Starting phenix.real_space_refine on Sat Aug 8 00:55:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298.map" model { file = "/net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oz5_17298/08_2026/8oz5_17298_trim.cif" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 K 6 8.98 5 Fe 12 7.16 5 P 24 5.49 5 S 174 5.16 5 C 15708 2.51 5 N 4266 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24994 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4049 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 29, 'TRANS': 484} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Unusual residues: {' K': 1, ' CA': 1, ' FE': 2, 'BYN': 1, 'WC8': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.29, per 1000 atoms: 0.17 Number of scatterers: 24994 At special positions: 0 Unit cell: (136.431, 148.149, 92.907, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 6 19.99 K 6 19.00 S 174 16.00 P 24 15.00 O 4798 8.00 N 4266 7.00 C 15708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 918.3 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 30 sheets defined 38.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.653A pdb=" N GLU A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 334 through 357 removed outlier: 4.856A pdb=" N VAL A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR A 371 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU B 122 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.694A pdb=" N THR B 371 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.519A pdb=" N ASN B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 430 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 504 through 514 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.901A pdb=" N SER B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.662A pdb=" N TRP C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 Processing helix chain 'C' and resid 188 through 197 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR C 371 " --> pdb=" O TYR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN C 393 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 430 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 504 through 514 Processing helix chain 'C' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 162 Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.694A pdb=" N THR D 371 " --> pdb=" O TYR D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 430 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 517 through 526 removed outlier: 3.901A pdb=" N SER D 521 " --> pdb=" O GLY D 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 92 through 106 Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.662A pdb=" N TRP E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 188 through 197 Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 234 through 244 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'E' and resid 334 through 357 removed outlier: 4.856A pdb=" N VAL E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR E 371 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 430 Processing helix chain 'E' and resid 450 through 455 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 504 through 514 Processing helix chain 'E' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER E 521 " --> pdb=" O GLY E 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 162 Processing helix chain 'F' and resid 188 through 197 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 234 through 244 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'F' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR F 371 " --> pdb=" O TYR F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 389 through 402 removed outlier: 3.519A pdb=" N ASN F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 504 through 514 Processing helix chain 'F' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER F 521 " --> pdb=" O GLY F 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL A 35 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 72 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL A 111 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 251 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA A 308 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG A 274 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 310 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 268 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE A 316 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 266 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 157 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 207 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN A 173 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN A 379 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 364 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 377 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 408 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA A 477 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 410 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL B 35 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 72 