Starting phenix.real_space_refine on Fri Mar 15 06:40:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kam_22775/03_2024/7kam_22775.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 7107 2.51 5 N 1873 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D GLU 460": "OE1" <-> "OE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10916 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3386 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3678 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 31, 'TRANS': 444} Chain breaks: 5 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1359 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 354 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 6.01, per 1000 atoms: 0.55 Number of scatterers: 10916 At special positions: 0 Unit cell: (107.16, 125.4, 139.08, 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 49 16.00 O 1887 8.00 N 1873 7.00 C 7107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 68.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.681A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 107 through 136 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 148 through 173 removed outlier: 3.711A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.685A pdb=" N ILE A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 removed outlier: 3.879A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.714A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.974A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.732A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 removed outlier: 4.080A pdb=" N ASP A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.663A pdb=" N THR A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.925A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 4.457A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 4.015A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 465 removed outlier: 3.671A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 67 Proline residue: C 61 - end of helix Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'D' and resid 14 through 28 removed outlier: 3.541A pdb=" N PHE D 18 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 removed outlier: 3.985A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 removed outlier: 4.116A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 98 removed outlier: 4.570A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.672A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.827A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.025A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.923A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.752A pdb=" N LYS D 275 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 276 " --> pdb=" O GLY D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.763A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.070A pdb=" N VAL D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 324 Processing helix chain 'D' and resid 331 through 358 removed outlier: 4.296A pdb=" N GLU D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 376 removed outlier: 3.587A pdb=" N ARG D 368 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.694A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.516A pdb=" N GLU D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.988A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 Proline residue: E 9 - end of helix removed outlier: 3.648A pdb=" N LEU E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 71 through 106 removed outlier: 4.503A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 138 removed outlier: 4.149A pdb=" N TRP E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 167 Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 3.858A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 89 removed outlier: 4.384A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 removed outlier: 3.501A pdb=" N GLY F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 removed outlier: 4.268A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 156 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'G' and resid 245 through 266 removed outlier: 3.711A pdb=" N LEU G 266 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 270 Processing helix chain 'G' and resid 274 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 7.047A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.781A pdb=" N GLU A 210 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 187 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.792A pdb=" N VAL A 325 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 457 removed