Starting phenix.real_space_refine on Fri Sep 11 18:49:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974.map" model { file = "/net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/4uis_2974/09_2026/4uis_2974_neut.cif" } resolution = 4.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2965 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5352 2.51 5 N 1523 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3757 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 457} Chain breaks: 7 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 615 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 4 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 210 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1302 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 1, 'TRANS': 205} Chain breaks: 6 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 969 Classifications: {'peptide': 196} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 185} Link IDs: {'CIS': 1, 'TRANS': 194} Chain breaks: 4 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 196} Unresolved non-hydrogen planarities: 196 Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 306 Classifications: {'peptide': 62} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 58} Link IDs: {'TRANS': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 62} Unresolved non-hydrogen planarities: 62 Chain: "G" Number of atoms: 1349 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 162, 1292 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'TRANS': 158} Chain breaks: 6 bond proxies already assigned to first conformer: 1250 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AGLU G 5 " occ=0.32 ... (16 atoms not shown) pdb=" OE2BGLU G 5 " occ=0.68 residue: pdb=" N AARG G 76 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG G 76 " occ=0.43 residue: pdb=" N ALYS G 135 " occ=0.29 ... (16 atoms not shown) pdb=" NZ BLYS G 135 " occ=0.71 residue: pdb=" N AARG G 137 " occ=0.41 ... (20 atoms not shown) pdb=" NH2BARG G 137 " occ=0.59 residue: pdb=" N AASN G 140 " occ=0.46 ... (14 atoms not shown) pdb=" ND2BASN G 140 " occ=0.54 residue: pdb=" N AGLN G 141 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN G 141 " occ=0.54 Time building chain proxies: 1.94, per 1000 atoms: 0.23 Number of scatterers: 8518 At special positions: 0 Unit cell: (122.76, 113.52, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1611 8.00 N 1523 7.00 C 5352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.04 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 Links applied TRANS " UNK B 101 " - " ILE B 100 " " UNK B 464 " - " HIS B 463 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 204.8 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 97.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.440A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.042A pdb=" N GLY A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 201 removed outlier: 4.087A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A 199 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.707A pdb=" N PHE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.652A pdb=" N VAL A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.753A pdb=" N SER A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.089A pdb=" N SER A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.774A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.988A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.583A pdb=" N ASP A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 542 " --> pdb=" O ARG A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 561 through 575 removed outlier: 3.584A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 665 through 687 removed outlier: 3.576A pdb=" N UNK A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 101 removed outlier: 3.723A pdb=" N UNK B 73 " --> pdb=" O UNK B 69 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.679A pdb=" N UNK B 171 " --> pdb=" O UNK B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.570A pdb=" N UNK B 198 " --> pdb=" O UNK B 194 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N UNK B 216 " --> pdb=" O UNK B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.671A pdb=" N GLN B 222 " --> pdb=" O UNK B 218 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N UNK B 241 " --> pdb=" O UNK B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.851A pdb=" N UNK B 250 " --> pdb=" O UNK B 246 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 257 " --> pdb=" O UNK B 253 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N UNK B 265 " --> pdb=" O UNK B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.941A pdb=" N UNK B 399 " --> pdb=" O UNK B 395 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK B 400 " --> pdb=" O UNK B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.505A pdb=" N UNK B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.672A pdb=" N UNK B 438 " --> pdb=" O UNK B 434 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 444 " --> pdb=" O UNK B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 3.645A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.389A pdb=" N UNK C 18 " --> pdb=" O UNK C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 36 through 56 removed outlier: 4.133A pdb=" N UNK C 40 " --> pdb=" O UNK C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 102 removed outlier: 3.851A pdb=" N UNK C 86 " --> pdb=" O UNK C 82 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N UNK C 87 " --> pdb=" O UNK C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 152 through 178 removed outlier: 4.032A pdb=" N UNK C 156 " --> pdb=" O UNK C 152 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK C 177 " --> pdb=" O UNK C 173 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N UNK C 178 " --> pdb=" O UNK C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.744A pdb=" N UNK C 183 " --> pdb=" O UNK C 179 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK C 184 " --> pdb=" O UNK C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 184' Processing helix chain 'C' and resid 184 through 198 removed outlier: 3.643A pdb=" N UNK C 188 " --> pdb=" O UNK C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 220 removed outlier: 4.123A pdb=" N UNK C 208 " --> pdb=" O UNK C 204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N UNK C 213 " --> pdb=" O UNK C 209 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N UNK C 214 " --> pdb=" O UNK C 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N UNK C 215 " --> pdb=" O UNK C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 removed outlier: 4.057A pdb=" N UNK D 13 " --> pdb=" O UNK D 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N UNK D 16 " --> pdb=" O UNK D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 31 removed outlier: 3.753A pdb=" N UNK D 25 " --> pdb=" O UNK D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 72 removed outlier: 4.028A pdb=" N UNK D 47 " --> pdb=" O UNK D 43 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N UNK D 49 " --> pdb=" O UNK D 45 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N UNK D 50 " --> pdb=" O UNK D 46 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N UNK D 51 " --> pdb=" O UNK D 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N UNK D 55 " --> pdb=" O UNK D 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N UNK D 65 " --> pdb=" O UNK D 61 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N UNK D 66 " --> pdb=" O UNK D 62 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N UNK D 67 " --> pdb=" O UNK D 63 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 38 through 51 removed outlier: 3.888A pdb=" N ALA G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 83 through 91 removed outlier: 3.924A pdb=" N VAL G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.969A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 142 through 156 Processing helix chain 'G' and resid 158 through 162 Processing sheet with id=AA, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AC, first strand: chain 'A' and resid 94 through 95 removed outlier: 6.378A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 248 through 250 Processing sheet with id=AE, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.813A pdb=" N ASP A 253 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.735A pdb=" N VAL A 276 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AH, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AI, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=GA, first strand: chain 'G' and resid 17 through 19 removed outlier: 7.694A pdb=" N TYR G 25 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS G 31 " --> pdb=" O ILE G 27 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1551 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: 1.14 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2891 1.34 - 1.46: 1592 1.46 - 1.58: 4089 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 8623 Sorted by residual: bond pdb=" CA PHE A 302 " pdb=" C PHE A 302 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.27e-02 6.20e+03 1.10e+01 bond pdb=" CA VAL A 256 " pdb=" CB VAL A 256 " ideal model delta sigma weight residual 1.540 1.503 0.037 1.36e-02 5.41e+03 7.32e+00 bond pdb=" N VAL A 303 " pdb=" CA VAL A 303 " ideal model delta sigma weight residual 1.459 1.427 0.032 1.25e-02 6.40e+03 6.39e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.51e-02 4.39e+03 5.94e+00 bond pdb=" C ALA A 556 " pdb=" O ALA A 556 " ideal model delta sigma weight residual 1.239 1.215 0.023 9.60e-03 1.09e+04 5.94e+00 ... (remaining 8618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11114 2.52 - 5.05: 536 5.05 - 7.57: 88 7.57 - 10.09: 16 10.09 - 12.62: 4 Bond angle restraints: 11758 Sorted by residual: angle pdb=" C GLY A 89 " pdb=" N PRO A 90 " pdb=" CA PRO A 90 " ideal model delta sigma weight residual 119.84 109.60 10.24 1.25e+00 6.40e-01 6.70e+01 angle pdb=" N VAL A 85 " pdb=" CA VAL A 85 " pdb=" C VAL A 85 " ideal model delta sigma weight residual 