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL B 111 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS B 251 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA B 308 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG B 274 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 310 " --> pdb=" O HIS B 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU B 268 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 316 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 266 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 157 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 207 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN B 173 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 361 through 365 removed outlier: 6.648A pdb=" N GLN B 379 " --> pdb=" O GLN B 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 364 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 377 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 408 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA B 477 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 410 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL C 35 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG C 72 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL C 111 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS C 251 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA C 308 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG C 274 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 310 " --> pdb=" O HIS C 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU C 268 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 316 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 266 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 157 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 207 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN C 173 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN C 379 " --> pdb=" O GLN C 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL C 364 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 377 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 408 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 477 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 410 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL D 35 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG D 72 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 112 removed outlier: 6.428A pdb=" N VAL D 111 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS D 251 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA D 308 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG D 274 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 310 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU D 268 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D 316 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 266 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 157 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 207 " --> pdb=" O CYS D 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN D 173 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN D 379 " --> pdb=" O GLN D 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 364 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 377 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 408 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA D 477 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA D 410 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL E 35 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG E 72 " --> pdb=" O ILE E 327 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL E 111 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS E 251 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 125 removed outlier: 8.950A pdb=" N ALA E 308 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ARG E 274 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR E 310 " --> pdb=" O HIS E 272 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU E 268 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 316 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL E 266 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 157 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR E 207 " --> pdb=" O CYS E 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN E 173 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 361 through 365 removed outlier: 6.648A pdb=" N GLN E 379 " --> pdb=" O GLN E 362 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL E 364 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 377 " --> pdb=" O VAL E 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA E 408 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA E 477 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA E 410 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL F 35 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG F 72 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.430A pdb=" N VAL F 111 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS F 251 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA F 308 