVERT: C 126 MET cc_start: 0.9190 (mtm) cc_final: 0.8876 (pmm) REVERT: C 154 MET cc_start: 0.8664 (ttm) cc_final: 0.8377 (ttm) REVERT: C 338 MET cc_start: 0.9019 (ttm) cc_final: 0.8728 (tmm) REVERT: C 383 MET cc_start: 0.8534 (mpp) cc_final: 0.8302 (mpp) REVERT: C 393 GLN cc_start: 0.9252 (mt0) cc_final: 0.8854 (mp10) REVERT: F 201 MET cc_start: 0.9209 (mmm) cc_final: 0.8730 (mpp) REVERT: F 304 TYR cc_start: 0.8125 (t80) cc_final: 0.7668 (t80) REVERT: F 383 MET cc_start: 0.7473 (mpp) cc_final: 0.7201 (mpp) REVERT: H 130 ASP cc_start: 0.9200 (t0) cc_final: 0.8906 (m-30) REVERT: H 326 MET cc_start: 0.9295 (mtt) cc_final: 0.8901 (ptp) REVERT: H 372 GLN cc_start: 0.8874 (mt0) cc_final: 0.8345 (mt0) REVERT: H 393 GLN cc_start: 0.8947 (mt0) cc_final: 0.8699 (mp10) REVERT: G 23 LEU cc_start: 0.8317 (tp) cc_final: 0.8019 (tp) REVERT: G 33 HIS cc_start: 0.9010 (m-70) cc_final: 0.8659 (m-70) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.3335 time to fit residues: 79.9363 Evaluate side-chains 118 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 0.0050 chunk 97 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN G 53 GLN G 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20961 Z= 0.168 Angle : 0.483 8.122 28259 Z= 0.264 Chirality : 0.042 0.231 3135 Planarity : 0.003 0.044 3581 Dihedral : 6.496 78.040 2914 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % 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: 1.68 (0.17), residues: 2492 helix: 2.06 (0.15), residues: 1285 sheet: -0.17 (0.25), residues: 415 loop : 0.41 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 158 HIS 0.005 0.001 HIS G 33 PHE 0.054 0.001 PHE B 234 TYR 0.016 0.001 TYR D 35 ARG 0.005 0.000 ARG G 31 *********************** 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 156 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.443 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 154 MET cc_start: 0.9115 (ttt) cc_final: 0.8399 (ttm) REVERT: A 201 MET cc_start: 0.8910 (ppp) cc_final: 0.8529 (ppp) REVERT: A 226 PHE cc_start: 0.8972 (t80) cc_final: 0.8606 (t80) REVERT: A 436 MET cc_start: 0.8702 (mtp) cc_final: 0.8457 (mtp) REVERT: B 129 MET cc_start: 0.8796 (mpp) cc_final: 0.8551 (mpp) REVERT: B 154 MET cc_start: 0.9218 (ttt) cc_final: 0.7798 (ttt) REVERT: D 62 MET cc_start: 0.8489 (ttp) cc_final: 0.8203 (ttt) REVERT: D 212 PHE cc_start: 0.9261 (t80) cc_final: 0.8914 (t80) REVERT: C 44 HIS cc_start: 0.9071 (m170) cc_final: 0.8811 (m90) REVERT: C 126 MET cc_start: 0.9170 (mtm) cc_final: 0.8864 (pmm) REVERT: C 129 MET cc_start: 0.9671 (mtm) cc_final: 0.9471 (mtt) REVERT: C 154 MET cc_start: 0.8551 (ttm) cc_final: 0.7828 (ttm) REVERT: C 383 MET cc_start: 0.8568 (mpp) cc_final: 0.8321 (mpp) REVERT: C 393 GLN cc_start: 0.9233 (mt0) cc_final: 0.8885 (mp10) REVERT: F 201 MET cc_start: 0.9214 (mmm) cc_final: 0.8729 (mpp) REVERT: F 304 TYR cc_start: 0.8066 (t80) cc_final: 0.7601 (t80) REVERT: F 383 MET cc_start: 0.7412 (mpp) cc_final: 0.7167 (mpp) REVERT: H 100 PHE cc_start: 0.8620 (p90) cc_final: 0.8174 (p90) REVERT: H 106 MET cc_start: 0.8434 (ppp) cc_final: 0.8133 (ppp) REVERT: H 130 ASP