111.67 104.39 7.28 9.50e-01 1.11e+00 5.87e+01 angle pdb=" N LEU A 542 " pdb=" CA LEU A 542 " pdb=" C LEU A 542 " ideal model delta sigma weight residual 108.23 117.36 -9.13 1.38e+00 5.25e-01 4.38e+01 angle pdb=" C ALA A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.78 126.51 -6.73 1.03e+00 9.43e-01 4.26e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 118.35 -7.65 1.22e+00 6.72e-01 3.93e+01 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4972 17.72 - 35.44: 120 35.44 - 53.16: 26 53.16 - 70.88: 3 70.88 - 88.60: 5 Dihedral angle restraints: 5126 sinusoidal: 1485 harmonic: 3641 Sorted by residual: dihedral pdb=" CA TYR B 451 " pdb=" C TYR B 451 " pdb=" N LEU B 452 " pdb=" CA LEU B 452 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLN A 552 " pdb=" C GLN A 552 " pdb=" N HIS A 553 " pdb=" CA HIS A 553 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N GLN A 454 " pdb=" CA GLN A 454 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 5123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.118: 365 0.118 - 0.177: 41 0.177 - 0.236: 7 0.236 - 0.295: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CB ILE A 338 " pdb=" CA ILE A 338 " pdb=" CG1 ILE A 338 " pdb=" CG2 ILE A 338 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA CYS A 159 " pdb=" N CYS A 159 " pdb=" C CYS A 159 " pdb=" CB CYS A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA UNK A 626 " pdb=" N UNK A 626 " pdb=" C UNK A 626 " pdb=" CB UNK A 626 " both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1435 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 164 " 0.018 2.00e-02 2.50e+03 1.64e-02 6.69e+00 pdb=" CG TRP A 164 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 164 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 164 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 473 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 138 " -0.018 2.00e-02 2.50e+03 1.33e-02 4.39e+00 pdb=" CG TRP G 138 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP G 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 138 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 138 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 138 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 138 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 138 " -0.001 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 17 2.22 - 2.89: 3660 2.89 - 3.56: 13505 3.56 - 4.23: 18841 4.23 - 4.90: 29789 Nonbonded interactions: 65812 Sorted by model distance: nonbonded pdb=" O UNK D 42 " pdb=" N UNK D 44 " model vdw 1.546 3.120 nonbonded pdb=" OE2 GLU G 11 " pdb=" NH1 ARG G 145 " model vdw 1.835 3.120 nonbonded pdb=" O GLN A 516 " pdb=" CD ARG A 520 " model vdw 1.874 3.440 nonbonded pdb=" CB SER A 219 " pdb=" CG2 ILE A 656 " model vdw 1.909 3.860 nonbonded pdb=" OD2 ASP G 10 " pdb=" ND2 ASN G 101 " model vdw 2.006 3.120 ... (remaining 65807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.29 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5618 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 : 0.009 0.068 8628 Z= 0.520 Angle : 1.455 46.125 11770 Z= 0.893 Chirality : 0.057 0.295 1438 Planarity : 0.005 0.055 1535 Dihedral : 9.919 88.595 2719 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 4.97 % Allowed : 7.65 % Favored : 87.38 % Rotamer: Outliers : 1.19 % Allowed : 1.04 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.30), residues: 750 helix: -1.94 (0.21), residues: 332 sheet: -3.07 (0.65), residues: 53 loop : -0.13 (0.37), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 629 TYR 0.017 0.003 TYR A 453 PHE 0.019 0.003 PHE A 335 TRP 0.041 0.004 TRP A 164 HIS 0.010 0.003 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.52 ( 8623) covalent geometry : angle 1.29458 / 0.83 (11758) SS BOND : bond 0.00450 / 0.19 ( 3) SS BOND : angle 29.49634 / 13.44 ( 6) hydrogen bonds : bond 0.15219 / 10.32 ( 527) hydrogen bonds : angle 9.36119 / 6.54 ( 1551) link_TRANS : bond 0.00373 / 0.18 ( 2) link_TRANS : angle 0.74334 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 226 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9238 (m-30) cc_final: 0.9019 (m-30) REVERT: A 84 TRP cc_start: 0.8763 (m100) cc_final: 0.8316 (m-90) REVERT: A 91 ASN cc_start: 0.9134 (m-40) cc_final: 0.8854 (m-40) REVERT: A 325 VAL cc_start: 0.9472 (t) cc_final: 0.9201 (p) REVERT: A 327 PHE cc_start: 0.9148 (m-80) cc_final: 0.8946 (m-80) REVERT: A 347 MET cc_start: 0.7453 (ptp) cc_final: 0.7222 (ptp) REVERT: A 401 VAL cc_start: 0.6247 (t) cc_final: 0.5894 (t) REVERT: A 552 GLN cc_start: 0.8863 (pm20) cc_final: 0.8459 (pm20) REVERT: B 173 LEU cc_start: 0.6682 (tt) cc_final: 0.5886 (tt) REVERT: B 176 PHE cc_start: 0.8457 (t80) cc_final: 0.8246 (t80) REVERT: B 202 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6913 (tt) REVERT: B 205 PHE cc_start: 0.6050 (t80) cc_final: 0.5766 (t80) REVERT: B 229 ILE cc_start: 0.9075 (mm) cc_final: 0.8673 (mm) REVERT: B 407 THR cc_start: 0.7762 (t) cc_final: 0.7073 (p) REVERT: B 447 PHE cc_start: 0.7973 (m-10) cc_final: 0.7566 (m-80) outliers start: 8 outliers final: 3 residues processed: 229 average time/residue: 0.0835 time to fit residues: 26.4886 Evaluate side-chains 149 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 4.