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG F 274 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 310 " --> pdb=" O HIS F 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU F 268 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE F 316 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL F 266 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL F 157 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 207 " --> pdb=" O CYS F 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN F 173 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN F 379 " --> pdb=" O GLN F 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL F 364 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 377 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA F 408 " --> pdb=" O ILE F 475 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 477 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA F 410 " --> pdb=" O ALA F 477 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2556 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: 4.77 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 4134 1.27 - 1.41: 6405 1.41 - 1.55: 14587 1.55 - 1.69: 86 1.69 - 1.82: 288 Bond restraints: 25500 Sorted by residual: bond pdb=" C ALA A 523 " pdb=" N ARG A 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.94e+02 bond pdb=" C ALA E 523 " pdb=" N ARG E 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.94e+02 bond pdb=" C ALA F 523 " pdb=" N ARG F 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.93e+02 bond pdb=" C ALA C 523 " pdb=" N ARG C 524 " ideal model delta sigma weight residual 1.334 1.643 -0.309 1.27e-02 6.20e+03 5.91e+02 bond pdb=" C ALA D 523 " pdb=" N ARG D 524 " ideal model delta sigma weight residual 1.334 1.643 -0.309 1.27e-02 6.20e+03 5.91e+02 ... (remaining 25495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 34335 3.87 - 7.74: 251 7.74 - 11.61: 94 11.61 - 15.48: 12 15.48 - 19.35: 12 Bond angle restraints: 34704 Sorted by residual: angle pdb=" O4A WC8 A 602 " pdb=" P2A WC8 A 602 " pdb=" O5A WC8 A 602 " ideal model delta sigma weight residual 120.63 101.28 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O4A WC8 D 602 " pdb=" P2A WC8 D 602 " pdb=" O5A WC8 D 602 " ideal model delta sigma weight residual 120.63 101.29 19.34 3.00e+00 1.11e-01 4.15e+01 angle pdb=" O4A WC8 B 602 " pdb=" P2A WC8 B 602 " pdb=" O5A WC8 B 602 " ideal model delta sigma weight residual 120.63 101.31 19.32 3.00e+00 1.11e-01 4.15e+01 angle pdb=" O4A WC8 F 602 " pdb=" P2A WC8 F 602 " pdb=" O5A WC8 F 602 " ideal model delta sigma weight residual 120.63 101.32 19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" O4A WC8 C 602 " pdb=" P2A WC8 C 602 " pdb=" O5A WC8 C 602 " ideal model delta sigma weight residual 120.63 101.33 19.30 3.00e+00 1.11e-01 4.14e+01 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 14295 20.58 - 41.17: 861 41.17 - 61.75: 300 61.75 - 82.34: 18 82.34 - 102.92: 18 Dihedral angle restraints: 15492 sinusoidal: 6672 harmonic: 8820 Sorted by residual: dihedral pdb=" CA ARG B 489 " pdb=" C ARG B 489 " pdb=" N PRO B 490 " pdb=" CA PRO B 490 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ARG C 489 " pdb=" C ARG C 489 " pdb=" N PRO C 490 " pdb=" CA PRO C 490 " ideal model delta harmonic sigma weight residual 180.00 -147.49 -32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ARG D 489 " pdb=" C ARG D 489 " pdb=" N PRO D 490 " pdb=" CA PRO D 490 " ideal model delta harmonic sigma weight residual -180.00 -147.50 -32.50 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 15489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 3672 0.965 - 1.930: 0 1.930 - 2.895: 0 2.895 - 3.860: 0 3.860 - 4.825: 6 Chirality restraints: 3678 Sorted by residual: chirality pdb=" C20 BYN F 601 " pdb=" C19 BYN F 601 " pdb=" C21 BYN F 601 " pdb=" O5 BYN F 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C20 BYN C 601 " pdb=" C19 BYN C 601 " pdb=" C21 BYN C 601 " pdb=" O5 BYN C 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C20 BYN E 601 " pdb=" C19 BYN E 601 " pdb=" C21 BYN E 601 " pdb=" O5 BYN E 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.81e+02 ... (remaining 3675 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BYN C 601 " -0.035 2.00e-02 2.50e+03 9.71e-02 2.59e+02 pdb=" C18 BYN C 601 " 0.103 2.00e-02 2.50e+03 pdb=" C2 BYN C 601 " 0.029 2.00e-02 2.50e+03 pdb=" C3 BYN C 601 " 0.070 2.00e-02 2.50e+03 pdb=" C4 BYN C 601 " 0.056 2.00e-02 2.50e+03 pdb=" C6 BYN C 601 " -0.251 2.00e-02 2.50e+03 pdb=" N1 BYN C 601 " -0.024 2.00e-02 2.50e+03 pdb=" N2 BYN C 601 " 0.005 2.00e-02 2.50e+03 pdb=" N4 BYN C 601 " 0.102 2.00e-02 2.50e+03 pdb=" O1 BYN C 601 " -0.088 2.00e-02 2.50e+03 pdb=" O3 BYN C 601 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN A 601 " 0.035 2.00e-02 2.50e+03 9.71e-02 2.59e+02 pdb=" C18 BYN A 601 " -0.103 2.00e-02 2.50e+03 pdb=" C2 BYN A 601 " -0.029 2.00e-02 2.50e+03 pdb=" C3 BYN A 601 " -0.070 2.00e-02 2.50e+03 pdb=" C4 BYN A 601 " -0.056 2.00e-02 2.50e+03 pdb=" C6 BYN A 601 " 0.251 2.00e-02 2.50e+03 pdb=" N1 BYN A 601 " 0.024 2.00e-02 2.50e+03 pdb=" N2 BYN A 601 " -0.004 2.00e-02 2.50e+03 pdb=" N4 BYN A 601 " -0.102 2.00e-02 2.50e+03 