Starting phenix.real_space_refine on Thu Mar 5 17:45:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ffq_31571/03_2026/7ffq_31571.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 15736 2.51 5 N 4243 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24808 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3257 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 30, 'TRANS': 385} Chain breaks: 1 Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3243 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 30, 'TRANS': 383} Chain breaks: 1 Chain: "R" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3249 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 30, 'TRANS': 384} Chain breaks: 1 Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Time building chain proxies: 6.14, per 1000 atoms: 0.25 Number of scatterers: 24808 At special positions: 0 Unit cell: (187.44, 201.96, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 4649 8.00 N 4243 7.00 C 15736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.04 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 123 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 27 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS J 151 " - pdb=" SG CYS J 266 " distance=2.03 Simple disulfide: pdb=" SG CYS J 200 " - pdb=" SG CYS J 226 " distance=2.03 Simple disulfide: pdb=" SG CYS J 202 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 67 sheets defined 16.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.092A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.857A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.238A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.541A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.729A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.647A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.567A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.589A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.757A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.543A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 222 through 224 No H-bonds generated for 'chain 'J' and resid 222 through 224' Processing helix chain 'J' and resid 351 through 363 removed outlier: 3.784A pdb=" N VAL J 355 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J 356 " --> pdb=" O PRO J 352 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR J 357 " --> pdb=" O HIS J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 398 removed outlier: 3.864A pdb=" N ILE J 368 " --> pdb=" O PRO J 364 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU J 369 " --> pdb=" O MET J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 416 Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.207A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.530A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.773A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.735A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.863A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 409 through 416 Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.100A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.734A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.098A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.753A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.308A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.646A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AB6, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.697A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC1, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.406A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC3, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AC4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'F' and resid 146 through 148 removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 170 Processing sheet with id=AC7, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.539A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.775A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD4, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.339A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AD6, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AD7, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AE1, first strand: chain 'J' and resid 33 through 37 removed outlier: 6.588A pdb=" N GLN J 48 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL J 36 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG J 46 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N SER J 50 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP J 69 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.504A pdb=" N ILE J 110 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 147 through 149 Processing sheet with id=AE4, first strand: chain 'J' and resid 152 through 154 Processing sheet with id=AE5, first strand: chain 'J' and resid 237 through 238 removed outlier: 3.532A pdb=" N VAL J 237 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY J 253 " --> pdb=" O MET J 167 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 179 through 181 Processing sheet with id=AE7, first strand: chain 'J' and resid 196 through 200 removed outlier: 3.982A pdb=" N LEU J 197 " --> pdb=" O TYR J 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AF1, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AF2, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.623A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF4, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF5, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.785A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AF8, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AF9, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AG3, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AG4, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.631A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 188 