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 HIS A 216 GLN A 290 ASN A 313 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.108784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080085 restraints weight = 124452.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.079981 restraints weight = 62827.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080862 restraints weight = 37970.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080226 restraints weight = 30102.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081126 restraints weight = 24966.857| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8628 Z= 0.242 Angle : 0.894 10.735 11770 Z= 0.453 Chirality : 0.044 0.309 1438 Planarity : 0.005 0.053 1535 Dihedral : 6.464 31.237 1289 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 1.74 % Allowed : 9.13 % Favored : 89.13 % Rotamer: Outliers : 0.59 % Allowed : 4.90 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.29), residues: 750 helix: -0.60 (0.25), residues: 331 sheet: -3.44 (0.57), residues: 58 loop : -1.16 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 629 TYR 0.020 0.002 TYR A 467 PHE 0.025 0.003 PHE G 153 TRP 0.026 0.003 TRP A 164 HIS 0.009 0.002 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.24 ( 8623) covalent geometry : angle 0.88981 / 0.45 (11758) SS BOND : bond 0.01128 / 0.51 ( 3) SS BOND : angle 3.90095 / 2.08 ( 6) hydrogen bonds : bond 0.04575 / 3.03 ( 527) hydrogen bonds : angle 5.68405 / 3.92 ( 1551) link_TRANS : bond 0.00363 / 0.17 ( 2) link_TRANS : angle 0.86359 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLN cc_start: 0.8415 (pp30) cc_final: 0.8129 (pm20) REVERT: A 81 ASP cc_start: 0.9172 (m-30) cc_final: 0.8803 (m-30) REVERT: A 84 TRP cc_start: 0.7783 (m100) cc_final: 0.7438 (m-90) REVERT: A 91 ASN cc_start: 0.9228 (m-40) cc_final: 0.8964 (p0) REVERT: A 201 LEU cc_start: 0.7369 (pp) cc_final: 0.7112 (tt) REVERT: A 213 CYS cc_start: 0.4812 (t) cc_final: 0.4367 (t) REVERT: A 215 MET cc_start: 0.8635 (ttt) cc_final: 0.8167 (ttm) REVERT: A 231 MET cc_start: 0.8822 (mmm) cc_final: 0.8504 (mmm) REVERT: A 282 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6708 (mp) REVERT: A 299 VAL cc_start: 0.9209 (p) cc_final: 0.8979 (p) REVERT: A 453 TYR cc_start: 0.8970 (t80) cc_final: 0.7936 (t80) REVERT: A 501 LEU cc_start: 0.9530 (tp) cc_final: 0.9057 (pp) REVERT: A 552 GLN cc_start: 0.8930 (pm20) cc_final: 0.8652 (pm20) REVERT: B 83 ILE cc_start: 0.8480 (mt) cc_final: 0.8230 (mt) REVERT: B 180 ILE cc_start: 0.9257 (mt) cc_final: 0.9051 (mt) REVERT: B 184 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8606 (tm-30) REVERT: B 202 ILE cc_start: 0.9546 (mp) cc_final: 0.9234 (tt) REVERT: B 205 PHE cc_start: 0.8764 (t80) cc_final: 0.8071 (t80) REVERT: B 229 ILE cc_start: 0.9520 (mm) cc_final: 0.9257 (mm) REVERT: G 6 MET cc_start: 0.5699 (ttm) cc_final: 0.5471 (ttm) outliers start: 4 outliers final: 0 residues processed: 190 average time/residue: 0.0704 time to fit residues: 19.6268 Evaluate side-chains 148 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 102 HIS A 139 GLN A 255 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078177 restraints weight = 157519.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079338 restraints weight = 73871.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079755 restraints weight = 39322.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079794 restraints weight = 28760.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.080144 restraints weight = 25971.503| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8628 Z= 0.258 Angle : 0.872 11.841 11770 Z= 0.439 Chirality : 0.044 0.340 1438 Planarity : 0.005 0.052 1535 Dihedral : 6.187 30.058 1289 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.34 % Favored : 88.05 % Rotamer: Outliers : 0.30 % Allowed : 5.65 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.74 (0.30), residues: 750 helix: -0.34 (0.27), residues: 332 sheet: -3.65 (0.56), residues: 52 loop : -1.48 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 119 TYR 0.023 0.002 TYR A 565 PHE 0.028 0.003 PHE A 181 TRP 0.021 0.003 TRP A 653 HIS 0.007 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 ( 8623) covalent geometry : angle 0.86992 / 0.44 (11758) SS BOND : bond 0.01114 / 0.52 ( 3) SS BOND : angle 2.77727 / 1.15 ( 6) hydrogen bonds : bond 0.04288 / 2.81 ( 527) hydrogen bonds : angle 5.42975 / 3.74 ( 1551) link_TRANS : bond 0.00400 / 0.19 ( 2) link_TRANS : angle 0.84039 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.9039 (m-30) cc_final: 0.8770 (m-30) REVERT: A 91 ASN cc_start: 0.9213 (m-40) cc_final: 0.9009 (m110) REVERT: A 201 LEU cc_start: 0.7446 (pp) cc_final: 0.7129 (tt) REVERT: A 291 VAL cc_start: 0.8218 (m) cc_final: 0.7996 (m) REVERT: A 305 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8866 (mm-40) REVERT: A 