Starting phenix.real_space_refine on Fri Sep 19 00:36:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8voa_43369/09_2025/8voa_43369.map" } resolution = 4.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 140 5.16 5 C 13504 2.51 5 N 3654 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21459 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.24 Number of scatterers: 21459 At special positions: 0 Unit cell: (214.24, 105.06, 156.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 12 15.00 Mg 6 11.99 O 4143 8.00 N 3654 7.00 C 13504 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: 1.86 Conformation dependent library (CDL) restraints added in 852.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 57 sheets defined 41.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.518A pdb=" N LEU A 119 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.968A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.868A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 4.080A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.516A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.798A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.955A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.087A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.804A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.427A pdb=" N ARG C 62 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.603A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.760A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.666A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.897A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.006A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.722A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.817A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.877A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.880A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.747A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.976A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 4.026A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.253A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.804A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.885A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.597A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.044A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.649A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.827A pdb=" N MET E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.894A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.588A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.892A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.516A pdb=" N TYR E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.121A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.545A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.654A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.811A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.670A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.850A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 4.023A pdb=" N MET F 305 " --> pdb=" O GLY F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 353 removed outlier: 3.691A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 350 through 353' Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 373 removed outlier: 4.308A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.579A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.584A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 260 removed outlier: 4.181A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 296 removed outlier: 3.999A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 349 through 356 removed outlier: 4.142A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.559A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.839A pdb=" N ALA A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 113 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS A 121 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 189 removed outlier: 3.619A pdb=" N SER A 187 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.626A pdb=" N ARG A 167 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 165 " --> pdb=" O HIS A 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 217 removed outlier: 3.511A pdb=" N ALA A 222 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 217 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 348 removed outlier: 3.500A pdb=" N THR A 346 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.745A pdb=" N SER A 274 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA A 283 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.777A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 366 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.656A pdb=" N ARG A 408 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY A 396 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA A 406 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 414 through 419 Processing sheet with id=AB8, first strand: chain 'A' and resid 432 through 434 removed outlier: 5.629A pdb=" N TYR A 432 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 444 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.553A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 13.062A pdb=" N VAL A 461 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLY A 472 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS A 471 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A 480 " --> pdb=" O LYS A 471 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP A 473 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU A 478 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.553A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.919A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.834A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.834A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.611A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.628A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.436A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AE2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.898A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AE4, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.158A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 135 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE7, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.336A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 162 " --> pdb=" O MET F 176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.336A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F 161 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.741A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.516A pdb=" N VAL E 298 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.638A pdb=" N ALA F 29 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AF8, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.792A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU G 107 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AG1, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AG2, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.969A pdb=" N VAL G 298 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 238 through 241 913 hydrogen bonds defined for protein. 2355 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: 4.47 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4614 1.33 - 1.45: 4910 1.45 - 1.57: 12143 1.57 - 1.69: 18 1.69 - 1.81: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" N ILE G 75 " pdb=" CA ILE G 75 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.34e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" N MET E 355 " pdb=" CA MET E 355 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.48e+00 bond pdb=" N ILE G 76 " pdb=" CA ILE G 76 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.27e+00 bond pdb=" N ILE A 395 " pdb=" CA ILE A 395 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.17e-02 7.31e+03 8.20e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 28730 1.41 - 2.82: 740 2.82 - 4.23: 197 4.23 - 5.64: 60 5.64 - 7.05: 12 Bond angle restraints: 29739 Sorted by residual: angle pdb=" C LYS A 399 " pdb=" CA LYS A 399 " pdb=" CB LYS A 399 " ideal model delta sigma weight residual 116.54 111.57 4.97 1.15e+00 7.56e-01 1.87e+01 angle pdb=" CA GLY A 393 " pdb=" C GLY A 393 " pdb=" O GLY A 393 " ideal model delta sigma weight residual 121.04 118.00 3.04 7.90e-01 1.60e+00 1.48e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 113.07 107.94 5.13 1.37e+00 5.33e-01 1.40e+01 angle pdb=" N GLU E 205 " pdb=" CA GLU E 205 " pdb=" C GLU E 205 " ideal model delta sigma weight residual 112.54 108.08 4.46 1.22e+00 6.72e-01 1.34e+01 angle pdb=" CA PHE A 394 " pdb=" CB PHE A 394 " pdb=" CG PHE A 394 " ideal model delta sigma weight residual 113.80 117.31 -3.51 1.00e+00 1.00e+00 1.23e+01 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 12113 22.19 - 44.37: 925 44.37 - 66.56: 89 66.56 - 88.74: 26 88.74 - 110.93: 7 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.93 110.93 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -169.63 109.63 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -168.84 108.84 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2668 0.056 - 0.113: 549 0.113 - 0.169: 56 0.169 - 0.225: 6 0.225 - 0.282: 2 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA PHE A 394 " pdb=" N PHE A 394 " pdb=" C PHE A 394 " pdb=" CB PHE A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU E 205 " pdb=" N GLU E 205 " pdb=" C GLU E 205 " pdb=" CB GLU E 205 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE G 71 " pdb=" N ILE G 71 " pdb=" C ILE G 71 " pdb=" CB ILE G 71 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 101 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO E 102 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 393 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C GLY A 393 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 393 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 394 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 204 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C ALA E 204 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA E 204 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU E 205 " 0.009 2.00e-02 2.50e+03 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 225 2.52 - 3.12: 16481 3.12 - 3.71: 34165 3.71 - 4.31: 46884 4.31 - 4.90: 78587 Nonbonded interactions: 176342 Sorted by model distance: nonbonded pdb=" CE MET F 132 " pdb=" N TYR F 133 " model vdw 1.925 3.540 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 1.993 2.170 nonbonded pdb=" O2A ADP F 401 " pdb="MG MG F 402 " model vdw 2.096 2.170 nonbonded pdb=" O2A ADP D 401 " pdb="MG MG D 402 " model vdw 2.103 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.120 2.170 ... (remaining 176337 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' 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: 0.010 Normalize map: mean=0, sd=1: 5.