Starting phenix.real_space_refine on Wed Feb 14 23:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kao_22778/02_2024/7kao_22778.pdb" } resolution = 4.0 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= 0.008 sd= 0.058 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 39 5.16 5 C 6860 2.51 5 N 1762 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 472": "OE1" <-> "OE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 186": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10502 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3369 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3869 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 28, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.71, per 1000 atoms: 0.54 Number of scatterers: 10502 At special positions: 0 Unit cell: (108.1, 126.5, 134.55, 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 39 16.00 O 1841 8.00 N 1762 7.00 C 6860 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: 4.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 67.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 63 through 70 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 107 through 137 removed outlier: 3.955A pdb=" N ARG A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.766A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.457A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.929A pdb=" N GLY A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.648A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 removed outlier: 3.635A pdb=" N TYR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 346' Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.573A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.568A pdb=" N CYS A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.521A pdb=" N TYR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.948A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.833A pdb=" N GLY B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.751A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.263A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.513A pdb=" N PHE D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.666A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.961A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.585A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.817A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.082A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.719A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.419A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.532A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.518A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.550A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 4.137A pdb=" N LEU E 92 " --> pdb=" O HIS E 88 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.911A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 4.125A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.429A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.579A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.731A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.865A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 91 removed outlier: 4.011A pdb=" N LEU F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.713A pdb=" N SER F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.623A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 175 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 284 removed outlier: 3.528A pdb=" N ILE A 269 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 281 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 6.726A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE D 435 " --> pdb=" O TYR D 450 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR D 450 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 659 hydrogen bonds defined for protein. 1926 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: 3.01 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3300 1.34 - 1.46: 2159 1.46 - 1.58: 5193 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 10713 Sorted by residual: bond pdb=" CB VAL C 54 " pdb=" CG1 VAL C 54 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.34e-01 bond pdb=" CG1 ILE D 280 " pdb=" CD1 ILE D 280 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.07e-01 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.54e-01 bond pdb=" CB LEU A 258 " pdb=" CG LEU A 258 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.45e-01 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.10e-02 2.27e+03 4.89e-01 ... (remaining 10708 