Starting phenix.real_space_refine on Sun Oct 12 03:43:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v47_42967/10_2025/8v47_42967.map" } resolution = 4.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 78 5.16 5 C 13109 2.51 5 N 3449 2.21 5 O 3932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 5.29, per 1000 atoms: 0.26 Number of scatterers: 20580 At special positions: 0 Unit cell: (100.045, 163.625, 195.415, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 12 15.00 O 3932 8.00 N 3449 7.00 C 13109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 900.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.78 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: 4.05 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6488 1.34 - 1.46: 4096 1.46 - 1.58: 10233 1.58 - 1.69: 7 1.69 - 1.81: 137 Bond restraints: 20961 Sorted by residual: bond pdb=" O3A ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 1.592 1.527 0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 1.600 1.541 0.059 2.80e-02 1.28e+03 4.51e+00 bond pdb=" C VAL H 30 " pdb=" N ILE H 31 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.97e-02 2.58e+03 4.43e+00 bond pdb=" O3B ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 1.592 1.533 0.059 3.00e-02 1.11e+03 3.89e+00 bond pdb=" C LEU D 177 " pdb=" N PRO D 178 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.25e+00 ... (remaining 20956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 27633 2.21 - 4.41: 566 4.41 - 6.62: 50 6.62 - 8.82: 9 8.82 - 11.03: 1 Bond angle restraints: 28259 Sorted by residual: angle pdb=" C ASP A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 121.54 128.76 -7.22 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA LEU A 374 " pdb=" CB LEU A 374 " pdb=" CG LEU A 374 " ideal model delta sigma weight residual 116.30 105.27 11.03 3.50e+00 8.16e-02 9.93e+00 angle pdb=" C PHE F 342 " pdb=" N ASP F 343 " pdb=" CA ASP F 343 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.81e+00 angle pdb=" C ASP C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta sigma weight residual 125.02 130.15 -5.13 1.76e+00 3.23e-01 8.49e+00 angle pdb=" C ASP F 83 " pdb=" N GLU F 84 " pdb=" CA GLU F 84 " ideal model delta sigma weight residual 125.02 130.08 -5.06 1.76e+00 3.23e-01 8.27e+00 ... (remaining 28254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11945 17.74 - 35.48: 621 35.48 - 53.22: 141 53.22 - 70.96: 41 70.96 - 88.70: 9 Dihedral angle restraints: 12757 sinusoidal: 5251 harmonic: 7506 Sorted by residual: dihedral pdb=" CA ASP H 23 " pdb=" C ASP H 23 " pdb=" N PHE H 24 " pdb=" CA PHE H 24 " ideal model delta harmonic sigma weight residual 180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS H 354 " pdb=" C LYS H 354 " pdb=" N PHE H 355 " pdb=" CA PHE H 355 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA SER H 427 " pdb=" C SER H 427 " pdb=" N ILE H 428 " pdb=" CA ILE H 428 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 12754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2072 0.045 - 0.089: 773 0.089 - 0.134: 249 0.134 - 0.178: 34 0.178 - 0.223: 7 Chirality restraints: 3135 Sorted by residual: chirality pdb=" CB VAL D 255 " pdb=" CA VAL D 255 " pdb=" CG1 VAL D 255 " pdb=" CG2 VAL D 255 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE G 204 " pdb=" N ILE G 204 " pdb=" C ILE G 204 " pdb=" CB ILE G 204 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3132 not shown) Planarity restraints: 3581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 223 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.70e+00 pdb=" C SER B 223 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 223 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG B 224 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 312 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C GLN C 312 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN C 312 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 313 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C LEU D 196 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE D 197 " 0.014 2.00e-02 2.50e+03 ... (remaining 3578 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5558 2.80 - 3.32: 19129 3.32 - 3.85: 35012 3.85 - 4.37: 40018 4.37 - 4.90: 69232 Nonbonded interactions: 168949 Sorted by model distance: nonbonded pdb=" O LYS D 60 " pdb=" OG SER D 63 " model vdw 2.275 3.040 nonbonded pdb=" O TYR C 221 " pdb=" OG1 THR C 225 