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.220 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.004 0.059 21924 Z= 0.194 Angle : 0.612 7.047 29739 Z= 0.320 Chirality : 0.046 0.282 3281 Planarity : 0.004 0.076 3827 Dihedral : 14.998 110.928 8126 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 4.19 % Favored : 95.54 % 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: 0.13 (0.17), residues: 2691 helix: 0.37 (0.18), residues: 900 sheet: 0.40 (0.24), residues: 494 loop : -0.11 (0.19), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.018 0.001 TYR B 279 PHE 0.017 0.001 PHE A 394 TRP 0.015 0.002 TRP G 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00384 (21924) covalent geometry : angle 0.61214 (29739) hydrogen bonds : bond 0.21829 ( 896) hydrogen bonds : angle 7.70823 ( 2355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 399 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 PHE cc_start: 0.7930 (m-80) cc_final: 0.7515 (m-80) REVERT: A 252 GLU cc_start: 0.8478 (mp0) cc_final: 0.8164 (mp0) REVERT: A 285 GLN cc_start: 0.7749 (mp10) cc_final: 0.7426 (mp10) REVERT: B 119 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8376 (ptp) REVERT: B 153 LEU cc_start: 0.9189 (tp) cc_final: 0.8970 (tp) REVERT: B 191 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7898 (ttmt) REVERT: B 356 TRP cc_start: 0.8149 (m100) cc_final: 0.7246 (m100) REVERT: C 54 VAL cc_start: 0.8911 (t) cc_final: 0.8638 (m) REVERT: C 93 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8098 (tm-30) REVERT: C 121 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6976 (tm-30) REVERT: C 217 CYS cc_start: 0.8442 (m) cc_final: 0.7701 (m) REVERT: D 137 GLN cc_start: 0.7993 (mp10) cc_final: 0.7712 (mp10) REVERT: D 151 ILE cc_start: 0.8518 (mm) cc_final: 0.8265 (mt) REVERT: D 192 ILE cc_start: 0.8345 (tp) cc_final: 0.8056 (tp) REVERT: D 234 SER cc_start: 0.8221 (m) cc_final: 0.7700 (p) REVERT: D 291 LYS cc_start: 0.8009 (tttm) cc_final: 0.7337 (mmtt) REVERT: D 355 MET cc_start: 0.8542 (mtt) cc_final: 0.8217 (mmp) REVERT: D 373 LYS cc_start: 0.8391 (tptm) cc_final: 0.8045 (tptm) REVERT: E 149 THR cc_start: 0.8297 (p) cc_final: 0.8071 (t) REVERT: E 252 ASN cc_start: 0.8290 (p0) cc_final: 0.7943 (p0) REVERT: E 328 LYS cc_start: 0.8297 (pptt) cc_final: 0.7734 (ptmm) REVERT: E 356 TRP cc_start: 0.6258 (m100) cc_final: 0.5885 (m100) REVERT: F 81 ASP cc_start: 0.8777 (m-30) cc_final: 0.8539 (m-30) REVERT: F 149 THR cc_start: 0.8897 (p) cc_final: 0.8688 (p) REVERT: F 217 CYS cc_start: 0.8184 (m) cc_final: 0.7870 (m) REVERT: F 246 GLN cc_start: 0.7945 (mt0) cc_final: 0.7668 (mt0) REVERT: F 289 ILE cc_start: 0.8207 (mm) cc_final: 0.7939 (mt) REVERT: F 299 MET cc_start: 0.8091 (mtm) cc_final: 0.7714 (mtm) REVERT: F 355 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6744 (mpp) REVERT: G 76 ILE cc_start: 0.8356 (mt) cc_final: 0.7935 (mt) REVERT: G 121 GLN cc_start: 0.8375 (tt0) cc_final: 0.7905 (tm-30) REVERT: G 195 GLU cc_start: 0.7889 (tp30) cc_final: 0.7671 (tt0) REVERT: G 222 ASP cc_start: 0.8545 (t0) cc_final: 0.8240 (t0) REVERT: G 237 GLU cc_start: 0.8323 (mp0) cc_final: 0.8057 (mp0) REVERT: G 362 TYR cc_start: 0.7885 (t80) cc_final: 0.7624 (t80) outliers start: 6 outliers final: 1 residues processed: 399 average time/residue: 0.1456 time to fit residues: 90.0226 Evaluate side-chains 285 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 310 HIS D 111 ASN D 128 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 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 = 0.3566 r_free = 0.3566 target = 0.108288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089690 restraints weight = 51629.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.090863 restraints weight = 31465.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091740 restraints weight = 23144.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092218 restraints weight = 19634.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092359 restraints weight = 17500.891| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21924 Z= 0.151 Angle : 0.631 7.372 29739 Z= 0.315 Chirality : 0.046 0.185 3281 Planarity : 0.004 0.043 3827 Dihedral : 8.023 101.811 3057 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.62 % Allowed : 9.26 % Favored : 89.12 % 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: 0.26 (0.17), residues: 2691 helix: 0.38 (0.17), residues: 948 sheet: 0.55 (0.25), residues: 488 loop : 0.02 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 147 TYR 0.033 0.001 TYR F 198 PHE 0.013 0.001 PHE G 223 TRP 0.011 0.001 TRP G 356 HIS 0.011 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00347 (21924) covalent geometry : angle 0.63122 (29739) hydrogen bonds : bond 0.04410 ( 896) hydrogen bonds : angle 5.78204 ( 2355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7562 (mp10) cc_final: 0.7138 (mp10) REVERT: B 82 MET cc_start: 0.8224 (tpt) cc_final: 0.7080 (tmm) REVERT: B 198 TYR cc_start: 0.8843 (m-80) cc_final: 0.8576 (m-80) REVERT: B 227 MET cc_start: 0.8249 (mmm) cc_final: 0.7857 (mmm) REVERT: B 356 TRP cc_start: 0.7955 (m100) cc_final: 0.7512 (m100) REVERT: C 54 VAL cc_start: 