outlier: 3.651A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 472 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 560 removed outlier: 3.617A pdb=" N VAL D 560 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU D 550 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 549 " --> pdb=" O HIS D 604 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2124 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: 2.85 Time building geometry restraints manager: 4.52 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: 3459 1.34 - 1.46: 1604 1.46 - 1.57: 6009 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 11157 Sorted by residual: bond pdb=" C GLY D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.332 1.351 -0.019 8.20e-03 1.49e+04 5.53e+00 bond pdb=" N GLY G 245 " pdb=" CA GLY G 245 " ideal model delta sigma weight residual 1.443 1.460 -0.017 1.37e-02 5.33e+03 1.54e+00 bond pdb=" N PRO G 246 " pdb=" CA PRO G 246 " ideal model delta sigma weight residual 1.471 1.458 0.013 1.29e-02 6.01e+03 1.08e+00 bond pdb=" CA ILE G 297 " pdb=" CB ILE G 297 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 9.37e-01 bond pdb=" CA VAL G 278 " pdb=" CB VAL G 278 " ideal model delta sigma weight residual 1.540 1.527 0.012 1.29e-02 6.01e+03 9.12e-01 ... (remaining 11152 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 406 107.11 - 113.83: 6366 113.83 - 120.55: 4597 120.55 - 127.27: 3667 127.27 - 133.98: 138 Bond angle restraints: 15174 Sorted by residual: angle pdb=" N PRO G 246 " pdb=" CA PRO G 246 " pdb=" CB PRO G 246 " ideal model delta sigma weight residual 103.44 110.18 -6.74 1.12e+00 7.97e-01 3.62e+01 angle pdb=" N VAL D 596 " pdb=" CA VAL D 596 " pdb=" C VAL D 596 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" N GLY D 426 " pdb=" CA GLY D 426 " pdb=" C GLY D 426 " ideal model delta sigma weight residual 112.34 119.30 -6.96 2.04e+00 2.40e-01 1.16e+01 angle pdb=" N PRO D 427 " pdb=" CA PRO D 427 " pdb=" C PRO D 427 " ideal model delta sigma weight residual 114.98 110.18 4.80 1.46e+00 4.69e-01 1.08e+01 angle pdb=" CA PRO D 427 " pdb=" C PRO D 427 " pdb=" O PRO D 427 " ideal model delta sigma weight residual 118.38 121.74 -3.36 1.13e+00 7.83e-01 8.83e+00 ... (remaining 15169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6197 17.89 - 35.78: 391 35.78 - 53.67: 62 53.67 - 71.56: 6 71.56 - 89.45: 4 Dihedral angle restraints: 6660 sinusoidal: 2486 harmonic: 4174 Sorted by residual: dihedral pdb=" CA GLY D 426 " pdb=" C GLY D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB GLU D 396 " pdb=" CG GLU D 396 " pdb=" CD GLU D 396 " pdb=" OE1 GLU D 396 " ideal model delta sinusoidal sigma weight residual 0.00 89.45 -89.45 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N PRO G 246 " pdb=" C PRO G 246 " pdb=" CA PRO G 246 " pdb=" CB PRO G 246 " ideal model delta harmonic sigma weight residual 115.10 122.75 -7.65 0 2.50e+00 1.60e-01 9.37e+00 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1429 0.045 - 0.091: 294 0.091 - 0.136: 49 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA PRO G 246 " pdb=" N PRO G 246 " pdb=" C PRO G 246 " pdb=" CB PRO G 246 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE D 478 " pdb=" CA ILE D 478 " pdb=" CG1 ILE D 478 " pdb=" CG2 ILE D 478 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1771 not shown) Planarity restraints: 1903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 426 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO D 427 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.014 2.00e-02 2.50e+03 9.16e-03 2.10e+00 pdb=" CG TRP E 141 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 391 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 392 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 392 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 392 " 0.020 5.00e-02 4.00e+02 ... (remaining 1900 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 187 2.70 - 3.25: 11047 3.25 - 3.80: 16763 3.80 - 4.35: 19014 4.35 - 4.90: 32652 Nonbonded interactions: 79663 Sorted by model distance: nonbonded pdb=" OH TYR A 287 " pdb=" OG SER A 385 " model vdw 2.150 2.440 nonbonded pdb=" NE2 GLN D 371 " pdb=" O TYR D 610 " model vdw 2.261 2.520 nonbonded pdb=" NE2 GLN D 63 " pdb=" OE2 GLU D 334 " model vdw 2.275 2.520 nonbonded pdb=" NE2 GLN D 386 " pdb=" O MET D 611 " model vdw 2.286 2.520 nonbonded pdb=" O ARG D 420 " pdb=" OG1 THR D 424 " model vdw 2.308 2.440 ... (remaining 79658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.120 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 30.040 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.003 0.035 11157 Z= 0.178 