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AG8, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AH1, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AH2, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.707A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.493A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.518A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 1947 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: 4.82 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7919 1.34 - 1.47: 6269 1.47 - 1.59: 11027 1.59 - 1.72: 0 1.72 - 1.84: 240 Bond restraints: 25455 Sorted by residual: bond pdb=" CB VAL G 148 " pdb=" CG2 VAL G 148 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.47e+00 bond pdb=" CB VAL C 148 " pdb=" CG2 VAL C 148 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.78e+00 bond pdb=" CB VAL G 42 " pdb=" CG1 VAL G 42 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.46e+00 bond pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.96e+00 bond pdb=" C ASN G 264 " pdb=" N PRO G 265 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.88e+00 ... (remaining 25450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 33899 2.63 - 5.27: 649 5.27 - 7.90: 83 7.90 - 10.54: 21 10.54 - 13.17: 3 Bond angle restraints: 34655 Sorted by residual: angle pdb=" N GLU R 148 " pdb=" CA GLU R 148 " pdb=" C GLU R 148 " ideal model delta sigma weight residual 107.69 119.40 -11.71 2.01e+00 2.48e-01 3.39e+01 angle pdb=" N THR R 140 " pdb=" CA THR R 140 " pdb=" C THR R 140 " ideal model delta sigma weight residual 114.56 108.29 6.27 1.27e+00 6.20e-01 2.44e+01 angle pdb=" C ILE B 369 " pdb=" N CYS B 370 " pdb=" CA CYS B 370 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C LEU A 132 " pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 120.38 127.01 -6.63 1.46e+00 4.69e-01 2.06e+01 angle pdb=" C SER R 87 " pdb=" N ARG R 88 " pdb=" CA ARG R 88 " ideal model delta sigma weight residual 122.48 129.83 -7.35 1.62e+00 3.81e-01 2.06e+01 ... (remaining 34650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 14425 14.31 - 28.63: 689 28.63 - 42.94: 165 42.94 - 57.25: 21 57.25 - 71.57: 17 Dihedral angle restraints: 15317 sinusoidal: 5996 harmonic: 9321 Sorted by residual: dihedral pdb=" CA ILE G 369 " pdb=" C ILE G 369 " pdb=" N CYS G 370 " pdb=" CA CYS G 370 " ideal model delta harmonic sigma weight residual -180.00 -130.00 -50.00 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA ASN B 264 " pdb=" C ASN B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual 180.00 131.45 48.55 0 5.00e+00 4.00e-02 9.43e+01 dihedral pdb=" CA ASN C 264 " pdb=" C ASN C 264 " pdb=" N PRO C 265 " pdb=" CA PRO C 265 " ideal model delta harmonic sigma weight residual 180.00 137.04 42.96 0 5.00e+00 4.00e-02 7.38e+01 ... (remaining 15314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3412 0.092 - 0.183: 426 0.183 - 0.274: 22 0.274 - 0.366: 2 0.366 - 0.457: 2 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CG LEU I 31 " pdb=" CB LEU I 31 " pdb=" CD1 LEU I 31 " pdb=" CD2 LEU I 31 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA HIS Q 156 " pdb=" N HIS Q 156 " pdb=" C HIS Q 156 " pdb=" CB HIS Q 156 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3861 not shown) Planarity restraints: 4455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 236 " 0.039 2.00e-02 2.50e+03 2.23e-02 1.25e+01 pdb=" CG TRP J 236 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J 236 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 236 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 236 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 236 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 236 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 236 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 264 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B 265 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.049 5.00e-02 4.00e+02 ... (remaining 4452 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5848 2.79 - 3.32: 20103 3.32 - 3.85: 39713 3.85 - 4.37: 44392 4.37 - 4.90: 79612 Nonbonded interactions: 189668 Sorted by model distance: nonbonded pdb=" OE1 GLU B 120 " pdb=" OH TYR B 122 " model vdw 2.267 3.040 nonbonded pdb=" O ALA C 401 " pdb=" OH TYR R 359 " model vdw 2.268 3.040 nonbonded pdb=" O ALA B 401 " pdb=" OH TYR Q 359 " model vdw 2.274 3.040 nonbonded pdb=" OG SER C 403 " pdb=" O PRO R 348 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR C 51 " pdb=" O ALA C 236 " model vdw 2.279 3.040 ... (remaining 189663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'S' } ncs_group { reference = (chain 'B' and resid 1 through 440) selection = (chain 'C' and resid 1 through 440) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'T' } ncs_group { reference = (chain 'J' and (resid 1 through 55 or resid 62 through 419)) selection = (chain 'Q' and (resid 1 through 55 or resid 62 through 419)) selection = (chain 'R' and (resid 1 through 55 or resid 62 through 419)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.640 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.008 0.469 25495 Z= 0.346 Angle : 0.952 33.305 34735 Z= 0.517 Chirality : 0.058 0.457 3864 Planarity : 0.008 0.102 4455 Dihedral : 9.309 71.568 9225 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -3.45 (0.12), residues: 3178 helix: -2.39 (0.18), residues: 434 sheet: -1.78 (0.15), residues: 928 loop : -2.61 (0.12), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 21 TYR 0.040 0.003 TYR C 308 PHE 0.030 0.004 PHE Q 328 TRP 0.047 0.004 TRP J 236 HIS 0.010 0.002 HIS B 381 Details of bonding type rmsd covalent geometry : bond 0.00749 (25455) covalent geometry : angle 0.92897 (34655) SS BOND : bond 0.07428 ( 40) SS BOND : angle 4.47966 ( 80) hydrogen bonds : bond 0.21130 ( 748) hydrogen bonds : angle 8.40001 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 676 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 PHE cc_start: 0.7499 (m-80) cc_final: 0.6694 (m-80) REVERT: B 109 MET cc_start: 0.6488 (ptt) cc_final: 0.6154 (ptt) REVERT: B 113 ASP cc_start: 0.8208 (m-30) cc_final: 0.7997 (m-30) REVERT: B 310 SER cc_start: 0.8360 (t) cc_final: 0.8090 (m) REVERT: C 136 THR cc_start: 0.8415 (m) cc_final: 0.8034 (p) REVERT: C 211 SER cc_start: 0.8926 (m) cc_final: 0.8489 (p) REVERT: C 389 THR cc_start: 0.8327 (p) cc_final: 0.8013 (p) REVERT: C 437 THR cc_start: 0.6501 (m) cc_final: 0.6019 (m) REVERT: Q 94 ASP cc_start: 0.5553 (t0) cc_final: 0.5258 (t0) REVERT: R 147 VAL cc_start: 0.8963 (m) cc_final: 0.8516 (p) REVERT: S 130 ILE cc_start: 0.3548 (mm) cc_final: 0.3314 (mt) REVERT: S 153 VAL cc_start: -0.0326 (t) cc_final: -0.1069 (t) REVERT: S 166 LYS cc_start: 0.7397 (tttt) cc_final: 0.7013 (pptt) outliers start: 5 outliers final: 2 residues processed: 679 average time/residue: 0.1745 time to fit residues: 180.9414 Evaluate side-chains 345 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain G residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN C 43 ASN C 304 ASN C 390 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN F 137 ASN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 HIS G 43 ASN G 235 GLN G 264 ASN G 360 ASN G 386 HIS G 394 HIS I 37 ASN J 239 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 HIS Q 160 ASN Q 168 HIS ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 349 HIS R 96 HIS R 121 HIS R 156 HIS R 216 GLN R 256 HIS T 37 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106253 restraints weight = 48676.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109065 restraints weight = 23225.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110743 restraints weight = 14794.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111753 restraints weight = 11375.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112122 restraints weight = 9817.116| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 25495 Z= 0.240 Angle : 0.718 9.679 34735 Z= 0.384 Chirality : 0.047 0.202 3864 Planarity : 0.006 0.101 4455 Dihedral : 6.158 73.227 3476 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.05 % Rotamer: Outliers : 2.99 % Allowed : 8.70 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -2.20 (0.14), residues: 3178 helix: -0.30 (0.25), residues: 436 sheet: -1.22 (0.16), residues: 946 loop : -1.91 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 401 TYR 0.026 0.002 TYR G 434 PHE 0.030 0.002 PHE P 14 TRP 0.021 0.002 TRP Q 236 HIS 0.006 0.002 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00539 (25455) covalent geometry : angle 0.71197 (34655) SS BOND : bond 0.00964 ( 40) SS BOND : angle 2.12188 ( 80) hydrogen bonds : bond 0.03965 ( 748) hydrogen bonds : angle 5.90101 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 377 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5723 (mtm) cc_final: 0.4975 (mmm) REVERT: A 204 HIS cc_start: 0.5787 (m170) cc_final: 0.5104 (m170) REVERT: A 209 TYR cc_start: 0.8517 (t80) cc_final: 0.8216 (t80) REVERT: A 257 MET cc_start: 0.8181 (ptp) cc_final: 0.7605 (ptp) REVERT: B 310 SER cc_start: 0.9026 (t) cc_final: 0.8753 (m) REVERT: C 88 MET cc_start: 0.8380 (tpp) cc_final: 0.8063 (mmm) REVERT: C 136 THR cc_start: 0.8675 (m) cc_final: 0.8154 (p) REVERT: C 211 SER cc_start: 0.8873 (m) cc_final: 0.8508 (p) REVERT: C 433 MET cc_start: 0.6426 (tmm) cc_final: 0.6143 (mmt) REVERT: F 174 ASP cc_start: 0.6613 (t0) cc_final: 0.6375 (t0) REVERT: F 175 LEU cc_start: 0.8323 (mt) cc_final: 0.8102 (mt) REVERT: F 176 GLU cc_start: 0.7312 (tt0) cc_final: 0.6532 (tp30) REVERT: F 184 MET cc_start: 0.7364 (tmm) cc_final: 0.7097 (tmm) REVERT: J 88 ARG cc_start: 0.6481 (mmt180) cc_final: 0.6100 (mmt180) REVERT: J 117 ASP cc_start: 0.7163 (p0) cc_final: 0.6929 (p0) REVERT: Q 225 GLN cc_start: 0.6726 (mt0) cc_final: 0.6521 (mt0) REVERT: Q 275 MET cc_start: 0.7490 (mpp) cc_final: 0.7139 (mpp) REVERT: R 88 ARG cc_start: 0.6061 (mmt180) cc_final: 0.5728 (mmt180) REVERT: R 181 LEU cc_start: 0.7321 (tp) cc_final: 0.7029 (tp) REVERT: R 212 ASN cc_start: 0.6783 (t0) cc_final: 0.6581 (t0) REVERT: S 131 MET cc_start: 0.6307 (mmp) cc_final: 0.5674 (ppp) outliers start: 81 outliers final: 54 residues processed: 440 average time/residue: 0.1586 time to fit residues: 110.6468 Evaluate side-chains 349 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 295 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 236 TRP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 203 HIS Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 110 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 295 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 331 HIS B 394 HIS C 140 HIS C 360 ASN C 386 HIS ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 HIS Q 216 GLN ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS Q 361 HIS R 361 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106218 restraints weight = 48521.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106805 restraints weight = 27275.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106984 restraints weight = 19195.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108192 restraints weight = 18035.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107948 restraints weight = 15265.356| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25495 Z= 0.176 Angle : 0.636 9.885 34735 Z= 0.332 Chirality : 0.045 0.164 3864 Planarity : 0.005 0.085 4455 Dihedral : 5.790 74.301 3476 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 3.46 % Allowed : 11.02 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.69 (0.14), residues: 3178 helix: 0.43 (0.26), residues: 432 sheet: -0.84 (0.17), residues: 918 loop : -1.70 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 67 TYR 0.022 0.002 TYR J 400 PHE 0.054 0.002 PHE Q 217 TRP 0.023 0.002 TRP Q 236 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00408 (25455) covalent geometry : angle 0.63112 (34655) SS BOND : bond 0.00422 ( 40) SS BOND : angle 1.75100 ( 80) hydrogen bonds : bond 0.03551 ( 748) hydrogen bonds : angle 5.50256 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 321 time to evaluate : 0.756 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 177 TYR cc_start: 0.6186 (p90) cc_final: 0.5580 (p90) REVERT: A 209 TYR cc_start: 0.8599 (t80) cc_final: 0.8257 (t80) REVERT: A 257 MET cc_start: 0.8223 (ptp) cc_final: 0.7722 (ptp) REVERT: C 136 THR cc_start: 0.8774 (m) cc_final: 0.8398 (p) REVERT: C 211 SER cc_start: 0.8830 (m) cc_final: 0.8561 (p) REVERT: C 366 ARG cc_start: 0.8364 (ptm160) cc_final: 0.7705 (ptm160) REVERT: C 433 MET cc_start: 0.6653 (tmm) cc_final: 0.6241 (mmt) REVERT: F 174 ASP cc_start: 0.6530 (t0) cc_final: 0.6299 (t0) REVERT: F 176 GLU cc_start: 0.7189 (tt0) cc_final: 0.6316 (tp30) REVERT: F 184 MET cc_start: 0.7469 (tmm) cc_final: 0.7253 (tmm) REVERT: F 189 PHE cc_start: 0.5353 (m-80) cc_final: 0.4719 (m-10) REVERT: F 273 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7176 (tm-30) REVERT: G 73 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7632 (mpt-90) REVERT: J 88 ARG cc_start: 0.6526 (mmt180) cc_final: 0.6229 (mmt180) REVERT: Q 225 GLN cc_start: 0.6414 (mt0) cc_final: 0.5992 (mt0) REVERT: Q 401 ARG cc_start: 0.7356 (ptp90) cc_final: 0.7026 (ptt-90) REVERT: R 88 ARG cc_start: 0.6286 (mmt180) cc_final: 0.6074 (mmt180) REVERT: R 212 ASN cc_start: 0.7053 (t0) cc_final: 0.6816 (t0) REVERT: S 135 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7481 (tppt) REVERT: S 184 MET cc_start: 0.7463 (ptp) cc_final: 0.7210 (ptt) REVERT: S 200 TYR cc_start: 0.6703 (m-80) cc_final: 0.6420 (m-80) outliers start: 94 outliers final: 61 residues processed: 392 average time/residue: 0.1592 time to fit residues: 98.5801 Evaluate side-chains 344 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 168 HIS Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 226 CYS Chi-restraints excluded: chain Q residue 261 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 212 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 126 optimal weight: 40.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 239 ASN J 347 ASN Q 216 GLN ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 197 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102067 restraints weight = 48310.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101458 restraints weight = 28512.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102290 restraints weight = 20955.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102705 restraints weight = 17554.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102795 restraints weight = 15815.590| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25495 Z= 0.231 Angle : 0.662 10.067 34735 Z= 0.344 Chirality : 0.046 0.195 3864 Planarity : 0.005 0.081 4455 Dihedral : 5.868 75.907 3476 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 3.61 % Allowed : 12.02 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.56 (0.14), residues: 3178 helix: 0.74 (0.26), residues: 433 sheet: -0.82 (0.16), residues: 930 loop : -1.62 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 67 TYR 0.021 0.002 TYR G 308 PHE 0.018 0.002 PHE Q 217 TRP 0.035 0.002 TRP Q 236 HIS 0.030 0.002 HIS Q 168 Details of bonding type rmsd covalent geometry : bond 0.00546 (25455) covalent geometry : angle 0.65847 (34655) SS BOND : bond 0.00494 ( 40) SS BOND : angle 1.48559 ( 80) hydrogen bonds : bond 0.03644 ( 748) hydrogen bonds : angle 5.39276 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 325 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6342 (p90) cc_final: 0.6030 (p90) REVERT: A 257 MET cc_start: 0.8295 (ptp) cc_final: 0.7929 (ptp) REVERT: B 252 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8736 (ttmm) REVERT: C 88 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8168 (mtt) REVERT: C 136 THR cc_start: 0.8850 (m) cc_final: 0.8583 (p) REVERT: C 211 SER cc_start: 0.8807 (m) cc_final: 0.8531 (p) REVERT: C 366 ARG cc_start: 0.8294 (ptm160) cc_final: 0.8093 (ptm160) REVERT: C 433 MET cc_start: 0.6861 (tmm) cc_final: 0.6509 (mmt) REVERT: F 130 ILE cc_start: 0.6335 (mm) cc_final: 0.5523 (mt) REVERT: F 131 MET cc_start: 0.6781 (mmm) cc_final: 0.6577 (mpp) REVERT: F 174 ASP cc_start: 0.6823 (t0) cc_final: 0.6609 (t0) REVERT: F 176 GLU cc_start: 0.7219 (tt0) cc_final: 0.6529 (tp30) REVERT: F 184 MET cc_start: 0.7561 (tmm) cc_final: 0.7287 (tmm) REVERT: F 189 PHE cc_start: 0.6236 (m-80) cc_final: 0.5410 (m-80) REVERT: F 240 ILE cc_start: 0.8377 (mt) cc_final: 0.8085 (mp) REVERT: F 247 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6539 (mp0) REVERT: G 73 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7779 (mpt-90) REVERT: J 55 LEU cc_start: 0.7855 (mp) cc_final: 0.6531 (mt) REVERT: J 88 ARG cc_start: 0.6504 (mmt180) cc_final: 0.6130 (mmt180) REVERT: J 199 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: J 239 ASN cc_start: 0.8799 (t0) cc_final: 0.8500 (t0) REVERT: P 45 GLU cc_start: 0.8604 (mp0) cc_final: 0.8282 (mp0) REVERT: Q 70 MET cc_start: 0.8688 (tpp) cc_final: 0.8434 (tpp) REVERT: Q 225 GLN cc_start: 0.6258 (mt0) cc_final: 0.6024 (mt0) REVERT: R 88 ARG cc_start: 0.6470 (mmt180) cc_final: 0.5915 (mmt180) REVERT: R 212 ASN cc_start: 0.7366 (t0) cc_final: 0.7091 (t0) REVERT: S 177 TYR cc_start: 0.8502 (p90) cc_final: 0.8261 (p90) REVERT: S 272 CYS cc_start: 0.7498 (t) cc_final: 0.6529 (m) outliers start: 98 outliers final: 74 residues processed: 398 average time/residue: 0.1652 time to fit residues: 103.6440 Evaluate side-chains 374 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 297 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 167 MET Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 55 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 239 optimal weight: 30.0000 chunk 87 optimal weight: 0.0020 chunk 270 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN G 125 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 HIS ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 GLN ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097434 restraints weight = 48107.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100127 restraints weight = 23162.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101840 restraints weight = 14714.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102689 restraints weight = 11289.