0.8604 (t) cc_final: 0.8317 (m) REVERT: C 121 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6940 (tm-30) REVERT: C 132 MET cc_start: 0.8672 (ptt) cc_final: 0.8450 (ptt) REVERT: C 217 CYS cc_start: 0.7946 (m) cc_final: 0.7348 (m) REVERT: D 192 ILE cc_start: 0.8846 (tp) cc_final: 0.8550 (tp) REVERT: D 234 SER cc_start: 0.8270 (m) cc_final: 0.7590 (p) REVERT: D 291 LYS cc_start: 0.8139 (tttm) cc_final: 0.7864 (mmtt) REVERT: D 360 GLN cc_start: 0.8380 (pm20) cc_final: 0.8133 (pp30) REVERT: E 265 SER cc_start: 0.8131 (p) cc_final: 0.7844 (t) REVERT: F 149 THR cc_start: 0.8892 (p) cc_final: 0.8641 (p) REVERT: F 257 CYS cc_start: 0.8772 (t) cc_final: 0.8314 (t) REVERT: F 289 ILE cc_start: 0.8531 (mm) cc_final: 0.8154 (mt) REVERT: F 355 MET cc_start: 0.7089 (mpp) cc_final: 0.6832 (mpp) REVERT: G 121 GLN cc_start: 0.7918 (tt0) cc_final: 0.7715 (tm-30) REVERT: G 362 TYR cc_start: 0.7568 (t80) cc_final: 0.7266 (t80) outliers start: 37 outliers final: 26 residues processed: 330 average time/residue: 0.1340 time to fit residues: 71.1755 Evaluate side-chains 284 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 270 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 121 optimal weight: 0.0970 chunk 43 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 204 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS D 111 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN ** G 371 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 = 0.3577 r_free = 0.3577 target = 0.109047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.089890 restraints weight = 51230.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091292 restraints weight = 33097.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092504 restraints weight = 22753.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092935 restraints weight = 19320.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092925 restraints weight = 17232.073| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21924 Z= 0.123 Angle : 0.590 7.179 29739 Z= 0.291 Chirality : 0.045 0.157 3281 Planarity : 0.004 0.039 3827 Dihedral : 7.755 99.356 3048 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.44 % Allowed : 11.88 % Favored : 86.68 % 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: 0.44 (0.17), residues: 2691 helix: 0.56 (0.18), residues: 924 sheet: 0.55 (0.24), residues: 498 loop : 0.14 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.018 0.001 TYR F 198 PHE 0.014 0.001 PHE G 352 TRP 0.011 0.001 TRP E 356 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00280 (21924) covalent geometry : angle 0.58956 (29739) hydrogen bonds : bond 0.03778 ( 896) hydrogen bonds : angle 5.43282 ( 2355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.794 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: A 285 GLN cc_start: 0.7570 (mp10) cc_final: 0.6954 (mp10) REVERT: B 198 TYR cc_start: 0.8921 (m-80) cc_final: 0.8710 (m-80) REVERT: B 286 ASP cc_start: 0.6716 (t0) cc_final: 0.6240 (t0) REVERT: B 356 TRP cc_start: 0.7887 (m100) cc_final: 0.7453 (m100) REVERT: C 54 VAL cc_start: 0.8523 (t) cc_final: 0.8216 (m) REVERT: C 121 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6927 (tm-30) REVERT: C 132 MET cc_start: 0.8746 (ptt) cc_final: 0.8517 (ptt) REVERT: C 217 CYS cc_start: 0.8144 (m) cc_final: 0.7555 (m) REVERT: D 192 ILE cc_start: 0.8866 (tp) cc_final: 0.8516 (tp) REVERT: D 234 SER cc_start: 0.8270 (m) cc_final: 0.7549 (p) REVERT: D 313 MET cc_start: 0.8928 (tpp) cc_final: 0.8438 (ttm) REVERT: E 265 SER cc_start: 0.8232 (p) cc_final: 0.8001 (t) REVERT: F 257 CYS cc_start: 0.8724 (t) cc_final: 0.8296 (t) REVERT: F 289 ILE cc_start: 0.8598 (mm) cc_final: 0.8242 (mt) REVERT: F 355 MET cc_start: 0.7142 (mpp) cc_final: 0.6854 (mpp) REVERT: G 103 THR cc_start: 0.9109 (t) cc_final: 0.8829 (t) REVERT: G 121 GLN cc_start: 0.8056 (tt0) cc_final: 0.7776 (tm-30) REVERT: G 362 TYR cc_start: 0.7706 (t80) cc_final: 0.7405 (t80) outliers start: 33 outliers final: 26 residues processed: 317 average time/residue: 0.1418 time to fit residues: 72.5734 Evaluate side-chains 282 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 270 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 46 optimal weight: 0.0030 chunk 181 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN B 59 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 59 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085670 restraints weight = 52453.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085911 restraints weight = 34162.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086777 restraints weight = 28549.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087436 restraints weight = 23082.