pdb=" O1 BYN A 601 " 0.088 2.00e-02 2.50e+03 pdb=" O3 BYN A 601 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN D 601 " -0.035 2.00e-02 2.50e+03 9.70e-02 2.59e+02 pdb=" C18 BYN D 601 " 0.103 2.00e-02 2.50e+03 pdb=" C2 BYN D 601 " 0.029 2.00e-02 2.50e+03 pdb=" C3 BYN D 601 " 0.069 2.00e-02 2.50e+03 pdb=" C4 BYN D 601 " 0.057 2.00e-02 2.50e+03 pdb=" C6 BYN D 601 " -0.251 2.00e-02 2.50e+03 pdb=" N1 BYN D 601 " -0.024 2.00e-02 2.50e+03 pdb=" N2 BYN D 601 " 0.004 2.00e-02 2.50e+03 pdb=" N4 BYN D 601 " 0.102 2.00e-02 2.50e+03 pdb=" O1 BYN D 601 " -0.089 2.00e-02 2.50e+03 pdb=" O3 BYN D 601 " 0.034 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 276 2.56 - 3.21: 23612 3.21 - 3.85: 52351 3.85 - 4.50: 77442 4.50 - 5.14: 121438 Nonbonded interactions: 275119 Sorted by model distance: nonbonded pdb=" O9 BYN B 601 " pdb="FE FE B 603 " model vdw 1.920 2.260 nonbonded pdb=" O9 BYN F 601 " pdb="FE FE F 603 " model vdw 1.920 2.260 nonbonded pdb=" O9 BYN A 601 " pdb="FE FE A 603 " model vdw 1.920 2.260 nonbonded pdb=" O9 BYN E 601 " pdb="FE FE E 603 " model vdw 1.921 2.260 nonbonded pdb=" O9 BYN D 601 " pdb="FE FE D 603 " model vdw 1.921 2.260 ... (remaining 275114 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 2.670 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 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 : 0.011 0.309 25500 Z= 0.620 Angle : 1.012 19.350 34704 Z= 0.459 Chirality : 0.199 4.825 3678 Planarity : 0.005 0.097 4470 Dihedral : 15.008 102.923 9852 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.34 % Favored : 97.07 % Rotamer: Outliers : 2.08 % Allowed : 1.39 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.21 % 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: -1.59 (0.14), residues: 3072 helix: -0.45 (0.15), residues: 996 sheet: -1.82 (0.22), residues: 486 loop : -1.12 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.010 0.001 TYR C 226 PHE 0.011 0.001 PHE A 449 TRP 0.005 0.001 TRP A 90 HIS 0.013 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.62 (25500) covalent geometry : angle 1.01235 / 0.46 (34704) hydrogen bonds : bond 0.16736 / 11.04 ( 918) hydrogen bonds : angle 6.71841 / 4.78 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.982 Fit side-chains REVERT: A 511 MET cc_start: 0.8832 (mtp) cc_final: 0.8563 (mtm) REVERT: B 18 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: D 511 MET cc_start: 0.8860 (mtp) cc_final: 0.8597 (mtm) outliers start: 54 outliers final: 15 residues processed: 245 average time/residue: 0.8565 time to fit residues: 235.5953 Evaluate side-chains 188 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 500 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 183 GLN A 293 HIS A 295 HIS A 393 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 293 HIS B 295 HIS B 393 ASN ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 293 HIS C 295 HIS C 393 ASN ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 293 HIS D 295 HIS D 393 ASN ** D 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 293 HIS E 295 HIS E 393 ASN ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 293 HIS F 295 HIS F 393 ASN ** F 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.059966 restraints weight = 41137.940| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.95 r_work: 0.2573 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9292 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 25500 Z= 0.173 Angle : 0.623 7.621 34704 Z= 0.316 Chirality : 0.047 0.175 3678 Planarity : 0.004 0.028 4470 Dihedral : 11.859 117.354 4064 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.09 % Favored : 96.32 % Rotamer: Outliers : 0.58 % Allowed : 5.63 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.21 % 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: -0.64 (0.15), residues: 3072 helix: 0.36 (0.16), residues: 1002 sheet: -1.47 (0.21), residues: 498 loop : -0.48 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 524 TYR 0.016 0.001 TYR A 218 PHE 0.013 0.001 PHE F 224 TRP 0.005 0.001 TRP D 425 HIS 0.006 0.002 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (25500) covalent geometry : angle 0.62286 / 0.32 (34704) hydrogen bonds : bond 0.05673 / 3.67 ( 918) hydrogen bonds : angle 5.19229 / 3.70 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.040 Fit side-chains REVERT: A 147 MET cc_start: 0.9304 (mtm) cc_final: 0.9052 (mtt) REVERT: B 302 MET cc_start: 0.8919 (tpt) cc_final: 0.8706 (mmm) REVERT: B 491 VAL cc_start: 0.7366 (p) cc_final: 0.7165 (t) REVERT: C 491 VAL cc_start: 0.7375 (p) cc_final: 0.7168 (t) REVERT: D 147 MET cc_start: 0.9294 (mtm) cc_final: 0.9057 (mtt) REVERT: F 453 GLU cc_start: 0.8007 (tt0) cc_final: 0.7405 (mt-10) REVERT: F 515 MET cc_start: 0.9045 (mtp) cc_final: 0.8781 (mtp) outliers start: 15 outliers final: 2 residues processed: 209 average time/residue: 0.7221 time to fit residues: 173.6297 Evaluate side-chains 176 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain D residue 422 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 9 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 225 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 271 