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103292 restraints weight = 9844.517| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25495 Z= 0.163 Angle : 0.605 8.091 34735 Z= 0.313 Chirality : 0.045 0.190 3864 Planarity : 0.004 0.072 4455 Dihedral : 5.447 77.085 3475 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 3.58 % Allowed : 13.20 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.24 (0.15), residues: 3178 helix: 1.09 (0.26), residues: 428 sheet: -0.61 (0.17), residues: 904 loop : -1.43 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 67 TYR 0.020 0.001 TYR G 308 PHE 0.016 0.002 PHE I 14 TRP 0.018 0.002 TRP G 409 HIS 0.005 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00382 (25455) covalent geometry : angle 0.60292 (34655) SS BOND : bond 0.00279 ( 40) SS BOND : angle 1.26117 ( 80) hydrogen bonds : bond 0.03207 ( 748) hydrogen bonds : angle 5.23281 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 328 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6558 (pptt) REVERT: A 168 LYS cc_start: 0.7149 (tppt) cc_final: 0.6827 (mppt) REVERT: A 177 TYR cc_start: 0.6312 (p90) cc_final: 0.6079 (p90) REVERT: A 257 MET cc_start: 0.8165 (ptp) cc_final: 0.7948 (ptp) REVERT: B 55 MET cc_start: 0.8173 (mtm) cc_final: 0.7968 (mtm) REVERT: C 88 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: C 136 THR cc_start: 0.8873 (m) cc_final: 0.8582 (p) REVERT: C 366 ARG cc_start: 0.8290 (ptm160) cc_final: 0.7632 (ptm160) REVERT: C 433 MET cc_start: 0.6830 (tmm) cc_final: 0.6506 (mmt) REVERT: F 130 ILE cc_start: 0.6301 (mm) cc_final: 0.5247 (mt) REVERT: F 131 MET cc_start: 0.6968 (mmm) cc_final: 0.6581 (mpp) REVERT: F 139 TYR cc_start: 0.7218 (m-80) cc_final: 0.6822 (m-80) REVERT: F 175 LEU cc_start: 0.8292 (mt) cc_final: 0.7942 (pp) REVERT: F 176 GLU cc_start: 0.7506 (tt0) cc_final: 0.6685 (tp30) REVERT: F 189 PHE cc_start: 0.6580 (m-80) cc_final: 0.5582 (m-80) REVERT: F 190 LYS cc_start: 0.7535 (mttt) cc_final: 0.7225 (mtmm) REVERT: F 225 ASP cc_start: 0.7251 (p0) cc_final: 0.7010 (p0) REVERT: F 240 ILE cc_start: 0.8211 (mt) cc_final: 0.7937 (mp) REVERT: F 247 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6477 (mp0) REVERT: F 257 MET cc_start: 0.7354 (ptp) cc_final: 0.7118 (ptp) REVERT: G 247 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7898 (tttt) REVERT: J 27 CYS cc_start: 0.4350 (t) cc_final: 0.3877 (t) REVERT: J 88 ARG cc_start: 0.5965 (mmt180) cc_final: 0.5450 (mmt180) REVERT: J 199 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: J 239 ASN cc_start: 0.9067 (t0) cc_final: 0.8714 (t0) REVERT: P 45 GLU cc_start: 0.8565 (mp0) cc_final: 0.8251 (mp0) REVERT: R 88 ARG cc_start: 0.6185 (mmt180) cc_final: 0.5599 (mmt180) REVERT: R 323 GLU cc_start: 0.7793 (pm20) cc_final: 0.7345 (pm20) REVERT: S 166 LYS cc_start: 0.7853 (pptt) cc_final: 0.7482 (tttt) REVERT: S 247 GLU cc_start: 0.2766 (tm-30) cc_final: 0.2281 (tp30) outliers start: 97 outliers final: 75 residues processed: 398 average time/residue: 0.1586 time to fit residues: 100.8528 Evaluate side-chains 373 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 295 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain J residue 407 ARG Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 385 SER Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 106 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 303 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100320 restraints weight = 48288.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100914 restraints weight = 27628.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101413 restraints weight = 19205.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101986 restraints weight = 17682.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102019 restraints weight = 15252.108| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25495 Z= 0.175 Angle : 0.612 7.466 34735 Z= 0.317 Chirality : 0.045 0.206 3864 Planarity : 0.004 0.076 4455 Dihedral : 5.384 78.376 3475 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 4.09 % Allowed : 13.45 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.18 (0.15), residues: 3178 helix: 1.18 (0.27), residues: 428 sheet: -0.60 (0.17), residues: 967 loop : -1.40 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 250 TYR 0.031 0.002 TYR Q 306 PHE 0.020 0.002 PHE I 14 TRP 0.017 0.001 TRP G 409 HIS 0.005 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00412 (25455) covalent geometry : angle 0.61013 (34655) SS BOND : bond 0.00334 ( 40) SS BOND : angle 1.18797 ( 80) hydrogen bonds : bond 0.03241 ( 748) hydrogen bonds : angle 5.20359 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 305 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6596 (pptt) REVERT: A 168 LYS cc_start: 0.7225 (tppt) cc_final: 0.6797 (mppt) REVERT: A 177 TYR cc_start: 0.6316 (p90) cc_final: 0.6087 (p90) REVERT: B 252 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8768 (ttmm) REVERT: C 136 THR cc_start: 0.8861 (m) cc_final: 0.8626 (p) REVERT: C 366 ARG cc_start: 0.8282 (ptm160) cc_final: 0.7628 (ptm160) REVERT: C 433 MET cc_start: 0.6889 (tmm) cc_final: 0.6564 (mmt) REVERT: F 130 ILE cc_start: 0.6407 (mm) cc_final: 0.5289 (mt) REVERT: F 131 MET cc_start: 0.6888 (mmm) cc_final: 0.6524 (mpp) REVERT: F 136 ILE cc_start: 0.8802 (tp) cc_final: 0.8542 (tp) REVERT: F 174 ASP cc_start: 0.7438 (t0) cc_final: 0.7215 (t0) REVERT: F 176 GLU cc_start: 0.7644 (tt0) cc_final: 0.6545 (tp30) REVERT: F 189 PHE cc_start: 0.6565 (m-80) cc_final: 0.5578 (m-80) REVERT: F 193 HIS cc_start: 0.6879 (p90) cc_final: 0.6658 (p-80) REVERT: F 240 ILE cc_start: 0.8261 (mt) cc_final: 0.7986 (mp) REVERT: F 247 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6686 (mp0) REVERT: G 247 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7893 (tttt) REVERT: I 29 GLU cc_start: 0.8286 (mp0) cc_final: 0.7758 (mp0) REVERT: J 88 ARG cc_start: 0.6116 (mmt180) cc_final: 0.5655 (mmt180) REVERT: J 199 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: P 33 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7371 (ptt) REVERT: P 45 GLU cc_start: 0.8689 (mp0) cc_final: 0.7965 (mp0) REVERT: Q 401 ARG cc_start: 0.7837 (ptp90) cc_final: 0.7143 (ptm160) REVERT: R 88 ARG cc_start: 0.6294 (mmt180) cc_final: 0.5632 (mmt180) REVERT: S 151 MET cc_start: 0.7814 (tpp) cc_final: 0.7390 (mpp) REVERT: S 166 LYS cc_start: 0.8040 (pptt) cc_final: 0.7548 (tttt) outliers start: 111 outliers final: 84 residues processed: 394 average time/residue: 0.1599 time to fit residues: 100.0930 Evaluate side-chains 373 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 285 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 385 SER Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 194 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 275 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 HIS ** R 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100087 restraints weight = 48266.