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087702 restraints weight = 20662.325| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21924 Z= 0.260 Angle : 0.704 7.741 29739 Z= 0.352 Chirality : 0.049 0.210 3281 Planarity : 0.005 0.052 3827 Dihedral : 8.321 109.362 3048 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.71 % Allowed : 13.76 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.02 (0.17), residues: 2691 helix: 0.14 (0.17), residues: 960 sheet: 0.33 (0.24), residues: 488 loop : -0.11 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 39 TYR 0.017 0.002 TYR F 166 PHE 0.018 0.002 PHE B 200 TRP 0.013 0.002 TRP C 79 HIS 0.008 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00607 (21924) covalent geometry : angle 0.70392 (29739) hydrogen bonds : bond 0.04528 ( 896) hydrogen bonds : angle 5.58920 ( 2355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7876 (mp10) cc_final: 0.7177 (mp10) REVERT: B 41 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 82 MET cc_start: 0.8523 (mmm) cc_final: 0.6401 (tmm) REVERT: B 86 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: B 110 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8689 (tt) REVERT: B 286 ASP cc_start: 0.6923 (t0) cc_final: 0.6364 (t0) REVERT: B 356 TRP cc_start: 0.8028 (m100) cc_final: 0.7559 (m100) REVERT: C 54 VAL cc_start: 0.8662 (t) cc_final: 0.8391 (m) REVERT: D 192 ILE cc_start: 0.8877 (tp) cc_final: 0.8508 (tp) REVERT: D 234 SER cc_start: 0.8356 (m) cc_final: 0.7638 (p) REVERT: D 313 MET cc_start: 0.9029 (tpp) cc_final: 0.8514 (ttm) REVERT: E 132 MET cc_start: 0.7960 (ppp) cc_final: 0.7737 (ppp) REVERT: E 244 ASP cc_start: 0.7720 (p0) cc_final: 0.7486 (p0) REVERT: E 354 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8269 (mp10) REVERT: F 162 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8363 (m-40) REVERT: F 289 ILE cc_start: 0.8760 (mm) cc_final: 0.8491 (mt) REVERT: F 349 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6235 (mp) REVERT: F 355 MET cc_start: 0.7092 (mpp) cc_final: 0.6890 (mpp) REVERT: G 103 THR cc_start: 0.9198 (t) cc_final: 0.8952 (t) REVERT: G 121 GLN cc_start: 0.8123 (tt0) cc_final: 0.7780 (tm-30) REVERT: G 305 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: G 362 TYR cc_start: 0.7991 (t80) cc_final: 0.7592 (t80) outliers start: 62 outliers final: 42 residues processed: 311 average time/residue: 0.1409 time to fit residues: 70.8908 Evaluate side-chains 280 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 135 optimal weight: 0.4980 chunk 235 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087513 restraints weight = 51945.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088769 restraints weight = 32894.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089749 restraints weight = 23611.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089849 restraints weight = 20117.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089902 restraints weight = 18712.020| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21924 Z= 0.158 Angle : 0.616 7.675 29739 Z= 0.303 Chirality : 0.046 0.170 3281 Planarity : 0.004 0.047 3827 Dihedral : 8.033 104.607 3048 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.66 % Allowed : 15.68 % Favored : 81.65 % 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: 0.06 (0.17), residues: 2691 helix: 0.23 (0.17), residues: 960 sheet: 0.32 (0.24), residues: 488 loop : -0.07 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 183 TYR 0.012 0.001 TYR F 337 PHE 0.018 0.001 PHE E 352 TRP 0.011 0.002 TRP B 340 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00370 (21924) covalent geometry : angle 0.61551 (29739) hydrogen bonds : bond 0.03724 ( 896) hydrogen bonds : angle 5.33815 ( 2355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8491 (mmm) cc_final: 0.6397 (tmm) REVERT: B 86 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: B 286 ASP cc_start: 0.6908 (t0) cc_final: 0.6437 (t0) REVERT: B 356 TRP cc_start: 0.7967 (m100) cc_final: 0.7719 (m100) REVERT: C 54 VAL cc_start: 0.8479 (t) cc_final: 0.8244 (m) REVERT: C 121 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7107 (tm-30) REVERT: D 192 ILE cc_start: 0.8938 (tp) cc_final: 0.8567 (tp) REVERT: D 234 SER cc_start: 0.8379 (m) cc_final: 0.7714 (p) REVERT: D 313 MET cc_start: 0.8929 (tpp) cc_final: 0.8457 (ttm) REVERT: E 132 MET cc_start: 0.7809 (ppp) cc_final: 0.6963 (ppp) REVERT: F 289 ILE cc_start: 0.8755 (mm) cc_final: 0.8432 (mt) REVERT: F 349 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6269 (mp) REVERT: G 65 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8329 (pp) REVERT: G 103 THR cc_start: 0.9070 (t) cc_final: 0.8831 (t) REVERT: G 305 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7237 (mpp) REVERT: G 362 TYR cc_start: 0.7726 (t80) cc_final: 0.7315 (t80) REVERT: G 372 ARG cc_start: 0.7239 (mtm110) cc_final: 0.6629 (mtm110) outliers start: 61 outliers final: 39 residues processed: 302 average time/residue: 0.1410 time to fit residues: 69.6888 Evaluate side-chains 280 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 228 optimal weight: 0.0070 chunk 84 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN C 246 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 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 = 0.3557 r_free = 0.3557 target = 0.107846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088924 restraints weight = 51602.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089917 restraints weight = 33145.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091003 restraints weight = 24120.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091358 restraints weight = 20887.