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR G 11 " pdb=" OD2 ASP G 50 " model vdw 2.288 3.040 nonbonded pdb=" O SER H 328 " pdb=" OG SER H 331 " model vdw 2.302 3.040 nonbonded pdb=" O PRO C 149 " pdb=" NH1 ARG C 152 " model vdw 2.316 3.120 ... (remaining 168944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) selection = (chain 'B' and (resid 3 through 236 or resid 249 through 288 or resid 295 throug \ h 444)) selection = (chain 'C' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) selection = (chain 'F' and (resid 3 through 112 or resid 126 through 162 or resid 175 throug \ h 236 or resid 249 through 270 or (resid 271 through 272 and (name N or name CA \ or name C or name O or name CB )) or resid 273 through 310 or (resid 311 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name NE \ or name NH1 or name NH2)) or resid 312 through 342 or resid 348 through 444)) } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.600 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20961 Z= 0.286 Angle : 0.787 11.028 28259 Z= 0.448 Chirality : 0.051 0.223 3135 Planarity : 0.006 0.053 3581 Dihedral : 12.058 88.705 7881 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.85 % Allowed : 4.81 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 78 TYR 0.026 0.003 TYR A 69 PHE 0.031 0.003 PHE B 191 TRP 0.025 0.003 TRP A 402 HIS 0.010 0.002 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00604 (20961) covalent geometry : angle 0.78670 (28259) hydrogen bonds : bond 0.15770 ( 1122) hydrogen bonds : angle 6.35523 ( 3210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 0.783 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: A 39 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9056 (mtmm) REVERT: A 154 MET cc_start: 0.9209 (ttt) cc_final: 0.8944 (ttm) REVERT: A 213 ARG cc_start: 0.9189 (mtp-110) cc_final: 0.8983 (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: 0.7974 (ttm) REVERT: A 436 MET cc_start: 0.8740 (mtp) cc_final: 0.8429 (mtp) REVERT: B 3 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7692 (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: 0.8441 (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: 0.8655 (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 136 GLN cc_start: 0.9748 (tt0) cc_final: 0.9519 (tp-100) REVERT: D 212 PHE cc_start: 0.9524 (t80) cc_final: 0.9213 (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: 0.8779 (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: 0.8727 (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: 0.7771 (t80) 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: 0.9304 (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: 0.7885 (t80) outliers start: 64 outliers final: 17 residues processed: 384 average time/residue: 0.1938 time to fit residues: 107.2305 Evaluate side-chains 191 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 262 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 32 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 268 ASN C 315 GLN C 324 ASN F 32 HIS F 262 GLN F 268 ASN G 190 ASN G 306 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.066203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046401 restraints weight = 149264.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.047611 restraints weight = 82150.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.048323 restraints weight = 56128.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.048839 restraints weight = 44186.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049077 restraints weight = 38013.735| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20961 Z= 0.207 Angle : 0.581 11.142 28259 Z= 0.317 Chirality : 0.043 0.195 3135 Planarity : 0.004 0.050 3581 Dihedral : 8.140 87.519 2914 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.17), residues: 2492 helix: 1.61 (0.14), residues: 1275 sheet: 0.19 (0.25), residues: 421 loop : -0.11 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 78 TYR 0.015 0.002 TYR C 18 PHE 0.049 0.002 PHE B 234 TRP 0.013 0.001 TRP A 402 HIS 0.009 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00430 (20961) covalent geometry : angle 0.58063 (28259) hydrogen bonds : bond 0.03887 ( 1122) hydrogen bonds : angle 4.63961 ( 3210) *********************** 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 209 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8600 (ppp) cc_final: 0.8256 (ppp) REVERT: A 213 ARG cc_start: 