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 308 107.03 - 113.76: 6236 113.76 - 120.50: 4203 120.50 - 127.24: 3672 127.24 - 133.98: 107 Bond angle restraints: 14526 Sorted by residual: angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 112.96 110.12 2.84 1.00e+00 1.00e+00 8.09e+00 angle pdb=" CA LEU A 162 " pdb=" CB LEU A 162 " pdb=" CG LEU A 162 " ideal model delta sigma weight residual 116.30 125.19 -8.89 3.50e+00 8.16e-02 6.46e+00 angle pdb=" C THR A 288 " pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta sigma weight residual 120.82 124.48 -3.66 1.50e+00 4.44e-01 5.94e+00 angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 114.00 110.89 3.11 1.31e+00 5.83e-01 5.63e+00 angle pdb=" CA ILE E 126 " pdb=" C ILE E 126 " pdb=" N GLY E 127 " ideal model delta sigma weight residual 116.60 120.02 -3.42 1.45e+00 4.76e-01 5.55e+00 ... (remaining 14521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 5970 17.35 - 34.70: 404 34.70 - 52.06: 60 52.06 - 69.41: 9 69.41 - 86.76: 4 Dihedral angle restraints: 6447 sinusoidal: 2528 harmonic: 3919 Sorted by residual: dihedral pdb=" CB GLU D 472 " pdb=" CG GLU D 472 " pdb=" CD GLU D 472 " pdb=" OE1 GLU D 472 " ideal model delta sinusoidal sigma weight residual 0.00 86.76 -86.76 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" N LYS A 26 " pdb=" CA LYS A 26 " pdb=" CB LYS A 26 " pdb=" CG LYS A 26 " ideal model delta sinusoidal sigma weight residual -180.00 -120.51 -59.49 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 158 " pdb=" CG MET A 158 " pdb=" SD MET A 158 " pdb=" CE MET A 158 " ideal model delta sinusoidal sigma weight residual 60.00 114.89 -54.89 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 6444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1052 0.028 - 0.056: 440 0.056 - 0.084: 150 0.084 - 0.113: 72 0.113 - 0.141: 10 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CA THR A 291 " pdb=" N THR A 291 " pdb=" C THR A 291 " pdb=" CB THR A 291 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE D 573 " pdb=" N ILE D 573 " pdb=" C ILE D 573 " pdb=" CB ILE D 573 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1721 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO F 94 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO F 48 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO D 463 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.016 5.00e-02 4.00e+02 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1107 2.74 - 3.28: 10975 3.28 - 3.82: 17200 3.82 - 4.36: 18852 4.36 - 4.90: 33379 Nonbonded interactions: 81513 Sorted by model distance: nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.202 2.520 nonbonded pdb=" OG SER A 179 " pdb=" OG SER A 182 " model vdw 2.206 2.440 nonbonded pdb=" O LYS E 79 " pdb=" OG SER E 82 " model vdw 2.207 2.440 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.219 2.440 nonbonded pdb=" OG1 THR A 441 " pdb=" O GLY A 443 " model vdw 2.250 2.440 ... (remaining 81508 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: 1.440 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: 4.100 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 30.810 Find NCS groups from input model: 0.310 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 0.030 10713 Z= 0.185 Angle : 0.531 10.125 14526 Z= 0.297 Chirality : 0.038 0.141 1724 Planarity : 0.003 0.035 1806 Dihedral : 11.866 86.758 3903 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: -1.25 (0.22), residues: 1325 helix: 0.01 (0.17), residues: 817 sheet: -2.62 (0.48), residues: 80 loop : -1.95 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 513 HIS 0.004 0.001 HIS D 330 PHE 0.014 0.001 PHE A 304 TYR 0.009 0.001 TYR F 190 ARG 0.003 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.9054 (mtmt) cc_final: 0.8845 (ptpt) REVERT: C 66 TYR cc_start: 0.8708 (t80) cc_final: 0.8330 (t80) REVERT: B 59 PHE cc_start: 0.8215 (m-10) cc_final: 0.7816 (t80) REVERT: D 14 TRP cc_start: 0.8789 (p-90) cc_final: 0.8333 (p-90) REVERT: D 19 LEU cc_start: 0.9416 (mt) cc_final: 0.9157 (mt) REVERT: D 491 MET cc_start: 0.9312 (ttp) cc_final: 0.9061 (tmm) REVERT: D 608 MET cc_start: 0.8568 (ptp) cc_final: 0.8256 (ttp) REVERT: E 75 TYR cc_start: 0.8500 (t80) cc_final: 0.8217 (t80) REVERT: F 114 ASP cc_start: 0.9326 (t0) cc_final: 0.8947 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2359 time to fit residues: 33.5487 Evaluate side-chains 57 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 192 GLN A 403 ASN D 282 HIS D 288 HIS D 292 GLN D 307 GLN D 494 GLN D 558 HIS E 98 ASN E 123 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10713 Z= 0.296 Angle : 0.600 12.545 14526 Z= 0.297 Chirality : 0.040 