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091721 restraints weight = 19217.107| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21924 Z= 0.122 Angle : 0.591 7.704 29739 Z= 0.290 Chirality : 0.045 0.170 3281 Planarity : 0.004 0.045 3827 Dihedral : 7.813 100.860 3048 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.49 % Allowed : 16.51 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.17), residues: 2691 helix: 0.39 (0.17), residues: 954 sheet: 0.36 (0.24), residues: 498 loop : -0.01 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 95 TYR 0.012 0.001 TYR G 53 PHE 0.007 0.001 PHE G 262 TRP 0.012 0.002 TRP E 356 HIS 0.005 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00283 (21924) covalent geometry : angle 0.59139 (29739) hydrogen bonds : bond 0.03367 ( 896) hydrogen bonds : angle 5.15913 ( 2355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.910 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: A 493 TYR cc_start: 0.8325 (p90) cc_final: 0.8057 (p90) REVERT: B 82 MET cc_start: 0.8541 (mmm) cc_final: 0.6266 (tmm) REVERT: B 86 TRP cc_start: 0.8417 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: B 286 ASP cc_start: 0.6945 (t0) cc_final: 0.6439 (t0) REVERT: B 356 TRP cc_start: 0.7918 (m100) cc_final: 0.7585 (m100) REVERT: C 54 VAL cc_start: 0.8437 (t) cc_final: 0.8199 (m) REVERT: C 121 GLN cc_start: 0.7296 (tm-30) cc_final: 0.7017 (tm-30) REVERT: C 123 MET cc_start: 0.8089 (ttm) cc_final: 0.7776 (ttm) REVERT: C 217 CYS cc_start: 0.8132 (m) cc_final: 0.7301 (m) REVERT: D 123 MET cc_start: 0.8544 (tpp) cc_final: 0.7968 (ttm) REVERT: D 192 ILE cc_start: 0.8892 (tp) cc_final: 0.8533 (tp) REVERT: D 234 SER cc_start: 0.8386 (m) cc_final: 0.7684 (p) REVERT: D 313 MET cc_start: 0.8940 (tpp) cc_final: 0.8482 (ttm) REVERT: E 132 MET cc_start: 0.7444 (ppp) cc_final: 0.7069 (ppp) REVERT: E 354 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8232 (mp10) REVERT: F 289 ILE cc_start: 0.8731 (mm) cc_final: 0.8474 (mt) REVERT: F 349 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6107 (mp) REVERT: G 305 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: G 362 TYR cc_start: 0.7832 (t80) cc_final: 0.7426 (t80) outliers start: 57 outliers final: 40 residues processed: 304 average time/residue: 0.1410 time to fit residues: 69.9838 Evaluate side-chains 288 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN E 137 GLN F 115 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.085098 restraints weight = 52215.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086195 restraints weight = 31798.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087013 restraints weight = 24457.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.087431 restraints weight = 21678.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087695 restraints weight = 19877.700| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21924 Z= 0.253 Angle : 0.701 8.947 29739 Z= 0.349 Chirality : 0.049 0.196 3281 Planarity : 0.005 0.048 3827 Dihedral : 8.305 109.505 3048 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.84 % Allowed : 17.17 % Favored : 79.99 % 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: -0.05 (0.17), residues: 2691 helix: 0.20 (0.17), residues: 954 sheet: 0.23 (0.24), residues: 488 loop : -0.18 (0.19), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 95 TYR 0.015 0.002 TYR E 188 PHE 0.017 0.002 PHE B 200 TRP 0.016 0.002 TRP E 356 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00594 (21924) covalent geometry : angle 0.70133 (29739) hydrogen bonds : bond 0.04278 ( 896) hydrogen bonds : angle 5.39923 ( 2355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8487 (mmm) cc_final: 0.6241 (tmm) REVERT: B 86 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7029 (m-10) REVERT: B 110 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (tt) REVERT: B 286 ASP cc_start: 0.7017 (t0) cc_final: 0.6439 (t0) REVERT: B 356 TRP cc_start: 0.8119 (m100) cc_final: 0.7753 (m100) REVERT: C 54 VAL cc_start: 0.8650 (t) cc_final: 0.8415 (m) REVERT: C 299 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7516 (mmt) REVERT: D 192 ILE cc_start: 0.8922 (tp) cc_final: 0.8567 (tp) REVERT: D 234 SER cc_start: 0.8425 (m) cc_final: 0.7729 (p) REVERT: D 313 MET cc_start: 0.9021 (tpp) cc_final: 0.8575 (ttm) REVERT: D 340 TRP cc_start: 0.7546 (t60) cc_final: 0.7262 (t60) REVERT: D 373 LYS cc_start: 0.8090 (tptm) cc_final: 0.7876 (tptt) REVERT: E 132 MET cc_start: 0.7510 (ppp) cc_final: 0.7287 (ppp) REVERT: E 186 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8403 (t) REVERT: E 328 LYS cc_start: 0.8184 (pptt) cc_final: 0.7494 (ptmt) REVERT: E 354 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8194 (mp10) REVERT: F 107 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: F 132 MET cc_start: 0.8124 (tmm) cc_final: 0.7865 (tmm) REVERT: F 162 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: F 289 ILE cc_start: 0.8826 (mm) cc_final: 0.8586 (mt) REVERT: F 349 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6214 (mp) REVERT: F 375 PHE cc_start: 0.4486 (t80) cc_final: 0.3856 (t80) REVERT: G 120 THR cc_start: 0.8427 (m) cc_final: 0.8225 (p) REVERT: G 305 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7356 (mpp) REVERT: G 362 TYR cc_start: 0.7797 (t80) cc_final: 0.7221 (t80) outliers start: 65 outliers final: 47 residues processed: 296 average time/residue: 0.1403 time to fit residues: 68.1398 Evaluate side-chains 286 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 90 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 260 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 212 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 115 ASN ** G 111 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 = 0.3562 r_free = 0.3562 target = 0.108120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089015 restraints weight = 51257.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090772 restraints weight = 31530.