optimal weight: 0.0980 chunk 159 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 357 GLN C 293 HIS C 357 GLN D 293 HIS ** D 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS F 293 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.060970 restraints weight = 41486.713| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.99 r_work: 0.2590 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9259 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25500 Z= 0.132 Angle : 0.576 8.118 34704 Z= 0.292 Chirality : 0.046 0.212 3678 Planarity : 0.003 0.032 4470 Dihedral : 11.238 133.201 4038 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.39 % Favored : 96.42 % Rotamer: Outliers : 1.12 % Allowed : 5.13 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.21 % 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: -0.26 (0.15), residues: 3072 helix: 0.72 (0.17), residues: 1002 sheet: -1.14 (0.21), residues: 528 loop : -0.30 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 320 TYR 0.013 0.001 TYR F 218 PHE 0.013 0.001 PHE A 292 TRP 0.009 0.001 TRP B 373 HIS 0.009 0.002 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25500) covalent geometry : angle 0.57553 / 0.29 (34704) hydrogen bonds : bond 0.04708 / 3.06 ( 918) hydrogen bonds : angle 4.86961 / 3.48 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.061 Fit side-chains REVERT: A 147 MET cc_start: 0.9311 (mtm) cc_final: 0.9087 (mtt) REVERT: A 302 MET cc_start: 0.8832 (mmm) cc_final: 0.7986 (mmm) REVERT: C 202 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8804 (pm20) REVERT: C 302 MET cc_start: 0.8878 (tpt) cc_final: 0.8641 (tpt) REVERT: D 147 MET cc_start: 0.9293 (mtm) cc_final: 0.9064 (mtt) REVERT: D 302 MET cc_start: 0.8859 (mmm) cc_final: 0.8004 (mmm) REVERT: E 322 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: E 422 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9100 (t0) REVERT: F 422 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.9079 (t0) REVERT: F 450 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8790 (mmt) REVERT: F 453 GLU cc_start: 0.7900 (tt0) cc_final: 0.7400 (mt-10) outliers start: 29 outliers final: 10 residues processed: 209 average time/residue: 0.6901 time to fit residues: 166.0732 Evaluate side-chains 188 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 422 ASP Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 126 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS C 293 HIS D 293 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.059586 restraints weight = 41189.440| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.96 r_work: 0.2551 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25500 Z= 0.192 Angle : 0.608 7.595 34704 Z= 0.312 Chirality : 0.047 0.272 3678 Planarity : 0.004 0.033 4470 Dihedral : 11.232 135.508 4038 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.42 % Rotamer: Outliers : 1.23 % Allowed : 5.63 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.21 % 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: -0.14 (0.15), residues: 3072 helix: 0.78 (0.17), residues: 1002 sheet: -1.01 (0.22), residues: 528 loop : -0.22 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 320 TYR 0.013 0.001 TYR B 218 PHE 0.016 0.001 PHE F 224 TRP 0.008 0.001 TRP A 373 HIS 0.010 0.002 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (25500) covalent geometry : angle 0.60823 / 0.31 (34704) hydrogen bonds : bond 0.05335 / 3.45 ( 918) hydrogen bonds : angle 4.88211 / 3.49 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.087 Fit side-chains REVERT: C 302 MET cc_start: 0.8900 (tpt) cc_final: 0.8667 (tpt) REVERT: E 422 ASP cc_start: 0.9398 (OUTLIER) cc_final: 0.9094 (t0) REVERT: F 302 MET cc_start: 0.8875 (mmm) cc_final: 0.8612 (mmm) REVERT: F 453 GLU cc_start: 0.7926 (tt0) cc_final: 0.7416 (mt-10) outliers start: 32 outliers final: 18 residues processed: 207 average time/residue: 0.7579 time to fit residues: 179.8184 Evaluate side-chains 198 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 263 optimal weight: 6.9990 chunk 304 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 284 optimal weight: 0.7980 chunk 257 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS A 357 GLN B 293 HIS C 293 HIS D 293 HIS D 357 GLN E 293 HIS F 293 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.061189 restraints weight = 41152.132| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.99 r_work: 0.2610 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9264 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25500 Z= 0.131 Angle : 0.575 7.323 34704 Z= 0.293 Chirality : 0.045 0.195 3678 Planarity : 0.003 0.034 4470 Dihedral : 11.068 136.651 4038 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.90 % Rotamer: Outliers : 1.54 % Allowed : 5.94 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.03 (0.16), residues: 3072 helix: 0.87 (0.17), residues: 1002 sheet: -0.97 (0.22), residues: 528 loop : -0.14 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 320 TYR 0.013 0.001 TYR A 218 PHE 0.011 0.001 PHE A 292 TRP 0.009 0.001 TRP F 373 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (25500) covalent geometry : angle 0.57512 / 0.29 (34704) hydrogen bonds : bond 0.04524 / 2.94 ( 918) hydrogen bonds : angle 4.74876 / 3.40 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.080 Fit side-chains REVERT: C 202 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8765 (pm20) REVERT: C 302 MET cc_start: 0.8924 (tpt) cc_final: 0.8708 (tpt) REVERT: D 453 GLU cc_start: 0.7798 (tt0) cc_final: 0.7263 (mt-10) REVERT: E 422 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9108 (t0) REVERT: E 515 MET cc_start: 0.8920 (mtp) cc_final: 0.8670 (mtp) REVERT: F 453 GLU cc_start: 0.7870 (tt0) cc_final: 0.7474 (mt-10) REVERT: F 515 MET cc_start: 0.8958 (mtp) cc_final: 0.8730 (mtp) outliers start: 40 outliers final: 14 residues processed: 211 average time/residue: 0.7172 time to fit residues: 173.6592 Evaluate side-chains 200 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 473 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 201 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS A 333 HIS B 293 HIS C 293 HIS D 293 HIS D 333 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.059558 restraints weight = 41278.929| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.98 r_work: 0.2554 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25500 Z= 0.189 Angle : 0.599 7.524 34704 Z= 0.305 Chirality : 0.046 0.218 3678 Planarity : 0.004 0.034 4470 Dihedral : 11.089 137.005 4038 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 1.20 % Allowed : 6.60 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.06 (0.16), residues: 3072 helix: 0.89 (0.17), residues: 1002 sheet: -0.90 (0.22), residues: 528 loop : -0.05 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 320 TYR 0.013 0.001 TYR B 218 PHE 0.014 0.001 PHE F 224 TRP 0.007 0.001 TRP B 373 HIS 0.010 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (25500) covalent geometry : angle 0.59857 / 0.30 (34704) hydrogen bonds : bond 0.05181 / 3.36 ( 918) hydrogen bonds : angle 4.79503 / 3.43 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.976 Fit side-chains REVERT: C 302 MET cc_start: 0.8926 (tpt) cc_final: 0.8665 (tpt) REVERT: E 422 ASP cc_start: 0.9402 (OUTLIER) cc_final: 0.9121 (t0) REVERT: E 515 MET cc_start: 0.9003 (mtp) cc_final: 0.8737 (mtp) REVERT: F 453 GLU cc_start: 0.7916 (tt0) cc_final: 0.7427 (mt-10) REVERT: F 498 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8849 (mttm) REVERT: F 515 MET cc_start: 0.9023 (mtp) cc_final: 0.8756 (mtp) outliers start: 31 outliers final: 19 residues processed: 207 average time/residue: 0.7065 time to fit residues: 167.2692 Evaluate side-chains 204 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 498 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 5 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 262 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS C 293 HIS C 333 HIS D 293 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.058852 restraints weight = 41328.761| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 1.98 r_work: 0.2536 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9289 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25500 Z= 0.225 Angle : 0.617 7.608 34704 Z= 0.316 Chirality : 0.047 0.211 3678 Planarity : 0.004 0.034 4470 Dihedral : 11.136 136.399 4038 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.91 % Favored : 95.77 % Rotamer: Outliers : 1.43 % Allowed : 6.48 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.08 (0.16), residues: 3072 helix: 0.92 (0.17), residues: 996 sheet: -0.85 (0.22), residues: 528 loop : -0.05 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 320 TYR 0.013 0.001 TYR B 218 PHE 0.015 0.001 PHE F 224 TRP 0.006 0.001 TRP E 390 HIS 0.010 0.002 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (25500) covalent geometry : angle 0.61739 / 0.32 (34704) hydrogen bonds : bond 0.05517 / 3.58 ( 918) hydrogen bonds : angle 4.84334 / 3.46 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 1.083 Fit side-chains REVERT: F 453 GLU cc_start: 0.7893 (tt0) cc_final: 0.7412 (mt-10) REVERT: F 515 MET cc_start: 0.9043 (mtp) cc_final: 0.8765 (mtp) outliers start: 37 outliers final: 21 residues processed: 205 average time/residue: 0.6654 time to fit residues: 155.8610 Evaluate side-chains 202 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 220 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS C 293 HIS D 293 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.060534 restraints weight = 41229.227| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 1.99 r_work: 0.2574 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9265 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25500 Z= 0.149 Angle : 0.587 7.495 34704 Z= 0.297 Chirality : 0.045 0.174 3678 Planarity : 0.003 0.035 4470 Dihedral : 11.013 136.895 4038 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.07 % Favored : 95.74 % Rotamer: Outliers : 1.31 % Allowed : 6.56 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.12 (0.16), residues: 3072 helix: 0.93 (0.17), residues: 1002 sheet: -0.84 (0.22), residues: 528 loop : -0.01 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 320 TYR 0.013 0.001 TYR F 218 PHE 0.011 0.001 