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100077 restraints weight = 27488.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100848 restraints weight = 18682.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101257 restraints weight = 17345.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101340 restraints weight = 15031.485| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25495 Z= 0.177 Angle : 0.615 8.748 34735 Z= 0.317 Chirality : 0.045 0.194 3864 Planarity : 0.004 0.070 4455 Dihedral : 5.358 79.577 3475 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 3.76 % Allowed : 14.49 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.14 (0.15), residues: 3178 helix: 1.12 (0.26), residues: 435 sheet: -0.59 (0.17), residues: 943 loop : -1.34 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 250 TYR 0.028 0.001 TYR Q 306 PHE 0.019 0.002 PHE I 14 TRP 0.017 0.002 TRP G 409 HIS 0.006 0.001 HIS Q 353 Details of bonding type rmsd covalent geometry : bond 0.00419 (25455) covalent geometry : angle 0.61277 (34655) SS BOND : bond 0.00310 ( 40) SS BOND : angle 1.24259 ( 80) hydrogen bonds : bond 0.03210 ( 748) hydrogen bonds : angle 5.23058 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 301 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.6947 (pptt) REVERT: A 168 LYS cc_start: 0.7250 (tppt) cc_final: 0.6770 (mppt) REVERT: B 252 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8792 (ttmm) REVERT: C 366 ARG cc_start: 0.8323 (ptm160) cc_final: 0.7799 (ptm160) REVERT: C 404 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7971 (ptmm) REVERT: C 433 MET cc_start: 0.7273 (tmm) cc_final: 0.7061 (mmt) REVERT: F 130 ILE cc_start: 0.6642 (mm) cc_final: 0.5749 (mt) REVERT: F 131 MET cc_start: 0.7108 (mmm) cc_final: 0.6586 (mpp) REVERT: F 136 ILE cc_start: 0.8812 (tp) cc_final: 0.8566 (tp) REVERT: F 175 LEU cc_start: 0.7978 (mt) cc_final: 0.7746 (pp) REVERT: F 176 GLU cc_start: 0.7757 (tt0) cc_final: 0.6821 (tp30) REVERT: F 189 PHE cc_start: 0.6619 (m-80) cc_final: 0.5699 (m-80) REVERT: F 240 ILE cc_start: 0.8425 (mt) cc_final: 0.8156 (mp) REVERT: F 247 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6855 (mp0) REVERT: G 247 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7860 (tttt) REVERT: J 88 ARG cc_start: 0.6262 (mmt180) cc_final: 0.5910 (mmt180) REVERT: J 199 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: J 256 HIS cc_start: 0.7969 (p-80) cc_final: 0.7468 (p-80) REVERT: P 33 MET cc_start: 0.8228 (ptp) cc_final: 0.7359 (ptt) REVERT: P 45 GLU cc_start: 0.8731 (mp0) cc_final: 0.8057 (mp0) REVERT: Q 354 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: Q 401 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7308 (ptm160) REVERT: R 88 ARG cc_start: 0.6377 (mmt180) cc_final: 0.5757 (mmt180) REVERT: S 120 MET cc_start: 0.7456 (tmm) cc_final: 0.7071 (mtt) REVERT: S 151 MET cc_start: 0.7700 (tpp) cc_final: 0.6969 (mmp) REVERT: S 166 LYS cc_start: 0.7924 (pptt) cc_final: 0.7543 (tttt) REVERT: S 234 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8401 (tm-30) REVERT: T 14 PHE cc_start: 0.6991 (p90) cc_final: 0.6511 (p90) outliers start: 102 outliers final: 88 residues processed: 384 average time/residue: 0.1540 time to fit residues: 94.4682 Evaluate side-chains 383 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 291 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 354 GLU Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 117 optimal weight: 50.0000 chunk 233 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 HIS ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS P 37 ASN ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098334 restraints weight = 48523.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099558 restraints weight = 26764.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099705 restraints weight = 17453.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100156 restraints weight = 17809.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100153 restraints weight = 15445.934| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25495 Z= 0.192 Angle : 0.620 7.308 34735 Z= 0.321 Chirality : 0.046 0.214 3864 Planarity : 0.004 0.075 4455 Dihedral : 5.406 80.429 3475 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 3.87 % Allowed : 15.11 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.15 (0.15), residues: 3178 helix: 1.16 (0.26), residues: 433 sheet: -0.61 (0.17), residues: 975 loop : -1.34 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 67 TYR 0.021 0.002 TYR G 308 PHE 0.020 0.002 PHE I 14 TRP 0.017 0.002 TRP G 409 HIS 0.005 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00456 (25455) covalent geometry : angle 0.61843 (34655) SS BOND : bond 0.00305 ( 40) SS BOND : angle 1.20630 ( 80) hydrogen bonds : bond 0.03258 ( 748) hydrogen bonds : angle 5.26717 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 299 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6976 (pptt) REVERT: A 148 PHE cc_start: 0.7825 (m-80) cc_final: 0.7520 (m-80) REVERT: A 168 LYS cc_start: 0.6959 (tppt) cc_final: 0.6737 (mptt) REVERT: B 305 GLU cc_start: 0.7379 (tt0) cc_final: 0.7145 (tt0) REVERT: C 346 LEU cc_start: 0.8277 (mt) cc_final: 0.7935 (mt) REVERT: C 366 ARG cc_start: 0.8315 (ptm160) cc_final: 0.7749 (ptm160) REVERT: C 433 MET cc_start: 0.7430 (tmm) cc_final: 0.7002 (mmt) REVERT: F 130 ILE cc_start: 0.7828 (mm) cc_final: 0.7218 (mm) REVERT: F 131 MET cc_start: 0.6952 (mmm) cc_final: 0.6736 (mpp) REVERT: F 136 ILE cc_start: 0.8806 (tp) cc_final: 0.8520 (tp) REVERT: F 175 