336 ASP cc_start: 0.7241 (p0) cc_final: 0.6897 (p0) REVERT: A 552 GLN cc_start: 0.9141 (pm20) cc_final: 0.8848 (pm20) REVERT: A 574 LEU cc_start: 0.9296 (tp) cc_final: 0.9034 (tp) REVERT: B 180 ILE cc_start: 0.9324 (mt) cc_final: 0.9060 (mt) REVERT: B 184 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8659 (tm-30) REVERT: B 205 PHE cc_start: 0.8775 (t80) cc_final: 0.7984 (t80) REVERT: B 229 ILE cc_start: 0.9539 (mm) cc_final: 0.9247 (mm) REVERT: B 404 TRP cc_start: 0.6493 (m100) cc_final: 0.6024 (m-10) REVERT: G 6 MET cc_start: 0.6063 (ttm) cc_final: 0.5715 (ttm) REVERT: G 120 MET cc_start: 0.7050 (mmp) cc_final: 0.6801 (mmp) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.0708 time to fit residues: 16.9309 Evaluate side-chains 143 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075141 restraints weight = 128263.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077812 restraints weight = 61115.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.077795 restraints weight = 31403.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077927 restraints weight = 25161.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078367 restraints weight = 21564.704| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8628 Z= 0.269 Angle : 0.872 13.738 11770 Z= 0.435 Chirality : 0.044 0.317 1438 Planarity : 0.005 0.054 1535 Dihedral : 6.067 29.815 1289 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 1.61 % Allowed : 10.20 % Favored : 88.19 % Rotamer: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.30), residues: 750 helix: -0.26 (0.27), residues: 332 sheet: -3.28 (0.48), residues: 70 loop : -1.74 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 543 TYR 0.021 0.002 TYR A 565 PHE 0.028 0.003 PHE A 218 TRP 0.022 0.003 TRP A 164 HIS 0.006 0.002 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.27 ( 8623) covalent geometry : angle 0.86907 / 0.43 (11758) SS BOND : bond 0.00828 / 0.41 ( 3) SS BOND : angle 3.50774 / 1.57 ( 6) hydrogen bonds : bond 0.04279 / 2.83 ( 527) hydrogen bonds : angle 5.20484 / 3.57 ( 1551) link_TRANS : bond 0.00408 / 0.20 ( 2) link_TRANS : angle 0.88198 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9403 (p) cc_final: 0.8674 (p) REVERT: A 81 ASP cc_start: 0.9082 (m-30) cc_final: 0.8811 (m-30) REVERT: A 91 ASN cc_start: 0.9225 (m-40) cc_final: 0.8976 (m110) REVERT: A 95 MET cc_start: 0.8715 (ppp) cc_final: 0.8476 (ppp) REVERT: A 121 LEU cc_start: 0.9312 (mt) cc_final: 0.9069 (mt) REVERT: A 201 LEU cc_start: 0.7568 (pp) cc_final: 0.7240 (tt) REVERT: A 213 CYS cc_start: 0.3818 (m) cc_final: 0.3274 (m) REVERT: A 231 MET cc_start: 0.8756 (mmp) cc_final: 0.7928 (mmm) REVERT: A 305 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8703 (mm-40) REVERT: A 327 PHE cc_start: 0.8083 (m-10) cc_final: 0.7850 (m-10) REVERT: A 336 ASP cc_start: 0.7186 (p0) cc_final: 0.6639 (p0) REVERT: A 364 GLU cc_start: 0.7320 (tp30) cc_final: 0.6973 (tm-30) REVERT: A 365 LEU cc_start: 0.8931 (mp) cc_final: 0.8679 (mp) REVERT: A 552 GLN cc_start: 0.9028 (pm20) cc_final: 0.8698 (pm20) REVERT: B 180 ILE cc_start: 0.9253 (mt) cc_final: 0.8982 (mm) REVERT: B 229 ILE cc_start: 0.9535 (mm) cc_final: 0.9225 (mm) REVERT: B 454 GLN cc_start: 0.9269 (mt0) cc_final: 0.8869 (mp10) REVERT: G 6 MET cc_start: 0.6414 (ttm) cc_final: 0.6130 (ttm) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.0777 time to fit residues: 17.8597 Evaluate side-chains 125 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 82 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 141 GLN A Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080976 restraints weight = 116514.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080812 restraints weight = 57722.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081592 restraints weight = 37797.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.081827 restraints weight = 26642.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082254 restraints weight = 23946.747| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8628 Z= 0.147 Angle : 0.739 11.291 11770 Z= 0.366 Chirality : 0.040 0.303 1438 Planarity : 0.004 0.059 1535 Dihedral : 5.383 27.003 1289 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.48 % Allowed : 8.32 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.31), residues: 750 helix: 0.28 (0.28), residues: 336 sheet: -3.30 (0.44), residues: 79 loop : -1.44 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 119 TYR 0.012 0.001 TYR A 196 PHE 0.026 0.002 PHE A 302 TRP 0.050 0.002 TRP A 164 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8623) covalent geometry : angle 0.73418 / 0.36 (11758) SS BOND : bond 0.00563 / 0.27 ( 3) SS BOND : angle 3.66083 / 1.39 ( 6) hydrogen bonds : bond 0.03568 / 2.36 ( 527) hydrogen bonds : angle 4.64497 / 3.18 ( 1551) link_TRANS : bond 0.00147 / 0.07 ( 2) link_TRANS : angle 0.59619 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9413 (p) cc_final: 0.8765 (p) REVERT: A 81 ASP cc_start: 0.9117 (m-30) cc_final: 0.8799 (m-30) REVERT: A 91 ASN cc_start: 0.9134 (m-40) cc_final: 0.8926 (m-40) REVERT: A 231 MET cc_start: 0.8649 (mmp) cc_final: 0.8059 (mmm) REVERT: A 327 PHE cc_start: 0.8153 (m-10) cc_final: 0.7757 (m-10) REVERT: A 367 GLN cc_start: 0.8446 (mm110) cc_final: 0.8231 (mm110) REVERT: A 400 GLN cc_start: 0.9186 (mp10) cc_final: 0.8978 (mp10) REVERT: A 404 LEU cc_start: 0.8725 (mm) cc_final: 0.8489 (mm) REVERT: A 489 ASP cc_start: 0.8606 (m-30) cc_final: 0.8165 (t0) REVERT: A 552 GLN cc_start: 0.8990 (pm20) cc_final: 0.8777 (pm20) REVERT: B 205 PHE cc_start: 0.8604 (t80) cc_final: 0.8161 (t80) REVERT: B 229 ILE cc_start: 0.9532 (mm) cc_final: 0.9287 (mm) REVERT: B 454 GLN cc_start: 0.9276 (mt0) cc_final: 0.8840 (mp10) REVERT: B 460 LEU cc_start: 0.8986 (tp) cc_final: 0.8701 (mt) REVERT: G 6 MET cc_start: 0.6288 (ttm) cc_final: 0.5881 (ttm) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0732 time to fit residues: 18.4590 Evaluate side-chains 131 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 45 optimal weight: 0.0030 chunk 66 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 overall best weight: 1.7952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 216 GLN A 305 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.109653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083099 restraints weight = 127588.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082323 restraints weight = 72989.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083454 restraints weight = 48850.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084090 restraints weight = 32959.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084617 restraints weight = 28273.276| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8628 Z= 0.148 Angle : 0.736 11.369 11770 Z= 0.366 Chirality : 0.039 0.316 1438 Planarity : 0.004 0.055 1535 Dihedral : 5.203 25.042 1289 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 1.34 % Allowed : 9.13 % Favored : 89.53 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.31), residues: 750 helix: 0.47 (0.28), residues: 334 sheet: -3.06 (0.46), residues: 79 loop : -1.42 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 95 TYR 0.021 0.002 TYR A 565 PHE 0.018 0.002 PHE A 335 TRP 0.041 0.002 TRP A 164 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8623) covalent geometry : angle 0.73275 / 0.36 (11758) SS BOND : bond 0.00171 / 0.08 ( 3) SS BOND : angle 2.96671 / 1.14 ( 6) hydrogen bonds : bond 0.03385 / 2.26 ( 527) hydrogen bonds : angle 4.57946 / 3.13 ( 1551) link_TRANS : bond 0.00182 / 0.09 ( 2) link_TRANS : angle 0.53016 / 0.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9419 (p) cc_final: 0.8831 (p) REVERT: A 81 ASP cc_start: 0.9087 (m-30) cc_final: 0.8792 (m-30) REVERT: A 95 MET cc_start: 0.8747 (ppp) cc_final: 0.7486 (ppp) REVERT: A 213 CYS cc_start: 0.3446 (m) cc_final: 0.2903 (m) REVERT: A 231 MET cc_start: 0.8543 (mmp) cc_final: 0.7995 (mmm) REVERT: A 327 PHE cc_start: 0.8176 (m-10) cc_final: 0.7943 (m-10) REVERT: A 343 MET cc_start: 0.8619 (tpt) cc_final: 0.8396 (tpp) REVERT: A 489 ASP cc_start: 0.8672 (m-30) cc_final: 0.8161 (t0) REVERT: A 518 VAL cc_start: 0.9627 (t) cc_final: 0.9363 (t) REVERT: B 173 LEU cc_start: 0.9116 (tt) cc_final: 0.8738 (tt) REVERT: B 180 ILE cc_start: 0.9224 (mm) cc_final: 0.8824 (mm) REVERT: B 205 PHE cc_start: 0.8685 (t80) cc_final: 0.8052 (t80) REVERT: B 229 ILE cc_start: 0.9542 (mm) cc_final: 0.9276 (mm) REVERT: B 454 GLN cc_start: 0.9336 (mt0) cc_final: 0.8867 (mp10) REVERT: G 6 MET cc_start: 0.6149 (ttm) cc_final: 0.5765 (ttm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0759 time to fit residues: 17.9784 Evaluate side-chains 135 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 91 ASN A 313 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.109827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.080232 restraints weight = 113209.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081025 restraints weight = 68762.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081568 restraints weight = 40086.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082406 restraints weight = 27305.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.082872 restraints weight = 21274.245| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8628 Z= 0.144 Angle : 0.713 11.468 11770 Z= 0.355 Chirality : 0.039 0.316 1438 Planarity : 0.004 0.055 1535 Dihedral : 5.018 24.373 1289 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 1.34 % Allowed : 8.72 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.31), residues: 750 helix: 0.56 (0.28), residues: 335 sheet: -2.82 (0.52), residues: 66 loop : -1.58 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 398 TYR 0.015 0.002 TYR B 181 PHE 0.020 0.002 PHE B 177 TRP 0.050 0.002 TRP A 164 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8623) covalent geometry : angle 0.71060 / 0.35 (11758) SS BOND : bond 0.00279 / 0.13 ( 3) SS BOND : angle 2.94061 / 1.13 ( 6) hydrogen bonds : bond 0.03400 / 2.25 ( 527) hydrogen bonds : angle 4.43683 / 3.04 ( 1551) link_TRANS : bond 0.00154 / 0.07 ( 2) link_TRANS : angle 0.56537 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9388 (p) cc_final: 0.8620 (p) REVERT: A 81 ASP cc_start: 0.9034 (m-30) cc_final: 0.8815 (m-30) REVERT: A 213 CYS cc_start: 0.3419 (m) cc_final: 0.2882 (m) REVERT: A 231 MET cc_start: 0.8568 (mmp) cc_final: 0.7940 (mmm) REVERT: A 327 PHE cc_start: 0.8416 (m-10) cc_final: 0.8155 (m-10) REVERT: A 343 MET cc_start: 0.8535 (tpt) cc_final: 0.8300 (tpp) REVERT: A 376 LEU cc_start: 0.8278 (tp) cc_final: 0.7839 (tt) REVERT: A 489 ASP cc_start: 0.8669 (m-30) cc_final: 0.8162 (t0) REVERT: A 518 VAL cc_start: 0.9630 (t) cc_final: 0.9347 (t) REVERT: B 180 ILE cc_start: 0.9203 (mm) cc_final: 0.8816 (mm) REVERT: B 205 PHE cc_start: 0.8649 (t80) cc_final: 0.8128 (t80) REVERT: B 229 ILE cc_start: 0.9512 (mm) cc_final: 0.9228 (mm) REVERT: B 454 GLN cc_start: 0.9257 (mt0) cc_final: 0.8774 (mp10) REVERT: G 6 MET cc_start: 0.6443 (ttm) cc_final: 0.6132 (ttm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0793 time to fit residues: 18.3014 Evaluate side-chains 140 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.0070 chunk 34 optimal weight: 0.0980 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 216 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN A Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.110784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081839 restraints weight = 128101.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082388 restraints weight = 60952.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.083407 restraints weight = 36495.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083410 restraints weight = 27198.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084277 restraints weight = 21874.564| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8628 Z= 0.134 Angle : 0.700 11.376 11770 Z= 0.349 Chirality : 0.040 0.320 1438 Planarity : 0.004 0.055 1535 Dihedral : 4.908 23.076 1289 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 1.34 % Allowed : 8.19 % Favored : 90.47 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.31), residues: 750 helix: 0.69 (0.28), residues: 334 sheet: -2.42 (0.56), residues: 67 loop : -1.56 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 95 TYR 0.017 0.001 TYR B 181 PHE 0.026 0.002 PHE B 86 TRP 0.036 0.002 TRP A 164 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8623) covalent geometry : angle 0.69691 / 0.35 (11758) SS BOND : bond 0.00197 / 0.09 ( 3) SS BOND : angle 2.97469 / 1.13 ( 6) hydrogen bonds : bond 0.03274 / 2.16 ( 527) hydrogen bonds : angle 4.31687 / 2.97 ( 1551) link_TRANS : bond 0.00121 / 0.06 ( 2) link_TRANS : angle 0.45951 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8832 (tptp) cc_final: 0.8349 (tptm) REVERT: A 72 VAL cc_start: 0.9354 (p) cc_final: 0.8594 (p) REVERT: A 81 ASP cc_start: 0.9030 (m-30) cc_final: 0.8749 (m-30) REVERT: A 91 ASN cc_start: 0.9196 (m-40) cc_final: 0.8934 (m-40) REVERT: A 213 CYS cc_start: 0.3327 (m) cc_final: 0.2780 (m) REVERT: A 231 MET cc_start: 0.8404 (mmp) cc_final: 0.7710 (mmm) REVERT: A 430 PHE cc_start: 0.8269 (m-10) cc_final: 0.7687 (m-10) REVERT: A 489 ASP cc_start: 0.8420 (m-30) cc_final: 0.8039 (t0) REVERT: B 180 ILE cc_start: 0.9203 (mm) cc_final: 0.8844 (mm) REVERT: B 229 ILE cc_start: 0.9524 (mm) cc_final: 0.9275 (mm) REVERT: B 454 GLN cc_start: 0.9249 (mt0) cc_final: 0.8855 (mp10) REVERT: G 6 MET cc_start: 0.6362 (ttm) cc_final: 0.5998 (ttm) REVERT: G 106 MET cc_start: 0.3608 (ttt) cc_final: 0.3231 (ttm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0842 time to fit residues: 20.0240 Evaluate side-chains 138 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 0.0040 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 GLN A Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.109746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080815 restraints weight = 111610.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081754 restraints weight = 54050.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081663 restraints weight = 37253.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082646 restraints weight = 24887.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083692 restraints weight = 19694.009| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8628 Z= 0.149 Angle : 0.707 11.461 11770 Z= 0.353 Chirality : 0.040 0.357 1438 Planarity : 0.004 0.049 1535 Dihedral : 4.839 23.351 1289 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 1.48 % Allowed : 8.59 % Favored : 89.93 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.31), residues: 750 helix: 0.71 (0.28), residues: 340 sheet: -2.24 (0.66), residues: 58 loop : -1.68 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 95 TYR 0.015 0.002 TYR A 565 PHE 0.024 0.002 PHE B 205 TRP 0.031 0.002 TRP A 164 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8623) covalent geometry : angle 0.70407 / 0.35 (11758) SS BOND : bond 0.00168 / 0.07 ( 3) SS BOND : angle 3.09015 / 1.19 ( 6) hydrogen bonds : bond 0.03330 / 2.16 ( 527) hydrogen bonds : angle 4.31120 / 2.95 ( 1551) link_TRANS : bond 0.00172 / 0.08 ( 2) link_TRANS : angle 0.55300 / 0.