PHE B 224 TRP 0.007 0.001 TRP C 373 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (25500) covalent geometry : angle 0.58668 / 0.30 (34704) hydrogen bonds : bond 0.04732 / 3.08 ( 918) hydrogen bonds : angle 4.74954 / 3.40 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.098 Fit side-chains REVERT: C 202 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8731 (pm20) REVERT: E 450 MET cc_start: 0.9060 (mmm) cc_final: 0.8848 (mmt) REVERT: F 453 GLU cc_start: 0.7908 (tt0) cc_final: 0.7435 (mt-10) REVERT: F 515 MET cc_start: 0.9034 (mtp) cc_final: 0.8755 (mtp) outliers start: 34 outliers final: 19 residues processed: 205 average time/residue: 0.7130 time to fit residues: 167.2505 Evaluate side-chains 201 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS B 333 HIS C 293 HIS D 293 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.060005 restraints weight = 41283.428| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 1.97 r_work: 0.2553 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2438 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9276 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 25500 Z= 0.197 Angle : 0.609 7.544 34704 Z= 0.310 Chirality : 0.046 0.197 3678 Planarity : 0.004 0.035 4470 Dihedral : 11.060 137.051 4038 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.00 % Favored : 95.77 % Rotamer: Outliers : 1.16 % Allowed : 6.67 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.18 (0.16), residues: 3072 helix: 0.99 (0.17), residues: 996 sheet: -0.81 (0.22), residues: 528 loop : 0.02 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 320 TYR 0.013 0.001 TYR B 218 PHE 0.015 0.001 PHE F 224 TRP 0.007 0.001 TRP C 373 HIS 0.010 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (25500) covalent geometry : angle 0.60863 / 0.31 (34704) hydrogen bonds : bond 0.05196 / 3.37 ( 918) hydrogen bonds : angle 4.79846 / 3.43 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.985 Fit side-chains REVERT: A 370 MET cc_start: 0.9079 (mtt) cc_final: 0.8862 (mtt) REVERT: F 453 GLU cc_start: 0.7947 (tt0) cc_final: 0.7427 (mt-10) REVERT: F 515 MET cc_start: 0.9061 (mtp) cc_final: 0.8777 (mtp) outliers start: 30 outliers final: 17 residues processed: 198 average time/residue: 0.7291 time to fit residues: 164.7990 Evaluate side-chains 197 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 170 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS C 293 HIS D 293 HIS E 293 HIS F 293 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.058865 restraints weight = 41253.562| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 1.99 r_work: 0.2536 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9288 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25500 Z= 0.227 Angle : 0.627 9.058 34704 Z= 0.320 Chirality : 0.047 0.198 3678 Planarity : 0.004 0.038 4470 Dihedral : 11.106 136.398 4038 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 1.04 % Allowed : 6.87 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.17 % 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: 0.18 (0.16), residues: 3072 helix: 0.99 (0.17), residues: 996 sheet: -0.81 (0.22), residues: 528 loop : 0.02 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 320 TYR 0.013 0.001 TYR B 218 PHE 0.016 0.001 PHE F 224 TRP 0.006 0.001 TRP F 390 HIS 0.010 0.002 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (25500) covalent geometry : angle 0.62733 / 0.32 (34704) hydrogen bonds : bond 0.05480 / 3.55 ( 918) hydrogen bonds : angle 4.84080 / 3.46 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.982 Fit side-chains REVERT: A 370 MET cc_start: 0.9124 (mtt) cc_final: 0.8807 (mtt) REVERT: F 453 GLU cc_start: 0.7927 (tt0) cc_final: 0.7407 (mt-10) outliers start: 27 outliers final: 15 residues processed: 196 average time/residue: 0.7774 time to fit residues: 173.4410 Evaluate side-chains 195 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 166 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS B 293 HIS C 293 HIS D 293 HIS E 293 HIS F 293 HIS F 333 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.061696 restraints weight = 41023.033| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.99 r_work: 0.2604 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9248 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25500 Z= 0.122 Angle : 0.577 7.640 34704 Z= 0.291 Chirality : 0.045 0.164 3678 Planarity : 0.003 0.036 4470 Dihedral : 10.915 137.594 4038 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 0.89 % Allowed : 7.18 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.24 (0.16), residues: 3072 helix: 1.03 (0.17), residues: 1002 sheet: -0.81 (0.22), residues: 528 loop : 0.07 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 320 TYR 0.013 0.001 TYR F 218 PHE 0.009 0.001 PHE F 292 TRP 0.010 0.001 TRP C 373 HIS 0.008 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (25500) covalent geometry : angle 0.57738 / 0.29 (34704) hydrogen bonds : bond 0.04287 / 2.79 ( 918) hydrogen bonds : angle 4.67827 / 3.35 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9860.13 seconds wall clock time: 168 minutes 18.27 seconds (10098.27 seconds total)