cc_start: 0.9184 (t0) cc_final: 0.8914 (m-30) REVERT: H 326 MET cc_start: 0.9235 (mtt) cc_final: 0.8857 (ptp) REVERT: H 372 GLN cc_start: 0.8857 (mt0) cc_final: 0.8389 (mt0) REVERT: H 393 GLN cc_start: 0.8914 (mt0) cc_final: 0.8658 (mp10) REVERT: G 23 LEU cc_start: 0.8339 (tp) cc_final: 0.8040 (tp) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.3228 time to fit residues: 78.9276 Evaluate side-chains 117 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 214 optimal weight: 0.0870 chunk 226 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20961 Z= 0.304 Angle : 0.581 9.155 28259 Z= 0.316 Chirality : 0.043 0.221 3135 Planarity : 0.004 0.046 3581 Dihedral : 6.876 81.857 2914 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 1.29 (0.17), residues: 2492 helix: 1.75 (0.14), residues: 1307 sheet: -0.36 (0.25), residues: 428 loop : 0.16 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 158 HIS 0.008 0.001 HIS D 119 PHE 0.050 0.002 PHE B 234 TYR 0.020 0.002 TYR B 304 ARG 0.005 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 148 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.615 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 154 MET cc_start: 0.9186 (ttt) cc_final: 0.8501 (ttm) REVERT: A 201 MET cc_start: 0.8921 (ppp) cc_final: 0.8560 (ppp) REVERT: A 213 ARG cc_start: 0.9327 (mtp-110) cc_final: 0.9106 (tmm160) REVERT: A 226 PHE cc_start: 0.8958 (t80) cc_final: 0.8608 (t80) REVERT: A 304 TYR cc_start: 0.8018 (t80) cc_final: 0.7796 (t80) REVERT: A 366 LEU cc_start: 0.9746 (mt) cc_final: 0.9539 (mt) REVERT: A 436 MET cc_start: 0.8792 (mtp) cc_final: 0.8528 (mtp) REVERT: B 129 MET cc_start: 0.8823 (mpp) cc_final: 0.8494 (mpp) REVERT: B 154 MET cc_start: 0.9257 (ttt) cc_final: 0.8243 (ttt) REVERT: D 62 MET cc_start: 0.8613 (ttp) cc_final: 0.8312 (ttt) REVERT: C 44 HIS cc_start: 0.9019 (m170) cc_final: 0.8755 (m90) REVERT: C 126 MET cc_start: 0.9196 (mtm) cc_final: 0.8877 (pmm) REVERT: C 383 MET cc_start: 0.8614 (mpp) cc_final: 0.8339 (mpp) REVERT: C 393 GLN cc_start: 0.9278 (mt0) cc_final: 0.8918 (mp10) REVERT: F 201 MET cc_start: 0.9232 (mmm) cc_final: 0.8730 (mpp) REVERT: F 304 TYR cc_start: 0.8061 (t80) cc_final: 0.7662 (t80) REVERT: F 383 MET cc_start: 0.7450 (mpp) cc_final: 0.7009 (mpp) REVERT: H 106 MET cc_start: 0.8455 (ppp) cc_final: 0.8186 (ppp) REVERT: H 186 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8121 (tm-30) REVERT: H 326 MET cc_start: 0.9260 (mtt) cc_final: 0.8722 (ptp) REVERT: H 372 GLN cc_start: 0.8924 (mt0) cc_final: 0.8402 (mt0) REVERT: H 393 GLN cc_start: 0.9007 (mt0) cc_final: 0.8748 (mp10) REVERT: G 23 LEU cc_start: 0.8423 (tp) cc_final: 0.8103 (tp) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3427 time to fit residues: 79.4736 Evaluate side-chains 118 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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: 2.9990 chunk 146 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 167 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 ASN F 413 GLN H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20961 Z= 0.438 Angle : 0.712 8.773 28259 Z= 0.389 Chirality : 0.046 