0.184 1724 Planarity : 0.004 0.035 1806 Dihedral : 3.525 16.966 1429 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.98 % Allowed : 10.96 % Favored : 88.06 % 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: 0.11 (0.23), residues: 1325 helix: 1.10 (0.18), residues: 834 sheet: -1.42 (0.55), residues: 75 loop : -1.73 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 513 HIS 0.005 0.001 HIS C 72 PHE 0.018 0.001 PHE A 304 TYR 0.013 0.001 TYR F 190 ARG 0.007 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.8741 (t80) cc_final: 0.8295 (t80) REVERT: B 59 PHE cc_start: 0.8175 (m-10) cc_final: 0.7824 (t80) REVERT: D 14 TRP cc_start: 0.9028 (p-90) cc_final: 0.8513 (p-90) REVERT: D 19 LEU cc_start: 0.9411 (mt) cc_final: 0.9173 (mt) REVERT: F 114 ASP cc_start: 0.9309 (t0) cc_final: 0.9094 (t0) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.2138 time to fit residues: 24.2455 Evaluate side-chains 68 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 0.0170 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN E 69 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10713 Z= 0.370 Angle : 0.653 13.763 14526 Z= 0.323 Chirality : 0.041 0.189 1724 Planarity : 0.004 0.037 1806 Dihedral : 3.795 17.783 1429 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.52 % Allowed : 14.62 % Favored : 83.87 % 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: 0.55 (0.23), residues: 1325 helix: 1.38 (0.18), residues: 833 sheet: -1.09 (0.58), residues: 75 loop : -1.43 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 513 HIS 0.007 0.002 HIS C 72 PHE 0.014 0.001 PHE D 481 TYR 0.014 0.001 TYR F 190 ARG 0.003 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 66 TYR cc_start: 0.8824 (t80) cc_final: 0.8212 (t80) REVERT: B 59 PHE cc_start: 0.8443 (m-10) cc_final: 0.8034 (t80) REVERT: D 14 TRP cc_start: 0.9081 (p-90) cc_final: 0.8529 (p-90) REVERT: D 19 LEU cc_start: 0.9448 (mt) cc_final: 0.9195 (mt) REVERT: E 126 ILE cc_start: 0.9290 (mt) cc_final: 0.8756 (tt) REVERT: F 29 ASP cc_start: 0.9329 (t70) cc_final: 0.9099 (t70) REVERT: F 90 ARG cc_start: 0.8468 (mmp80) cc_final: 0.8194 (mmp80) REVERT: F 114 ASP cc_start: 0.9337 (t0) cc_final: 0.9126 (t0) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.1970 time to fit residues: 22.8932 Evaluate side-chains 73 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 0.0970 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10713 Z= 0.175 Angle : 0.549 11.293 14526 Z= 0.266 Chirality : 0.039 0.170 1724 Planarity : 0.003 0.032 1806 Dihedral : 3.551 16.983 1429 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.25 % Allowed : 16.22 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.24), residues: 1325 helix: 1.72 (0.19), residues: 836 sheet: -0.93 (0.59), residues: 75 loop : -1.19 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 35 HIS 0.004 0.001 HIS D 330 PHE 0.012 0.001 PHE A 304 TYR 0.010 0.001 TYR F 190 ARG 0.003 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9210 (tpp) cc_final: 0.8939 (tpp) REVERT: C 66 TYR cc_start: 0.8733 (t80) cc_final: 0.8052 (t80) REVERT: B 59 PHE cc_start: 0.8479 (m-10) cc_final: 0.8031 (t80) REVERT: D 14 TRP cc_start: 0.9063 (p-90) cc_final: 0.8468 (p-90) REVERT: D 19 LEU cc_start: 0.9445 (mt) cc_final: 0.9200 (mt) REVERT: D 265 ASN cc_start: 0.8427 (m-40) cc_final: 0.8203 (m-40) REVERT: E 76 PHE cc_start: 0.9003 (m-80) cc_final: 0.8733 (m-80) REVERT: F 87 MET cc_start: 0.8787 (mpp) cc_final: 0.8567 (mpp) REVERT: F 114 ASP cc_start: 0.9259 (t0) cc_final: 0.8914 (p0) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.2080 time to fit residues: 24.9539 Evaluate side-chains 70 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 201 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 115 optimal weight: 0.0060 chunk 32 optimal weight: 20.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10713 Z= 0.136 Angle : 0.534 11.000 14526 Z= 0.254 Chirality : 0.039 0.313 1724 Planarity : 0.003 0.031 1806 Dihedral : 3.369 16.633 1429 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.07 % Allowed : 17.02 % Favored : 81.91 % 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: 1.35 (0.24), residues: 1325 helix: 1.95 (0.18), residues: 836 sheet: -0.80 (0.60), residues: 75 loop : -0.97 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.003 0.001 HIS D 330 PHE 0.011 0.001 PHE A 304 TYR 0.009 0.001 TYR F 190 ARG 0.002 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7530 (ttt) cc_final: 0.6572 (ptm) REVERT: A 249 MET cc_start: 0.9223 (tpp) cc_final: 0.9015 (mmm) REVERT: A 400 MET cc_start: 0.8904 (tpp) cc_final: 0.8572 (tpp) REVERT: C 66 TYR cc_start: 0.8632 (t80) cc_final: 