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091751 restraints weight = 23254.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091892 restraints weight = 18568.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092055 restraints weight = 17117.261| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21924 Z= 0.113 Angle : 0.602 12.224 29739 Z= 0.295 Chirality : 0.045 0.168 3281 Planarity : 0.004 0.048 3827 Dihedral : 7.814 99.947 3048 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.01 % Allowed : 18.04 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.17), residues: 2691 helix: 0.33 (0.17), residues: 960 sheet: 0.33 (0.24), residues: 478 loop : -0.04 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 95 TYR 0.020 0.001 TYR G 279 PHE 0.007 0.001 PHE D 124 TRP 0.017 0.002 TRP A 491 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00260 (21924) covalent geometry : angle 0.60170 (29739) hydrogen bonds : bond 0.03244 ( 896) hydrogen bonds : angle 5.11947 ( 2355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.8386 (p90) cc_final: 0.8096 (p90) REVERT: B 82 MET cc_start: 0.8391 (mmm) cc_final: 0.7097 (tmm) REVERT: B 286 ASP cc_start: 0.6936 (t0) cc_final: 0.6419 (t0) REVERT: B 356 TRP cc_start: 0.7950 (m100) cc_final: 0.7703 (m100) REVERT: C 28 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7660 (tpp80) REVERT: C 54 VAL cc_start: 0.8426 (t) cc_final: 0.8190 (m) REVERT: C 121 GLN cc_start: 0.7330 (tm-30) cc_final: 0.7055 (tm-30) REVERT: C 123 MET cc_start: 0.8097 (ttm) cc_final: 0.7762 (ttm) REVERT: C 167 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: C 217 CYS cc_start: 0.8082 (m) cc_final: 0.7263 (m) REVERT: C 299 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7494 (mmt) REVERT: C 325 MET cc_start: 0.5971 (ptp) cc_final: 0.5687 (ptm) REVERT: D 81 ASP cc_start: 0.7794 (m-30) cc_final: 0.7392 (m-30) REVERT: D 123 MET cc_start: 0.8556 (tpp) cc_final: 0.8192 (ttm) REVERT: D 192 ILE cc_start: 0.8869 (tp) cc_final: 0.8519 (tp) REVERT: D 234 SER cc_start: 0.8362 (m) cc_final: 0.7686 (p) REVERT: D 246 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: D 313 MET cc_start: 0.8952 (tpp) cc_final: 0.8439 (ttm) REVERT: D 340 TRP cc_start: 0.7355 (t60) cc_final: 0.7153 (t60) REVERT: E 328 LYS cc_start: 0.8015 (pptt) cc_final: 0.7243 (ptmm) REVERT: F 107 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: F 132 MET cc_start: 0.7936 (tmm) cc_final: 0.7662 (tmm) REVERT: F 217 CYS cc_start: 0.7970 (m) cc_final: 0.7720 (m) REVERT: F 289 ILE cc_start: 0.8793 (mm) cc_final: 0.8517 (mt) REVERT: F 349 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6028 (mp) REVERT: F 375 PHE cc_start: 0.4289 (t80) cc_final: 0.3697 (t80) REVERT: G 65 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8374 (pp) REVERT: G 305 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7321 (mpp) REVERT: G 362 TYR cc_start: 0.7769 (t80) cc_final: 0.7285 (t80) outliers start: 46 outliers final: 33 residues processed: 298 average time/residue: 0.1431 time to fit residues: 69.4862 Evaluate side-chains 287 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 113 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 249 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086083 restraints weight = 52221.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087115 restraints weight = 33899.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088319 restraints weight = 24750.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.088611 restraints weight = 20643.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088729 restraints weight = 19364.764| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21924 Z= 0.216 Angle : 0.678 10.545 29739 Z= 0.335 Chirality : 0.048 0.193 3281 Planarity : 0.004 0.050 3827 Dihedral : 8.148 107.480 3048 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.27 % Allowed : 18.65 % Favored : 79.07 % 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: -0.04 (0.17), residues: 2691 helix: 0.21 (0.17), residues: 960 sheet: 0.21 (0.24), residues: 488 loop : -0.15 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.015 0.001 TYR D 362 PHE 0.022 0.001 PHE E 352 TRP 0.020 0.002 TRP A 491 HIS 0.007 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00508 (21924) covalent geometry : angle 0.67765 (29739) hydrogen bonds : bond 0.03951 ( 896) hydrogen bonds : angle 5.22476 ( 2355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.8351 (p90) cc_final: 0.8022 (p90) REVERT: B 57 GLU cc_start: 0.7462 (tp30) cc_final: 0.7228 (tp30) REVERT: B 82 MET cc_start: 0.8286 (mmm) cc_final: 0.7475 (mmm) REVERT: B 86 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: B 286 ASP cc_start: 0.6953 (t0) cc_final: 0.6540 (t0) REVERT: B 356 TRP cc_start: 0.8119 (m100) cc_final: 0.7863 (m100) REVERT: C 54 VAL cc_start: 0.8564 (t) cc_final: 0.8333 (m) REVERT: C 167 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: C 299 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7504 (mmt) REVERT: D 81 ASP cc_start: 0.7696 (m-30) cc_final: 0.7323 (m-30) REVERT: D 123 MET cc_start: 0.8461 (tpp) cc_final: 0.8004 (ttm) REVERT: D 192 ILE cc_start: 0.8994 (tp) cc_final: 0.8620 (tp) REVERT: D 234 SER cc_start: 0.8386 (m) cc_final: 0.7706 (p) REVERT: D 246 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: D 313 MET cc_start: 0.8898 (tpp) cc_final: 0.8572 (ttm) REVERT: D 340 TRP cc_start: 