Angle : 0.543 12.917 15174 Z= 0.295 Chirality : 0.037 0.227 1774 Planarity : 0.004 0.058 1903 Dihedral : 11.788 89.454 3966 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1414 helix: 0.23 (0.16), residues: 907 sheet: -2.34 (0.51), residues: 81 loop : -2.54 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 141 HIS 0.003 0.001 HIS B 114 PHE 0.013 0.001 PHE A 263 TYR 0.011 0.001 TYR A 237 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 MET cc_start: 0.8268 (tpp) cc_final: 0.7980 (ttt) REVERT: C 18 ASP cc_start: 0.8178 (m-30) cc_final: 0.7944 (m-30) REVERT: B 102 LEU cc_start: 0.8528 (tp) cc_final: 0.8108 (tp) REVERT: D 270 MET cc_start: 0.7891 (tmm) cc_final: 0.7436 (tmm) REVERT: E 92 ILE cc_start: 0.9544 (mt) cc_final: 0.9278 (mm) REVERT: E 110 ASP cc_start: 0.6936 (t70) cc_final: 0.6482 (t70) REVERT: E 151 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7836 (mm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2424 time to fit residues: 57.4327 Evaluate side-chains 106 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.0070 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN D 604 HIS E 56 HIS E 95 GLN E 97 GLN E 114 GLN E 166 GLN F 43 GLN F 127 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 11157 Z= 0.459 Angle : 0.725 13.155 15174 Z= 0.361 Chirality : 0.041 0.148 1774 Planarity : 0.005 0.050 1903 Dihedral : 3.664 18.822 1550 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.11 % Allowed : 15.58 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1414 helix: 1.25 (0.17), residues: 929 sheet: -2.39 (0.49), residues: 83 loop : -2.47 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 141 HIS 0.004 0.001 HIS D 604 PHE 0.030 0.002 PHE D 581 TYR 0.016 0.002 TYR A 237 ARG 0.011 0.001 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 90 MET cc_start: 0.8413 (mmm) cc_final: 0.8123 (mmp) REVERT: D 308 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8214 (p0) REVERT: E 92 ILE cc_start: 0.9556 (mt) cc_final: 0.9306 (mm) REVERT: F 137 MET cc_start: 0.7544 (mpp) cc_final: 0.7167 (mpp) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.2012 time to fit residues: 38.9048 Evaluate side-chains 124 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11157 Z= 0.187 Angle : 0.578 14.798 15174 Z= 0.278 Chirality : 0.037 0.136 1774 Planarity : 0.004 0.043 1903 Dihedral : 3.406 15.587 1550 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 18.88 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1414 helix: 1.80 (0.18), residues: 927 sheet: -2.09 (0.50), residues: 81 loop : -2.16 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 176 HIS 0.003 0.001 HIS C 59 PHE 0.027 0.001 PHE D 563 TYR 0.011 0.001 TYR A 237 ARG 0.004 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 92 ILE cc_start: 0.9539 (mt) cc_final: 0.9299 (mm) REVERT: F 137 MET cc_start: 0.7943 (mpp) cc_final: 0.7717 (mpp) outliers start: 16 outliers final: 11 residues processed: 132 average time/residue: 0.1907 time to fit residues: 38.1647 Evaluate side-chains 117 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain F residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11157 Z= 0.442 Angle : 0.700 14.466 15174 Z= 0.346 Chirality : 0.040 0.138 1774 Planarity : 0.004 0.048 1903 Dihedral : 3.646 16.730 1550 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 3.39 % Allowed : 21.26 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1414 helix: 1.82 (0.17), residues: 932 sheet: -2.06 (0.51), residues: 81 loop : -2.21 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 141 HIS 0.004 0.001 HIS C 59 PHE 0.027 0.002 PHE D 581 TYR 0.016 0.002 TYR A 237 ARG 0.004 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8718 (tt) REVERT: D 270 MET cc_start: 0.7856 (tmm) cc_final: 0.7637 (tmm) REVERT: E 92 ILE cc_start: 0.9544 (mt) cc_final: 0.9291 (mm) REVERT: E 121 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8296 (mtmm) REVERT: F 137 MET cc_start: 0.8048 (mpp) cc_final: 0.7700 (mpp) outliers start: 37 outliers final: 25 residues processed: 132 average time/residue: 0.1896 time to fit residues: 38.4857 Evaluate side-chains 132 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 581 PHE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 100 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11157 Z= 0.174 Angle : 0.585 15.179 15174 Z= 0.277 Chirality : 0.037 0.141 1774 Planarity : 0.004 0.047 1903 Dihedral : 3.413 16.004 1550 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 2.57 % Allowed : 23.28 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1414 helix: 2.13 (0.17), residues: 929 sheet: -1.85 (0.51), residues: 81 loop : -2.00 