0.9185 (mtp-110) cc_final: 0.8944 (tmm160) REVERT: A 226 PHE cc_start: 0.9188 (t80) cc_final: 0.8980 (t80) REVERT: A 310 ASP cc_start: 0.9215 (m-30) cc_final: 0.8940 (m-30) REVERT: A 317 LYS cc_start: 0.9569 (tttm) cc_final: 0.9335 (ptpp) REVERT: A 383 MET cc_start: 0.8522 (mtp) cc_final: 0.8290 (ttm) REVERT: B 154 MET cc_start: 0.8988 (ttp) cc_final: 0.8714 (ttm) REVERT: B 201 MET cc_start: 0.8594 (mpp) cc_final: 0.8299 (mpp) REVERT: D 62 MET cc_start: 0.8319 (ttp) cc_final: 0.8043 (ttt) REVERT: D 212 PHE cc_start: 0.9239 (t80) cc_final: 0.8823 (t80) REVERT: C 44 HIS cc_start: 0.8897 (m170) cc_final: 0.8688 (m90) REVERT: C 126 MET cc_start: 0.8862 (mtm) cc_final: 0.8622 (pmm) REVERT: C 129 MET cc_start: 0.9455 (mtm) cc_final: 0.9212 (mtt) REVERT: C 187 LEU cc_start: 0.9007 (mt) cc_final: 0.8655 (mt) REVERT: C 326 MET cc_start: 0.8803 (ptp) cc_final: 0.8602 (ptp) REVERT: C 338 MET cc_start: 0.8866 (ttm) cc_final: 0.8529 (tmm) REVERT: C 393 GLN cc_start: 0.9157 (mt0) cc_final: 0.8809 (mp10) REVERT: C 410 MET cc_start: 0.9008 (mtp) cc_final: 0.8738 (mtp) REVERT: F 201 MET cc_start: 0.9517 (mmm) cc_final: 0.9299 (mpp) REVERT: F 304 TYR cc_start: 0.9111 (t80) cc_final: 0.8500 (t80) REVERT: F 326 MET cc_start: 0.8452 (ptp) cc_final: 0.8227 (ptm) REVERT: F 383 MET cc_start: 0.8095 (mpp) cc_final: 0.7552 (mpp) REVERT: H 100 PHE cc_start: 0.8880 (p90) cc_final: 0.8678 (p90) REVERT: H 106 MET cc_start: 0.8646 (ppp) cc_final: 0.8310 (ppp) REVERT: H 326 MET cc_start: 0.9241 (mtt) cc_final: 0.9007 (mtp) REVERT: H 340 TYR cc_start: 0.8358 (p90) cc_final: 0.8112 (p90) REVERT: H 372 GLN cc_start: 0.9015 (mt0) cc_final: 0.8672 (mt0) REVERT: H 393 GLN cc_start: 0.9056 (mt0) cc_final: 0.8693 (mp10) REVERT: H 432 TYR cc_start: 0.8210 (m-80) cc_final: 0.8007 (m-80) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1722 time to fit residues: 53.3631 Evaluate side-chains 128 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 249 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN D 263 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.065697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.045900 restraints weight = 149893.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047137 restraints weight = 82415.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047907 restraints weight = 55925.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048311 restraints weight = 43663.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.048587 restraints weight = 37976.407| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20961 Z= 0.175 Angle : 0.531 9.660 28259 Z= 0.290 Chirality : 0.042 0.159 3135 Planarity : 0.004 0.067 3581 Dihedral : 7.399 79.331 2914 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.17), residues: 2492 helix: 1.80 (0.14), residues: 1291 sheet: 0.11 (0.26), residues: 404 loop : -0.08 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 144 TYR 0.014 0.001 TYR C 304 PHE 0.021 0.001 PHE H 191 TRP 0.008 0.001 TRP A 402 HIS 0.010 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00367 (20961) covalent geometry : angle 0.53073 (28259) hydrogen bonds : bond 0.03490 ( 1122) hydrogen bonds : angle 4.37706 ( 3210) *********************** 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 176 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9110 (mmm) cc_final: 0.8635 (mpp) REVERT: A 201 MET cc_start: 0.8638 (ppp) cc_final: 0.8243 (ppp) REVERT: A 213 ARG cc_start: 0.9215 (mtp-110) cc_final: 0.8967 (tmm160) REVERT: A 226 PHE cc_start: 0.9203 (t80) cc_final: 0.8994 (t80) REVERT: A 310 ASP cc_start: 0.9283 (m-30) cc_final: 0.9020 (m-30) REVERT: A 317 LYS cc_start: 0.9582 (tttm) cc_final: 0.9347 (ptpp) REVERT: A 383 MET cc_start: 0.8574 (mtp) cc_final: 0.8341 (ttm) REVERT: B 338 MET cc_start: 0.8183 (ttt) cc_final: 0.7774 (ttt) REVERT: D 62 MET cc_start: 0.8393 (ttp) cc_final: 0.8090 (ttt) REVERT: D 212 PHE cc_start: 0.9250 (t80) cc_final: 0.8796 (t80) REVERT: C 126 MET cc_start: 0.8912 (mtm) cc_final: 0.8684 (pmm) REVERT: C 129 MET cc_start: 0.9471 (mtm) cc_final: 0.9247 (mtt) REVERT: C 187 LEU cc_start: 0.9031 (mt) cc_final: 0.8675 (mt) REVERT: C 393 GLN cc_start: 0.9150 (mt0) cc_final: 0.8820 (mp10) REVERT: F 201 MET cc_start: 0.9506 (mmm) cc_final: 0.9288 (mpp) REVERT: F 304 TYR cc_start: 0.9071 (t80) cc_final: 0.8480 (t80) REVERT: F 326 MET cc_start: 0.8573 (ptp) cc_final: 0.8321 (ptm) REVERT: F 383 MET cc_start: 0.8041 (mpp) cc_final: 0.7456 (mpp) REVERT: F 436 MET cc_start: 0.6705 (tpt) cc_final: 0.6478 (mmm) REVERT: H 100 PHE cc_start: 0.8879 (p90) cc_final: 0.8556 (p90) REVERT: H 106 MET cc_start: 0.8647 (ppp) cc_final: 0.8320 (ppp) REVERT: H 326 MET cc_start: 0.9286 (mtt) cc_final: 0.9024 (mtp) REVERT: H 340 TYR cc_start: 0.8334 (p90) cc_final: 0.8038 (p90) REVERT: H 372 GLN cc_start: 0.8959 (mt0) cc_final: 0.8523 (mt0) REVERT: H 393 GLN cc_start: 0.9079 (mt0) cc_final: 0.8684 (mp10) REVERT: G 23 LEU cc_start: 0.9363 (tp) cc_final: 0.9136 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1692 time to fit residues: 45.3281 Evaluate side-chains 126 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 135 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 241 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 250 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** B 44 HIS D 306 ASN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 HIS H 19 ASN H 324 ASN ** H 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.062912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.043125 restraints weight = 155565.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.044192 restraints weight = 85586.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044833 restraints weight = 58628.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.045250 restraints weight = 46734.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.045462 restraints weight = 41153.052| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 20961 Z= 0.398 Angle : 0.806 11.619 28259 Z= 0.435 Chirality : 0.047 0.171 3135 Planarity : 0.006 0.061 3581 Dihedral : 7.937 79.008 2914 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2492 helix: 1.06 (0.14), residues: 1292 sheet: -0.41 (0.24), residues: 408 loop : -0.35 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 409 TYR 0.028 0.003 TYR D 35 PHE 0.044 0.003 PHE B 234 TRP 0.016 0.002 TRP F 402 HIS 0.009 0.002 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00821 (20961) covalent geometry : angle 0.80600 (28259) hydrogen bonds : bond 0.04602 ( 1122) hydrogen bonds : angle 5.35600 ( 3210) *********************** 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 141 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.842 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: 0.8770 (ttp) cc_final: 0.6724 (ttt) REVERT: A 201 MET cc_start: 0.8823 (ppp) cc_final: 0.8456 (ppp) REVERT: A 310 ASP cc_start: 0.9372 (m-30) cc_final: 0.9164 (m-30) REVERT: B 154 MET cc_start: 0.9082 (ttt) cc_final: 0.7420 (ttt) REVERT: D 62 MET cc_start: 0.8418 (ttp) cc_final: 0.8059 (ttt) REVERT: C 44 HIS cc_start: 0.8876 (m90) cc_final: 0.8572 (m90) REVERT: C 187 LEU cc_start: 0.9085 (mt) cc_final: 0.8747 (mt) REVERT: F 158 TRP cc_start: 0.7597 (t60) cc_final: 0.7375 (t-100) REVERT: F 304 TYR cc_start: 0.9061 (t80) cc_final: 0.8467 (t80) REVERT: F 326 MET cc_start: 0.8569 (ptp) cc_final: 0.7962 (ppp) REVERT: F 383 MET cc_start: 0.7672 (mpp) cc_final: 0.7152 (mpp) REVERT: H 100 PHE cc_start: 0.9116 (p90) cc_final: 0.8802 (p90) REVERT: H 106 MET cc_start: 0.8568 (ppp) cc_final: 0.8169 (ppp) REVERT: H 326 MET cc_start: 0.9293 (mtt) cc_final: 0.8964 (mtp) REVERT: H 372 GLN cc_start: 0.9021 (mt0) cc_final: 0.8658 (mt0) REVERT: H 393 GLN cc_start: 0.9077 (mt0) cc_final: 0.8657 (mp10) REVERT: G 23 LEU cc_start: 0.9362 (tp) cc_final: 0.9151 (tp) REVERT: G 33 HIS cc_start: 0.9543 (m-70) cc_final: 0.9343 (m-70) outliers start: 3 outliers final: 2 residues processed: 141 average time/residue: 0.1577 time to fit residues: 34.6905 Evaluate side-chains 109 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN B 44 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN H 19 ASN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.065407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.047022 restraints weight = 151502.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048155 restraints weight = 87038.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.048511 restraints weight = 50876.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048638 restraints weight = 47833.