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 VAL cc_start: 0.9313 (p) cc_final: 0.8503 (p) REVERT: A 81 ASP cc_start: 0.9000 (m-30) cc_final: 0.8707 (m-30) REVERT: A 91 ASN cc_start: 0.9215 (m-40) cc_final: 0.8937 (m-40) REVERT: A 201 LEU cc_start: 0.7430 (mp) cc_final: 0.7107 (tp) REVERT: A 213 CYS cc_start: 0.3572 (m) cc_final: 0.3128 (m) REVERT: A 231 MET cc_start: 0.8500 (mmp) cc_final: 0.7816 (mmm) REVERT: A 330 PHE cc_start: 0.9030 (m-80) cc_final: 0.8812 (m-80) REVERT: A 489 ASP cc_start: 0.8546 (m-30) cc_final: 0.8179 (t0) REVERT: A 518 VAL cc_start: 0.9670 (t) cc_final: 0.9389 (t) REVERT: B 180 ILE cc_start: 0.9223 (mm) cc_final: 0.8886 (mm) REVERT: B 229 ILE cc_start: 0.9522 (mm) cc_final: 0.9231 (mm) REVERT: B 454 GLN cc_start: 0.9268 (mt0) cc_final: 0.8808 (mp10) REVERT: G 6 MET cc_start: 0.6276 (ttm) cc_final: 0.5918 (ttm) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0817 time to fit residues: 19.1616 Evaluate side-chains 136 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 34 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.110607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082094 restraints weight = 132272.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082925 restraints weight = 61988.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083514 restraints weight = 33635.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083908 restraints weight = 23685.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.084237 restraints weight = 20534.549| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8628 Z= 0.135 Angle : 0.702 11.358 11770 Z= 0.348 Chirality : 0.039 0.341 1438 Planarity : 0.004 0.049 1535 Dihedral : 4.807 22.727 1289 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 1.61 % Allowed : 7.79 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.31), residues: 750 helix: 0.79 (0.28), residues: 340 sheet: -2.37 (0.56), residues: 73 loop : -1.60 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 398 TYR 0.016 0.001 TYR A 554 PHE 0.029 0.002 PHE B 86 TRP 0.032 0.002 TRP A 164 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8623) covalent geometry : angle 0.69903 / 0.35 (11758) SS BOND : bond 0.00190 / 0.09 ( 3) SS BOND : angle 3.02894 / 1.15 ( 6) hydrogen bonds : bond 0.03294 / 2.17 ( 527) hydrogen bonds : angle 4.21276 / 2.89 ( 1551) link_TRANS : bond 0.00135 / 0.06 ( 2) link_TRANS : angle 0.46582 / 0.23 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8129 (m-30) cc_final: 0.7770 (m-30) REVERT: A 72 VAL cc_start: 0.9310 (p) cc_final: 0.8485 (p) REVERT: A 81 ASP cc_start: 0.9021 (m-30) cc_final: 0.8729 (m-30) REVERT: A 91 ASN cc_start: 0.9198 (m-40) cc_final: 0.8934 (m-40) REVERT: A 201 LEU cc_start: 0.7418 (mp) cc_final: 0.7112 (tp) REVERT: A 213 CYS cc_start: 0.3845 (m) cc_final: 0.3524 (m) REVERT: A 231 MET cc_start: 0.8466 (mmp) cc_final: 0.7718 (mmm) REVERT: A 330 PHE cc_start: 0.9063 (m-80) cc_final: 0.8812 (m-80) REVERT: A 489 ASP cc_start: 0.8498 (m-30) cc_final: 0.8147 (t0) REVERT: A 518 VAL cc_start: 0.9673 (t) cc_final: 0.9420 (t) REVERT: B 180 ILE cc_start: 0.9171 (mm) cc_final: 0.8773 (mm) REVERT: B 229 ILE cc_start: 0.9511 (mm) cc_final: 0.9230 (mm) REVERT: B 454 GLN cc_start: 0.9244 (mt0) cc_final: 0.8810 (mp10) REVERT: G 6 MET cc_start: 0.6212 (ttm) cc_final: 0.5897 (ttm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0817 time to fit residues: 18.8608 Evaluate side-chains 141 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.107733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079445 restraints weight = 142835.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080315 restraints weight = 68363.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080012 restraints weight = 43500.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080893 restraints weight = 30297.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081096 restraints weight = 24236.135| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8628 Z= 0.190 Angle : 0.745 12.495 11770 Z= 0.373 Chirality : 0.040 0.360 1438 Planarity : 0.004 0.049 1535 Dihedral : 4.960 23.763 1289 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 1.61 % Allowed : 8.46 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.31), residues: 750 helix: 0.68 (0.28), residues: 341 sheet: -2.33 (0.66), residues: 58 loop : -1.74 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 160 TYR 0.024 0.002 TYR A 554 PHE 0.025 0.002 PHE A 218 TRP 0.035 0.003 TRP A 164 HIS 0.006 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 8623) covalent geometry : angle 0.74122 / 0.37 (11758) SS BOND : bond 0.00191 / 0.09 ( 3) SS BOND : angle 3.19477 / 1.24 ( 6) hydrogen bonds : bond 0.03464 / 2.28 ( 527) hydrogen bonds : angle 4.40671 / 3.01 ( 1551) link_TRANS : bond 0.00258 / 0.12 ( 2) link_TRANS : angle 0.73743 / 0.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.05 seconds wall clock time: 28 minutes 42.87 seconds (1722.87 seconds total)