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 84 HIS 0.003 0.001 HIS C 59 PHE 0.026 0.001 PHE D 563 TYR 0.013 0.001 TYR E 158 ARG 0.003 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8646 (tt) REVERT: C 16 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8224 (tt) REVERT: C 59 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.8011 (t-90) REVERT: D 308 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 415 MET cc_start: 0.6905 (tmm) cc_final: 0.6673 (tmm) REVERT: E 92 ILE cc_start: 0.9530 (mt) cc_final: 0.9298 (mm) REVERT: E 162 MET cc_start: 0.8997 (tpp) cc_final: 0.8497 (mpp) outliers start: 28 outliers final: 14 residues processed: 139 average time/residue: 0.1733 time to fit residues: 37.2177 Evaluate side-chains 126 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11157 Z= 0.189 Angle : 0.581 14.914 15174 Z= 0.275 Chirality : 0.037 0.189 1774 Planarity : 0.004 0.051 1903 Dihedral : 3.377 15.613 1550 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.66 % Allowed : 23.74 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1414 helix: 2.22 (0.17), residues: 929 sheet: -1.72 (0.52), residues: 81 loop : -1.91 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 65 HIS 0.003 0.001 HIS C 59 PHE 0.026 0.001 PHE D 15 TYR 0.011 0.001 TYR A 237 ARG 0.003 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 153 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8679 (tt) REVERT: C 16 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 59 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.8006 (t-90) REVERT: D 308 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 429 LEU cc_start: 0.7986 (mp) cc_final: 0.7762 (mp) REVERT: D 599 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7088 (p90) REVERT: E 92 ILE cc_start: 0.9539 (mt) cc_final: 0.9307 (mm) REVERT: E 121 LYS cc_start: 0.8875 (pptt) cc_final: 0.8482 (ptpp) outliers start: 29 outliers final: 19 residues processed: 140 average time/residue: 0.1820 time to fit residues: 39.5636 Evaluate side-chains 134 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 50.0000 chunk 85 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.0050 chunk 84 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11157 Z= 0.155 Angle : 0.582 15.109 15174 Z= 0.272 Chirality : 0.037 0.194 1774 Planarity : 0.004 0.052 1903 Dihedral : 3.279 16.341 1550 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 1.92 % Allowed : 23.83 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1414 helix: 2.30 (0.17), residues: 929 sheet: -1.58 (0.52), residues: 81 loop : -1.71 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 176 HIS 0.002 0.001 HIS C 59 PHE 0.024 0.001 PHE D 15 TYR 0.013 0.001 TYR E 158 ARG 0.003 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8750 (mm) REVERT: C 16 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8180 (tt) REVERT: D 308 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8088 (p0) REVERT: D 415 MET cc_start: 0.7134 (tmm) cc_final: 0.6906 (tmm) REVERT: D 599 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7072 (p90) REVERT: E 92 ILE cc_start: 0.9536 (mt) cc_final: 0.9303 (mm) REVERT: E 121 LYS cc_start: 0.8899 (pptt) cc_final: 0.8576 (ptpp) REVERT: F 170 MET cc_start: 0.8152 (tpp) cc_final: 0.7660 (mmp) outliers start: 21 outliers final: 13 residues processed: 132 average time/residue: 0.1805 time to fit residues: 37.0319 Evaluate side-chains 130 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11157 Z= 0.347 Angle : 0.655 14.726 15174 Z= 0.317 Chirality : 0.039 0.195 1774 Planarity : 0.004 0.052 1903 Dihedral : 3.434 15.951 1550 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 3.76 % Allowed : 23.01 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1414 helix: 2.21 (0.17), residues: 940 sheet: -1.71 (0.52), residues: 81 loop : -1.87 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 160 HIS 0.003 0.001 HIS C 59 PHE 0.023 0.002 PHE E 23 TYR 0.013 0.001 TYR A 237 ARG 0.003 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8897 (mm) REVERT: A 153 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8710 (tt) REVERT: C 16 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 59 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: D 308 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8158 (p0) REVERT: D 369 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8916 (tp) REVERT: D 415 MET cc_start: 0.7268 (tmm) cc_final: 0.6938 (tmm) REVERT: D 599 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7391 (p90) REVERT: E 92 ILE cc_start: 0.9540 (mt) cc_final: 0.9292 (mm) REVERT: E 121 LYS cc_start: 0.9007 (pptt) cc_final: 0.8696 (ptpp) outliers