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048671 restraints weight = 42724.446| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20961 Z= 0.113 Angle : 0.492 10.145 28259 Z= 0.271 Chirality : 0.042 0.170 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.797 71.538 2914 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.04 % Allowed : 1.78 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.17), residues: 2492 helix: 1.75 (0.14), residues: 1298 sheet: -0.10 (0.26), residues: 392 loop : 0.07 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.015 0.001 TYR C 278 PHE 0.031 0.001 PHE B 234 TRP 0.008 0.001 TRP C 158 HIS 0.013 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00237 (20961) covalent geometry : angle 0.49201 (28259) hydrogen bonds : bond 0.03229 ( 1122) hydrogen bonds : angle 4.39549 ( 3210) *********************** 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 164 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.825 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: 0.9242 (mmm) cc_final: 0.8787 (mpp) REVERT: A 201 MET cc_start: 0.8648 (ppp) cc_final: 0.8280 (ppp) REVERT: A 310 ASP cc_start: 0.9357 (m-30) cc_final: 0.9148 (m-30) REVERT: B 129 MET cc_start: 0.8707 (mpp) cc_final: 0.8300 (mpp) REVERT: B 326 MET cc_start: 0.8763 (tpp) cc_final: 0.8451 (tpp) REVERT: D 62 MET cc_start: 0.8316 (ttp) cc_final: 0.7965 (ttt) REVERT: C 44 HIS cc_start: 0.8969 (m90) cc_final: 0.8658 (m-70) REVERT: C 187 LEU cc_start: 0.8945 (mt) cc_final: 0.8495 (mt) REVERT: F 158 TRP cc_start: 0.7378 (t60) cc_final: 0.7086 (t-100) REVERT: F 304 TYR cc_start: 0.9202 (t80) cc_final: 0.8355 (t80) REVERT: F 383 MET cc_start: 0.7872 (mpp) cc_final: 0.7571 (mpp) REVERT: H 100 PHE cc_start: 0.9110 (p90) cc_final: 0.8847 (p90) REVERT: H 106 MET cc_start: 0.8552 (ppp) cc_final: 0.8227 (ppp) REVERT: H 326 MET cc_start: 0.9349 (mtt) cc_final: 0.9139 (mmm) REVERT: H 372 GLN cc_start: 0.8977 (mt0) cc_final: 0.8619 (mt0) REVERT: H 393 GLN cc_start: 0.8912 (mt0) cc_final: 0.8604 (mp10) REVERT: G 33 HIS cc_start: 0.9528 (m-70) cc_final: 0.9246 (m-70) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1550 time to fit residues: 39.9013 Evaluate side-chains 117 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 211 optimal weight: 7.9990 chunk 210 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 250 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 91 optimal weight: 0.0270 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 403 GLN ** G 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.064684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.046050 restraints weight = 153251.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047208 restraints weight = 93827.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047553 restraints weight = 54080.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047695 restraints weight = 50239.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047634 restraints weight = 43659.666| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4287 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= 0.162 Angle : 0.523 9.613 28259 Z= 0.286 Chirality : 0.042 0.189 3135 Planarity : 0.003 0.043 3581 Dihedral : 6.768 73.662 2914 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.13 % Allowed : 1.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.17), residues: 2492 helix: 1.82 (0.14), residues: 1294 sheet: -0.24 (0.24), residues: 424 loop : 0.12 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.016 0.002 TYR B 304 PHE 0.026 0.001 PHE B 234 TRP 0.010 0.001 TRP C 158 HIS 0.014 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00343 (20961) covalent geometry : angle 0.52285 (28259) hydrogen bonds : bond 0.03284 ( 1122) hydrogen bonds : angle 4.39426 ( 3210) *********************** 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 to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9208 (mmm) cc_final: 0.8779 (mpp) REVERT: A 154 MET cc_start: 0.8702 (ttm) cc_final: 0.8485 (ttm) REVERT: A 201 MET cc_start: 0.8695 (ppp) cc_final: 0.8336 (ppp) REVERT: B 106 MET cc_start: 0.9181 (mtm) cc_final: 0.8935 (ptp) REVERT: B 129 MET cc_start: 0.8774 (mpp) cc_final: 0.8343 (mpp) REVERT: B 338 MET cc_start: 0.8637 (ttt) cc_final: 0.8424 (ttm) REVERT: D 62 MET cc_start: 0.8386 (ttp) cc_final: 0.8032 (ttt) REVERT: C 44 HIS cc_start: 0.9023 (m90) cc_final: 0.8703 (m-70) REVERT: C 187 LEU cc_start: 0.8937 (mt) cc_final: 0.8698 (mt) REVERT: F 158 TRP cc_start: 0.7586 (t60) cc_final: 0.7156 (t-100) REVERT: F 304 TYR cc_start: 0.9237 (t80) cc_final: 0.8413 (t80) REVERT: F 383 MET cc_start: 0.7916 (mpp) cc_final: 0.7586 (mpp) REVERT: H 100 PHE cc_start: 0.9196 (p90) cc_final: 0.8919 (p90) REVERT: H 106 MET cc_start: 0.8563 (ppp) cc_final: 0.8249 (ppp) REVERT: H 209 GLU cc_start: 0.9275 (OUTLIER) cc_final: 0.9074 (pm20) REVERT: H 372 GLN cc_start: 0.8989 (mt0) cc_final: 0.8486 (mt0) REVERT: H 393 GLN cc_start: 0.9030 (mt0) cc_final: 0.8723 (mp10) REVERT: G 23 LEU cc_start: 0.9311 (tp) cc_final: 0.9011 (tp) outliers start: 3 outliers final: 0 residues processed: 152 average time/residue: 0.1555 time to fit residues: 37.3655 Evaluate side-chains 119 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 229 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 151 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 315 GLN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN H 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.064684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046149 restraints weight = 153213.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047149 restraints weight = 93847.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047520 restraints weight = 57070.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.047654 restraints weight = 48359.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.047649 restraints weight = 44652.472| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20961 Z= 0.155 Angle : 0.507 8.355 28259 Z= 0.279 Chirality : 0.042 0.218 3135 Planarity : 0.003 0.042 3581 Dihedral : 6.681 78.246 2914 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.04 % Allowed : 0.98 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.17), residues: 2492 helix: 1.87 (0.14), residues: 1296 sheet: -0.34 (0.25), residues: 403 loop : 0.13 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.016 0.001 TYR B 304 PHE 0.051 0.001 PHE B 234 TRP 0.009 0.001 TRP G 287 HIS 0.017 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00327 (20961) covalent geometry : angle 0.50663 (28259) hydrogen bonds : bond 0.03206 ( 1122) hydrogen bonds : angle 4.37974 ( 3210) *********************** 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 147 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9194 (mmm) cc_final: 0.8780 (mpp) REVERT: A 201 MET cc_start: 0.8700 (ppp) cc_final: 0.8345 (ppp) REVERT: A 326 MET cc_start: 0.8650 (mmm) cc_final: 0.8281 (mmm) REVERT: D 62 MET cc_start: 0.8394 (ttp) cc_final: 0.8025 (ttt) REVERT: C 44 HIS cc_start: 0.9017 (m90) cc_final: 0.8640 (m90) REVERT: C 410 MET cc_start: 0.8979 (mtp) cc_final: 0.8702 (mtp) REVERT: F 158 TRP cc_start: 0.7603 (t60) cc_final: 0.7124 (t-100) REVERT: F 304 TYR cc_start: 0.9215 (t80) cc_final: 0.8341 (t80) REVERT: F 383 MET cc_start: 0.7926 (mpp) cc_final: 0.7595 (mpp) REVERT: F 436 MET cc_start: 0.7329 (tpt) cc_final: 0.6964 (mmm) REVERT: H 130 ASP cc_start: 0.9315 (t0) cc_final: 0.8964 (m-30) REVERT: H 326 MET cc_start: 0.9040 (mmm) cc_final: 0.8741 (ptp) REVERT: H 372 GLN cc_start: 0.8972 (mt0) cc_final: 0.8413 (mt0) REVERT: H 393 GLN cc_start: 0.9080 (mt0) cc_final: 0.8768 (mp10) REVERT: G 23 LEU cc_start: 0.9307 (tp) cc_final: 0.9010 (tp) REVERT: G 33 HIS cc_start: 0.9548 (m-70) cc_final: 0.9186 (m90) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.1566 time to fit residues: 36.0935 Evaluate side-chains 113 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 202 optimal weight: 0.0370 chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 150 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.4662 ------------------------------------------------------------------------------- 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** H 19 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.065419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046935 restraints weight = 152458.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047854 restraints weight = 94332.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048120 restraints weight = 55939.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.048296 restraints weight = 50884.