0.7456 (t60) cc_final: 0.7246 (t60) REVERT: E 124 PHE cc_start: 0.7060 (m-10) cc_final: 0.6525 (m-10) REVERT: E 328 LYS cc_start: 0.7956 (pptt) cc_final: 0.7285 (ptmm) REVERT: F 107 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: F 132 MET cc_start: 0.7887 (tmm) cc_final: 0.7577 (tmm) REVERT: F 289 ILE cc_start: 0.8787 (mm) cc_final: 0.8522 (mt) REVERT: F 349 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6184 (mp) REVERT: F 375 PHE cc_start: 0.4555 (t80) cc_final: 0.3972 (t80) REVERT: G 227 MET cc_start: 0.8994 (mmm) cc_final: 0.8322 (mmm) REVERT: G 305 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7260 (mpp) REVERT: G 362 TYR cc_start: 0.7600 (t80) cc_final: 0.7051 (t80) outliers start: 52 outliers final: 38 residues processed: 276 average time/residue: 0.1422 time to fit residues: 64.5424 Evaluate side-chains 274 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 219 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 169 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086723 restraints weight = 52274.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087988 restraints weight = 30352.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089044 restraints weight = 23020.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089339 restraints weight = 20029.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089391 restraints weight = 17807.138| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21924 Z= 0.188 Angle : 0.656 11.009 29739 Z= 0.323 Chirality : 0.047 0.172 3281 Planarity : 0.004 0.053 3827 Dihedral : 8.107 105.206 3048 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.32 % Allowed : 19.00 % Favored : 78.68 % 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: -0.05 (0.17), residues: 2691 helix: 0.18 (0.17), residues: 960 sheet: 0.20 (0.24), residues: 488 loop : -0.14 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 95 TYR 0.026 0.001 TYR G 279 PHE 0.011 0.001 PHE E 352 TRP 0.025 0.002 TRP A 491 HIS 0.009 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00442 (21924) covalent geometry : angle 0.65551 (29739) hydrogen bonds : bond 0.03752 ( 896) hydrogen bonds : angle 5.19977 ( 2355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 TYR cc_start: 0.8413 (p90) cc_final: 0.8103 (p90) REVERT: B 57 GLU cc_start: 0.7545 (tp30) cc_final: 0.7323 (tp30) REVERT: B 82 MET cc_start: 0.8393 (mmm) cc_final: 0.7474 (mmm) REVERT: B 86 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: B 119 MET cc_start: 0.8800 (pmm) cc_final: 0.8579 (pmm) REVERT: B 286 ASP cc_start: 0.7156 (t0) cc_final: 0.6661 (t0) REVERT: B 356 TRP cc_start: 0.8153 (m100) cc_final: 0.7809 (m100) REVERT: C 54 VAL cc_start: 0.8536 (t) cc_final: 0.8308 (m) REVERT: C 167 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: C 299 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7524 (mmt) REVERT: D 123 MET cc_start: 0.8546 (tpp) cc_final: 0.8177 (ttm) REVERT: D 192 ILE cc_start: 0.8929 (tp) cc_final: 0.8548 (tp) REVERT: D 234 SER cc_start: 0.8432 (m) cc_final: 0.7771 (p) REVERT: D 313 MET cc_start: 0.8995 (tpp) cc_final: 0.8607 (ttm) REVERT: D 340 TRP cc_start: 0.7484 (t60) cc_final: 0.7282 (t60) REVERT: E 186 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8390 (t) REVERT: E 328 LYS cc_start: 0.8073 (pptt) cc_final: 0.7330 (ptmm) REVERT: F 107 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: F 132 MET cc_start: 0.8094 (tmm) cc_final: 0.7767 (tmm) REVERT: F 217 CYS cc_start: 0.7914 (m) cc_final: 0.7712 (m) REVERT: F 289 ILE cc_start: 0.8789 (mm) cc_final: 0.8547 (mt) REVERT: F 349 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6111 (mp) REVERT: F 375 PHE cc_start: 0.4595 (t80) cc_final: 0.3992 (t80) REVERT: G 227 MET cc_start: 0.8953 (mmm) cc_final: 0.8387 (mmm) REVERT: G 305 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7262 (mpp) REVERT: G 362 TYR cc_start: 0.7730 (t80) cc_final: 0.7294 (t80) outliers start: 53 outliers final: 42 residues processed: 272 average time/residue: 0.1369 time to fit residues: 60.5658 Evaluate side-chains 275 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 247 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.089030 restraints weight = 51500.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090410 restraints weight = 32479.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091423 restraints weight = 22613.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091995 restraints weight = 19809.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092264 restraints weight = 18178.233| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21924 Z= 0.119 Angle : 0.616 11.595 29739 Z= 0.302 Chirality : 0.045 0.165 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.797 99.422 3048 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.05 % Allowed : 19.53 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.14 (0.17), residues: 2691 helix: 0.35 (0.17), residues: 960 sheet: 0.29 (0.25), residues: 478 loop : -0.04 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 95 TYR 0.016 0.001 TYR D 362 PHE 0.028 0.001 PHE E 352 TRP 0.030 0.002 TRP A 491 HIS 0.010 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00276 (21924) covalent geometry : angle 0.61638 (29739) hydrogen bonds : bond 0.03214 ( 896) hydrogen bonds : angle 5.03095 ( 2355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.23 seconds wall clock time: 54 minutes 7.41 seconds (3247.41 seconds total)