LEU cc_start: 0.7860 (mt) cc_final: 0.7582 (pp) REVERT: F 176 GLU cc_start: 0.7547 (tt0) cc_final: 0.7068 (tp30) REVERT: F 189 PHE cc_start: 0.6747 (m-80) cc_final: 0.5807 (m-80) REVERT: F 240 ILE cc_start: 0.8409 (mt) cc_final: 0.8129 (mp) REVERT: F 247 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7051 (mp0) REVERT: G 247 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7904 (tttt) REVERT: I 29 GLU cc_start: 0.8351 (mp0) cc_final: 0.7900 (mp0) REVERT: J 88 ARG cc_start: 0.6306 (mmt180) cc_final: 0.5751 (mmt180) REVERT: J 199 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: J 256 HIS cc_start: 0.7819 (p-80) cc_final: 0.7453 (p-80) REVERT: P 33 MET cc_start: 0.7945 (ptp) cc_final: 0.7197 (ptt) REVERT: P 45 GLU cc_start: 0.8753 (mp0) cc_final: 0.8067 (mp0) REVERT: Q 354 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: R 88 ARG cc_start: 0.6448 (mmt180) cc_final: 0.5813 (mmt180) REVERT: S 120 MET cc_start: 0.7560 (tmm) cc_final: 0.7212 (mtt) REVERT: S 151 MET cc_start: 0.7675 (tpp) cc_final: 0.7410 (mpp) REVERT: S 166 LYS cc_start: 0.7980 (pptt) cc_final: 0.7568 (tttt) REVERT: S 234 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8371 (tm-30) outliers start: 105 outliers final: 90 residues processed: 386 average time/residue: 0.1564 time to fit residues: 96.5643 Evaluate side-chains 381 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 288 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 160 ASN Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 354 GLU Chi-restraints excluded: chain Q residue 385 SER Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 263 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 295 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 overall best weight: 7.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 396 GLN C 349 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 HIS ** J 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 HIS T 37 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096776 restraints weight = 48270.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097951 restraints weight = 25873.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.098351 restraints weight = 17202.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099038 restraints weight = 16255.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098989 restraints weight = 14313.947| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 25495 Z= 0.234 Angle : 0.667 10.201 34735 Z= 0.344 Chirality : 0.047 0.215 3864 Planarity : 0.005 0.070 4455 Dihedral : 5.599 82.457 3475 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 3.87 % Allowed : 15.37 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -1.32 (0.15), residues: 3178 helix: 1.05 (0.26), residues: 429 sheet: -0.64 (0.16), residues: 1060 loop : -1.56 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 67 TYR 0.023 0.002 TYR G 308 PHE 0.018 0.002 PHE I 14 TRP 0.022 0.002 TRP F 202 HIS 0.006 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00557 (25455) covalent geometry : angle 0.66432 (34655) SS BOND : bond 0.00377 ( 40) SS BOND : angle 1.37853 ( 80) hydrogen bonds : bond 0.03515 ( 748) hydrogen bonds : angle 5.36946 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 313 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7097 (pptt) REVERT: A 148 PHE cc_start: 0.7849 (m-80) cc_final: 0.7443 (m-80) REVERT: A 149 ARG cc_start: 0.7433 (ttt-90) cc_final: 0.7127 (ttt-90) REVERT: A 168 LYS cc_start: 0.6804 (tppt) cc_final: 0.6590 (mptt) REVERT: A 228 ARG cc_start: 0.6211 (mtt180) cc_final: 0.5659 (mtt-85) REVERT: A 257 MET cc_start: 0.8271 (ptp) cc_final: 0.7737 (mpp) REVERT: C 366 ARG cc_start: 0.8330 (ptm160) cc_final: 0.7832 (ptm160) REVERT: C 433 MET cc_start: 0.7524 (tmm) cc_final: 0.7063 (mmt) REVERT: F 175 LEU cc_start: 0.7748 (mt) cc_final: 0.7157 (pp) REVERT: F 176 GLU cc_start: 0.7490 (tt0) cc_final: 0.7019 (tp30) REVERT: F 189 PHE cc_start: 0.6613 (m-80) cc_final: 0.5524 (m-80) REVERT: F 190 LYS cc_start: 0.7929 (mttt) cc_final: 0.7443 (mtmm) REVERT: F 203 HIS cc_start: 0.8640 (t-90) cc_final: 0.8038 (t-90) REVERT: F 247 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7134 (mp0) REVERT: F 274 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7423 (mm-40) REVERT: G 247 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7960 (tttt) REVERT: I 29 GLU cc_start: 0.8333 (mp0) cc_final: 0.7849 (mp0) REVERT: J 88 ARG cc_start: 0.6045 (mmt180) cc_final: 0.5435 (mmt180) REVERT: J 199 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: P 33 MET cc_start: 0.8054 (ptp) cc_final: 0.7468 (ptt) REVERT: P 45 GLU cc_start: 0.8768 (mp0) cc_final: 0.8566 (mp0) REVERT: Q 225 GLN cc_start: 0.6152 (pt0) cc_final: 0.5931 (pt0) REVERT: Q 401 ARG cc_start: 0.7786 (ptp90) cc_final: 0.7496 (ptm160) REVERT: R 88 ARG cc_start: 0.6503 (mmt180) cc_final: 0.5792 (mmt180) REVERT: S 120 MET cc_start: 0.7698 (tmm) cc_final: 0.7283 (mtt) REVERT: S 234 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8373 (tm-30) outliers start: 105 outliers final: 90 residues processed: 398 average time/residue: 0.1545 time to fit residues: 98.0310 Evaluate side-chains 395 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 303 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 436 LEU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 137 GLU Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 160 ASN Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 179 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 282 SER Chi-restraints excluded: chain Q residue 385 SER Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 140 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 230 ILE Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 263 VAL Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 192 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 66 optimal weight: 40.0000 chunk 190 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 239 optimal weight: 0.0010 chunk 116 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 HIS ** Q 256 HIS ** 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 = 0.3795 r_free = 0.3795 target = 0.139080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105042 restraints weight = 47941.