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048337 restraints weight = 47879.079| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20961 Z= 0.120 Angle : 0.491 10.715 28259 Z= 0.271 Chirality : 0.042 0.236 3135 Planarity : 0.003 0.041 3581 Dihedral : 6.494 82.168 2914 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.17), residues: 2492 helix: 1.93 (0.15), residues: 1299 sheet: -0.24 (0.25), residues: 409 loop : 0.19 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.013 0.001 TYR B 304 PHE 0.047 0.001 PHE B 234 TRP 0.009 0.001 TRP G 287 HIS 0.017 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00254 (20961) covalent geometry : angle 0.49132 (28259) hydrogen bonds : bond 0.03134 ( 1122) hydrogen bonds : angle 4.28554 ( 3210) *********************** 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 155 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9222 (mmm) cc_final: 0.8784 (mpp) REVERT: A 201 MET cc_start: 0.8658 (ppp) cc_final: 0.8330 (ppp) REVERT: B 106 MET cc_start: 0.9137 (mtm) cc_final: 0.8918 (ptp) REVERT: B 129 MET cc_start: 0.8779 (mpp) cc_final: 0.8407 (mpp) REVERT: B 326 MET cc_start: 0.8771 (tpp) cc_final: 0.8536 (tpp) REVERT: D 62 MET cc_start: 0.8409 (ttp) cc_final: 0.8079 (ttt) REVERT: D 212 PHE cc_start: 0.9190 (t80) cc_final: 0.8907 (t80) REVERT: C 44 HIS cc_start: 0.9043 (m90) cc_final: 0.8671 (m90) REVERT: C 410 MET cc_start: 0.8964 (mtp) cc_final: 0.8693 (mtp) REVERT: F 209 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8827 (tm-30) REVERT: F 304 TYR cc_start: 0.9180 (t80) cc_final: 0.8293 (t80) REVERT: F 383 MET cc_start: 0.7920 (mpp) cc_final: 0.7593 (mpp) REVERT: F 436 MET cc_start: 0.7288 (tpt) cc_final: 0.6899 (mmm) REVERT: H 106 MET cc_start: 0.8323 (ppp) cc_final: 0.8076 (ppp) REVERT: H 130 ASP cc_start: 0.9325 (t0) cc_final: 0.9027 (m-30) REVERT: H 326 MET cc_start: 0.9436 (mtt) cc_final: 0.9102 (mtp) REVERT: H 372 GLN cc_start: 0.8977 (mt0) cc_final: 0.8417 (mt0) REVERT: H 393 GLN cc_start: 0.9008 (mt0) cc_final: 0.8718 (mp10) REVERT: G 23 LEU cc_start: 0.9327 (tp) cc_final: 0.9055 (tp) REVERT: G 33 HIS cc_start: 0.9571 (m-70) cc_final: 0.9358 (m90) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.1599 time to fit residues: 38.4046 Evaluate side-chains 124 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 232 optimal weight: 20.0000 chunk 68 optimal weight: 0.1980 chunk 19 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.065688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047418 restraints weight = 152887.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.048274 restraints weight = 90486.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048797 restraints weight = 55686.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048914 restraints weight = 45916.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.048992 restraints weight = 43736.762| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20961 Z= 0.113 Angle : 0.480 9.000 28259 Z= 0.264 Chirality : 0.042 0.237 3135 Planarity : 0.003 0.052 3581 Dihedral : 6.355 87.244 2914 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.17), residues: 2492 helix: 1.99 (0.15), residues: 1299 sheet: -0.05 (0.26), residues: 403 loop : 0.17 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 213 TYR 0.042 0.001 TYR C 304 PHE 0.039 0.001 PHE B 234 TRP 0.010 0.001 TRP C 158 HIS 0.015 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00240 (20961) covalent geometry : angle 0.47975 (28259) hydrogen bonds : bond 0.03054 ( 1122) hydrogen bonds : angle 4.22896 ( 3210) *********************** 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 151 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8702 (ppp) cc_final: 0.8333 (ppp) REVERT: A 304 TYR cc_start: 0.9076 (t80) cc_final: 0.8856 (t80) REVERT: A 326 MET cc_start: 0.8682 (mmm) cc_final: 0.8270 (mmm) REVERT: B 106 MET cc_start: 0.9148 (mtm) cc_final: 0.8927 (ptp) REVERT: B 129 MET cc_start: 0.8825 (mpp) cc_final: 0.8478 (mpp) REVERT: B 154 MET cc_start: 0.8735 (ptm) cc_final: 0.7254 (ptm) REVERT: D 62 MET cc_start: 0.8418 (ttp) cc_final: 0.8097 (ttt) REVERT: D 212 PHE cc_start: 0.9198 (t80) cc_final: 0.8958 (t80) REVERT: C 44 HIS cc_start: 0.9059 (m90) cc_final: 0.8712 (m90) REVERT: C 187 LEU cc_start: 0.9219 (mt) cc_final: 0.8864 (mt) REVERT: C 338 MET cc_start: 0.9010 (ttp) cc_final: 0.8463 (tmm) REVERT: C 393 GLN cc_start: 0.9166 (mt0) cc_final: 0.8825 (mp10) REVERT: F 209 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8802 (tm-30) REVERT: F 304 TYR cc_start: 0.9166 (t80) cc_final: 0.8274 (t80) REVERT: F 383 MET cc_start: 0.7877 (mpp) cc_final: 0.7385 (mpp) REVERT: F 436 MET cc_start: 0.7200 (tpt) cc_final: 0.6781 (mmm) REVERT: H 100 PHE cc_start: 0.8887 (p90) cc_final: 0.8271 (p90) REVERT: H 106 MET cc_start: 0.8327 (ppp) cc_final: 0.8106 (ppp) REVERT: H 130 ASP cc_start: 0.9316 (t0) cc_final: 0.9016 (m-30) REVERT: H 326 MET cc_start: 0.9497 (mtt) cc_final: 0.9048 (mtt) REVERT: H 372 GLN cc_start: 0.8998 (mt0) cc_final: 0.8486 (mt0) REVERT: H 393 GLN cc_start: 0.9049 (mt0) cc_final: 0.8708 (mp10) REVERT: G 23 LEU cc_start: 0.9334 (tp) cc_final: 0.9063 (tp) REVERT: G 33 HIS cc_start: 0.9561 (m-70) cc_final: 0.9345 (m90) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1600 time to fit residues: 37.4364 Evaluate side-chains 122 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 158 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 73 optimal weight: 0.3980 chunk 219 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.065855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046354 restraints weight = 152737.