start: 41 outliers final: 25 residues processed: 145 average time/residue: 0.1749 time to fit residues: 39.1458 Evaluate side-chains 143 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 581 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 134 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11157 Z= 0.214 Angle : 0.612 15.605 15174 Z= 0.290 Chirality : 0.038 0.162 1774 Planarity : 0.004 0.051 1903 Dihedral : 3.392 19.176 1550 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 3.02 % Allowed : 24.29 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1414 helix: 2.29 (0.17), residues: 935 sheet: -1.63 (0.52), residues: 81 loop : -1.74 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 160 HIS 0.002 0.000 HIS F 91 PHE 0.021 0.001 PHE D 15 TYR 0.013 0.001 TYR F 98 ARG 0.002 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8853 (mm) REVERT: C 16 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8262 (tt) REVERT: C 59 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.6975 (t-90) REVERT: D 308 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8233 (p0) REVERT: D 369 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8889 (tp) REVERT: D 415 MET cc_start: 0.7273 (tmm) cc_final: 0.6949 (tmm) REVERT: D 599 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7403 (p90) REVERT: E 92 ILE cc_start: 0.9526 (mt) cc_final: 0.9278 (mm) REVERT: E 121 LYS cc_start: 0.8969 (pptt) cc_final: 0.8754 (ptpp) REVERT: E 162 MET cc_start: 0.8931 (tpp) cc_final: 0.8411 (mpp) outliers start: 33 outliers final: 22 residues processed: 136 average time/residue: 0.1840 time to fit residues: 38.4329 Evaluate side-chains 139 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 581 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11157 Z= 0.233 Angle : 0.642 16.896 15174 Z= 0.302 Chirality : 0.038 0.160 1774 Planarity : 0.004 0.052 1903 Dihedral : 3.420 22.653 1550 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 24.20 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1414 helix: 2.29 (0.17), residues: 935 sheet: -1.61 (0.52), residues: 81 loop : -1.73 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 160 HIS 0.002 0.000 HIS F 91 PHE 0.022 0.001 PHE D 15 TYR 0.012 0.001 TYR E 165 ARG 0.002 0.000 ARG F 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 153 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8672 (tt) REVERT: C 16 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8265 (tt) REVERT: C 59 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.7058 (t-90) REVERT: D 308 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8256 (p0) REVERT: D 369 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8906 (tp) REVERT: D 415 MET cc_start: 0.7328 (tmm) cc_final: 0.6982 (tmm) REVERT: D 599 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7319 (p90) REVERT: E 92 ILE cc_start: 0.9532 (mt) cc_final: 0.9282 (mm) REVERT: E 141 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.6473 (t60) REVERT: E 162 MET cc_start: 0.8965 (tpp) cc_final: 0.8390 (mpp) REVERT: F 147 CYS cc_start: 0.7892 (m) cc_final: 0.7485 (m) REVERT: F 170 MET cc_start: 0.8262 (mmt) cc_final: 0.7919 (mmt) outliers start: 33 outliers final: 23 residues processed: 137 average time/residue: 0.1991 time to fit residues: 42.2597 Evaluate side-chains 141 residues out of total 1209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 564 THR Chi-restraints excluded: chain D residue 581 PHE Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 141 TRP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 99 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** D 63 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 = 0.3436 r_free = 0.3436 target = 0.068352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054337 restraints weight = 55260.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.055774 restraints weight = 29321.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056766 restraints weight = 19952.225| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11157 Z= 0.166 Angle : 0.624 15.798 15174 Z= 0.291 Chirality : 0.038 0.190 1774 Planarity : 0.004 0.054 1903 Dihedral : 3.341 20.528 1550 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 24.93 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1414 helix: 2.39 (0.17), residues: 929 sheet: -1.57 (0.52), residues: 81 loop : -1.56 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 179 HIS 0.002 0.000 HIS F 91 PHE 0.023 0.001 PHE D 15 TYR 0.012 0.001 TYR E 158 ARG 0.003 0.000 ARG F 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.58 seconds wall clock time: 34 minutes 31.98 seconds (2071.98 seconds total)