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105564 restraints weight = 28391.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106574 restraints weight = 18571.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106935 restraints weight = 16634.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107000 restraints weight = 14529.572| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25495 Z= 0.138 Angle : 0.613 14.111 34735 Z= 0.314 Chirality : 0.045 0.189 3864 Planarity : 0.004 0.071 4455 Dihedral : 5.309 82.186 3475 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 3.24 % Allowed : 15.81 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -1.12 (0.15), residues: 3178 helix: 1.23 (0.27), residues: 415 sheet: -0.56 (0.17), residues: 958 loop : -1.34 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 213 TYR 0.020 0.001 TYR G 308 PHE 0.023 0.001 PHE R 389 TRP 0.016 0.001 TRP J 236 HIS 0.004 0.001 HIS Q 28 Details of bonding type rmsd covalent geometry : bond 0.00322 (25455) covalent geometry : angle 0.60977 (34655) SS BOND : bond 0.00393 ( 40) SS BOND : angle 1.43426 ( 80) hydrogen bonds : bond 0.03063 ( 748) hydrogen bonds : angle 5.18727 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6356 Ramachandran restraints generated. 3178 Oldfield, 0 Emsley, 3178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7022 (pptt) REVERT: A 149 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7169 (ttt-90) REVERT: A 168 LYS cc_start: 0.6806 (tppt) cc_final: 0.6599 (mptt) REVERT: A 257 MET cc_start: 0.8240 (ptp) cc_final: 0.7682 (mpp) REVERT: C 346 LEU cc_start: 0.8134 (mt) cc_final: 0.7718 (mt) REVERT: C 404 LYS cc_start: 0.8238 (mtmt) cc_final: 0.8025 (ptmm) REVERT: C 433 MET cc_start: 0.7530 (tmm) cc_final: 0.7093 (mmt) REVERT: F 131 MET cc_start: 0.7113 (mmm) cc_final: 0.6851 (mpp) REVERT: F 176 GLU cc_start: 0.7531 (tt0) cc_final: 0.7103 (tp30) REVERT: F 189 PHE cc_start: 0.6808 (m-80) cc_final: 0.5807 (m-80) REVERT: F 202 TRP cc_start: 0.7520 (t60) cc_final: 0.7193 (t60) REVERT: F 223 LYS cc_start: 0.8444 (mptt) cc_final: 0.7623 (tptm) REVERT: F 247 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7141 (mp0) REVERT: F 274 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7463 (mm-40) REVERT: G 247 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7866 (tttt) REVERT: I 29 GLU cc_start: 0.8325 (mp0) cc_final: 0.7816 (mp0) REVERT: J 88 ARG cc_start: 0.6141 (mmt180) cc_final: 0.5585 (mmt180) REVERT: J 199 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: P 33 MET cc_start: 0.8006 (ptp) cc_final: 0.7251 (ptt) REVERT: P 45 GLU cc_start: 0.8743 (mp0) cc_final: 0.8018 (mp0) REVERT: R 88 ARG cc_start: 0.6359 (mmt180) cc_final: 0.5730 (mmt180) REVERT: R 323 GLU cc_start: 0.7724 (pm20) cc_final: 0.7367 (pm20) REVERT: R 389 PHE cc_start: 0.7481 (t80) cc_final: 0.7185 (t80) REVERT: S 119 VAL cc_start: 0.6911 (t) cc_final: 0.6665 (p) REVERT: S 120 MET cc_start: 0.7667 (tmm) cc_final: 0.7176 (mtt) REVERT: S 184 MET cc_start: 0.8106 (ptp) cc_final: 0.7866 (ptp) REVERT: S 191 TYR cc_start: 0.7333 (p90) cc_final: 0.7003 (p90) REVERT: S 234 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8331 (tm-30) REVERT: T 35 SER cc_start: 0.8097 (t) cc_final: 0.7716 (m) outliers start: 88 outliers final: 76 residues processed: 385 average time/residue: 0.1632 time to fit residues: 99.3762 Evaluate side-chains 380 residues out of total 2713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 68 CYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 407 TRP Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain F residue 152 HIS Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain G residue 413 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 199 GLU Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain J residue 402 LEU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 168 HIS Chi-restraints excluded: chain Q residue 189 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 397 LEU Chi-restraints excluded: chain Q residue 402 LEU Chi-restraints excluded: chain R residue 22 CYS Chi-restraints excluded: chain R residue 66 MET Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 263 VAL Chi-restraints excluded: chain T residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 306 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.0570 chunk 60 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 252 optimal weight: 9.9990 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** B 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN ** F 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103981 restraints weight = 47475.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105555 restraints weight = 25168.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105644 restraints weight = 16564.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106127 restraints weight = 16820.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106084 restraints weight = 14239.690| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25495 Z= 0.114 Angle : 0.609 13.753 34735 Z= 0.310 Chirality : 0.045 0.217 3864 Planarity : 0.004 0.070 4455 Dihedral : 5.123 81.804 3475 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 2.69 % Allowed : 16.70 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.95 (0.15), residues: 3178 helix: 1.46 (0.27), residues: 407 sheet: -0.43 (0.17), residues: 986 loop : -1.25 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 213 TYR 0.025 0.001 TYR B 434 PHE 0.021 0.001 PHE R 389 TRP 0.017 0.001 TRP J 236 HIS 0.017 0.001 HIS Q 168 Details of bonding type rmsd covalent geometry : bond 0.00260 (25455) covalent geometry : angle 0.60607 (34655) SS BOND : bond 0.00231 ( 40) SS BOND : angle 1.37287 ( 80) hydrogen bonds : bond 0.02918 ( 748) hydrogen bonds : angle 5.11618 ( 1947) =============================================================================== Job complete usr+sys time: 4336.76 seconds wall clock time: 75 minutes 42.24 seconds (4542.24 seconds total)