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.047557 restraints weight = 83393.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.048305 restraints weight = 56668.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.048654 restraints weight = 44664.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048935 restraints weight = 39297.627| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20961 Z= 0.116 Angle : 0.490 11.946 28259 Z= 0.269 Chirality : 0.042 0.213 3135 Planarity : 0.003 0.052 3581 Dihedral : 6.277 88.228 2914 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.17), residues: 2492 helix: 2.05 (0.15), residues: 1295 sheet: -0.01 (0.26), residues: 408 loop : 0.22 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.021 0.001 TYR G 6 PHE 0.041 0.001 PHE B 234 TRP 0.010 0.001 TRP C 158 HIS 0.016 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00246 (20961) covalent geometry : angle 0.49047 (28259) hydrogen bonds : bond 0.03068 ( 1122) hydrogen bonds : angle 4.20020 ( 3210) ********************** 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 150 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.764 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 201 MET cc_start: 0.8685 (ppp) cc_final: 0.8325 (ppp) REVERT: A 326 MET cc_start: 0.8652 (mmm) cc_final: 0.7919 (mmm) REVERT: B 129 MET cc_start: 0.8804 (mpp) cc_final: 0.8453 (mpp) REVERT: D 62 MET cc_start: 0.8334 (ttp) cc_final: 0.8030 (ttt) REVERT: C 44 HIS cc_start: 0.9006 (m90) cc_final: 0.8632 (m90) REVERT: C 187 LEU cc_start: 0.9210 (mt) cc_final: 0.8897 (mt) REVERT: C 338 MET cc_start: 0.8741 (ttp) cc_final: 0.8389 (tmm) REVERT: C 393 GLN cc_start: 0.9139 (mt0) cc_final: 0.8825 (mp10) REVERT: F 209 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8778 (tm-30) REVERT: F 383 MET cc_start: 0.7920 (mpp) cc_final: 0.7422 (mpp) REVERT: F 436 MET cc_start: 0.7555 (tpt) cc_final: 0.7202 (mmm) REVERT: H 106 MET cc_start: 0.8298 (ppp) cc_final: 0.8031 (ppp) REVERT: H 130 ASP cc_start: 0.9127 (t0) cc_final: 0.8914 (m-30) REVERT: H 326 MET cc_start: 0.9423 (mtt) cc_final: 0.8923 (mtt) REVERT: H 372 GLN cc_start: 0.8933 (mt0) cc_final: 0.8423 (mt0) REVERT: H 393 GLN cc_start: 0.9068 (mt0) cc_final: 0.8741 (mp10) REVERT: G 23 LEU cc_start: 0.9348 (tp) cc_final: 0.9078 (tp) REVERT: G 191 ASP cc_start: 0.8746 (m-30) cc_final: 0.8313 (t0) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1611 time to fit residues: 37.0290 Evaluate side-chains 117 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.065461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.046952 restraints weight = 152895.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.047812 restraints weight = 92381.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048322 restraints weight = 57370.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048467 restraints weight = 47380.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.048483 restraints weight = 43345.075| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20961 Z= 0.144 Angle : 0.517 10.045 28259 Z= 0.285 Chirality : 0.042 0.222 3135 Planarity : 0.003 0.052 3581 Dihedral : 6.351 86.756 2914 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.04 % Allowed : 0.13 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.17), residues: 2492 helix: 1.99 (0.15), residues: 1302 sheet: -0.13 (0.26), residues: 422 loop : 0.21 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 213 TYR 0.016 0.001 TYR G 11 PHE 0.041 0.001 PHE B 234 TRP 0.014 0.001 TRP C 158 HIS 0.010 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00306 (20961) covalent geometry : angle 0.51680 (28259) hydrogen bonds : bond 0.03237 ( 1122) hydrogen bonds : angle 4.32473 ( 3210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4028.56 seconds wall clock time: 70 minutes 31.77 seconds (4231.77 seconds total)