0.276 3135 Planarity : 0.005 0.049 3581 Dihedral : 7.486 79.623 2914 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % 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: 0.64 (0.17), residues: 2492 helix: 1.20 (0.14), residues: 1301 sheet: -0.67 (0.25), residues: 409 loop : -0.07 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 402 HIS 0.008 0.002 HIS B 32 PHE 0.050 0.002 PHE B 234 TYR 0.037 0.002 TYR D 35 ARG 0.007 0.001 ARG B 409 ********************** 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 141 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9263 (ttt) cc_final: 0.8450 (ttt) REVERT: A 201 MET cc_start: 0.9035 (ppp) cc_final: 0.8638 (ppp) REVERT: A 226 PHE cc_start: 0.8980 (t80) cc_final: 0.8731 (t80) REVERT: A 326 MET cc_start: 0.8929 (mmm) cc_final: 0.8088 (mmm) REVERT: A 436 MET cc_start: 0.8851 (mtp) cc_final: 0.8597 (mtp) REVERT: B 129 MET cc_start: 0.8889 (mpp) cc_final: 0.8550 (mpp) REVERT: B 154 MET cc_start: 0.9300 (ttt) cc_final: 0.7949 (ttt) REVERT: B 376 MET cc_start: 0.9537 (mtm) cc_final: 0.9248 (mtm) REVERT: D 62 MET cc_start: 0.8710 (ttp) cc_final: 0.7909 (tpp) REVERT: C 44 HIS cc_start: 0.9015 (m170) cc_final: 0.8780 (m90) REVERT: C 56 ARG cc_start: 0.9457 (mmp-170) cc_final: 0.9114 (mmm160) REVERT: C 126 MET cc_start: 0.9229 (mtm) cc_final: 0.8909 (pmm) REVERT: F 304 TYR cc_start: 0.8025 (t80) cc_final: 0.7647 (t80) REVERT: F 383 MET cc_start: 0.7207 (mpp) cc_final: 0.6665 (mpp) REVERT: F 436 MET cc_start: 0.7687 (mmm) cc_final: 0.7371 (mmm) REVERT: H 106 MET cc_start: 0.8493 (ppp) cc_final: 0.8208 (ppp) REVERT: H 326 MET cc_start: 0.9346 (mtt) cc_final: 0.8785 (ptp) REVERT: H 372 GLN cc_start: 0.8935 (mt0) cc_final: 0.8578 (mt0) REVERT: H 393 GLN cc_start: 0.9022 (mt0) cc_final: 0.8614 (mp10) REVERT: G 23 LEU cc_start: 0.8379 (tp) cc_final: 0.8022 (tp) REVERT: G 33 HIS cc_start: 0.9095 (m-70) cc_final: 0.8804 (m-70) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.3295 time to fit residues: 73.0392 Evaluate side-chains 106 residues out of total 2249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 185 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 HIS C 35 ASN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN G 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.064757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046724 restraints weight = 152284.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.047571 restraints weight = 89035.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047822 restraints weight = 59476.853| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20961 Z= 0.164 Angle : 0.514 9.857 28259 Z= 0.280 Chirality : 0.043 0.231 3135 Planarity : 0.003 0.044 3581 Dihedral : 6.673 83.945 2914 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2492 helix: 1.74 (0.14), residues: 1304 sheet: -0.35 (0.26), residues: 403 loop : 0.21 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 158 HIS 0.004 0.001 HIS G 119 PHE 0.036 0.001 PHE B 234 TYR 0.028 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: 3512.10 seconds wall clock time: 64 minutes 43.04 seconds (3883.04 seconds total)