0.7997 (t80) REVERT: B 59 PHE cc_start: 0.8496 (m-10) cc_final: 0.7958 (t80) REVERT: D 14 TRP cc_start: 0.8965 (p-90) cc_final: 0.8708 (p-90) REVERT: D 19 LEU cc_start: 0.9445 (mt) cc_final: 0.9187 (mt) REVERT: D 265 ASN cc_start: 0.8386 (m-40) cc_final: 0.8169 (m-40) REVERT: E 76 PHE cc_start: 0.9029 (m-80) cc_final: 0.8702 (m-80) REVERT: E 87 ILE cc_start: 0.7989 (pt) cc_final: 0.7642 (pt) REVERT: F 114 ASP cc_start: 0.9164 (t0) cc_final: 0.8731 (p0) outliers start: 12 outliers final: 5 residues processed: 80 average time/residue: 0.1976 time to fit residues: 24.4511 Evaluate side-chains 72 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 516 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 9.9990 chunk 115 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 192 GLN D 334 HIS E 123 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10713 Z= 0.328 Angle : 0.650 12.514 14526 Z= 0.313 Chirality : 0.041 0.281 1724 Planarity : 0.004 0.033 1806 Dihedral : 3.660 17.755 1429 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.58 % Allowed : 17.02 % Favored : 80.39 % 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: 1.27 (0.24), residues: 1325 helix: 1.80 (0.18), residues: 843 sheet: -0.78 (0.60), residues: 75 loop : -0.85 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 513 HIS 0.006 0.001 HIS D 334 PHE 0.015 0.001 PHE D 481 TYR 0.016 0.001 TYR F 190 ARG 0.006 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9295 (tpp) cc_final: 0.9057 (mmm) REVERT: C 66 TYR cc_start: 0.8629 (t80) cc_final: 0.8120 (t80) REVERT: B 59 PHE cc_start: 0.8535 (m-10) cc_final: 0.8049 (t80) REVERT: D 14 TRP cc_start: 0.9135 (p-90) cc_final: 0.8474 (p-90) REVERT: D 19 LEU cc_start: 0.9446 (mt) cc_final: 0.9189 (mt) REVERT: D 265 ASN cc_start: 0.8480 (m-40) cc_final: 0.8206 (m-40) REVERT: F 114 ASP cc_start: 0.9280 (t0) cc_final: 0.8910 (p0) outliers start: 29 outliers final: 15 residues processed: 85 average time/residue: 0.1963 time to fit residues: 26.1975 Evaluate side-chains 75 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10713 Z= 0.154 Angle : 0.566 11.168 14526 Z= 0.266 Chirality : 0.040 0.262 1724 Planarity : 0.003 0.031 1806 Dihedral : 3.443 17.052 1429 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.34 % Allowed : 18.45 % Favored : 80.21 % 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: 1.61 (0.24), residues: 1325 helix: 2.06 (0.18), residues: 838 sheet: -0.77 (0.61), residues: 75 loop : -0.64 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.003 0.001 HIS D 330 PHE 0.023 0.001 PHE A 304 TYR 0.010 0.001 TYR F 190 ARG 0.005 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7656 (ttt) cc_final: 0.6718 (ptm) REVERT: A 400 MET cc_start: 0.8923 (tpp) cc_final: 0.8678 (tpp) REVERT: C 66 TYR cc_start: 0.8553 (t80) cc_final: 0.7975 (t80) REVERT: B 59 PHE cc_start: 0.8530 (m-10) cc_final: 0.8046 (t80) REVERT: D 14 TRP cc_start: 0.9050 (p-90) cc_final: 0.8410 (p-90) REVERT: D 19 LEU cc_start: 0.9441 (mt) cc_final: 0.9161 (mt) REVERT: E 76 PHE cc_start: 0.9072 (m-80) cc_final: 0.8687 (m-80) REVERT: E 87 ILE cc_start: 0.8178 (pt) cc_final: 0.7773 (pt) REVERT: F 114 ASP cc_start: 0.9166 (t0) cc_final: 0.8966 (t0) outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.1962 time to fit residues: 24.9058 Evaluate side-chains 71 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10713 Z= 0.159 Angle : 0.580 10.469 14526 Z= 0.272 Chirality : 0.040 0.345 1724 Planarity : 0.003 0.040 1806 Dihedral : 3.377 16.622 1429 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.52 % Allowed : 19.34 % Favored : 79.14 % 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: 1.70 (0.24), residues: 1325 helix: 2.09 (0.18), residues: 840 sheet: -0.69 (0.61), residues: 75 loop : -0.52 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 283 HIS 0.004 0.001 HIS C 72 PHE 0.026 0.001 PHE A 304 TYR 0.010 0.001 TYR F 190 ARG 0.010 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7656 (ttt) cc_final: 0.6699 (ptm) REVERT: A 400 MET cc_start: 0.8927 (tpp) cc_final: 0.8656 (tpp) REVERT: C 66 TYR cc_start: 0.8497 (t80) cc_final: 0.7970 (t80) REVERT: B 59 PHE cc_start: 0.8526 (m-10) cc_final: 0.8043 (t80) REVERT: D 14 TRP cc_start: 0.9047 (p-90) cc_final: 0.8414 (p-90) REVERT: D 19 LEU cc_start: 0.9440 (mt) cc_final: 0.9155 (mt) REVERT: E 76 PHE cc_start: 0.9077 (m-80) cc_final: 0.8685 (m-80) REVERT: E 87 ILE cc_start: 0.8087 (pt) cc_final: 0.7817 (pt) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.1753 time to fit residues: 21.7150 Evaluate side-chains 70 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10713 Z= 0.154 Angle : 0.603 12.424 14526 Z= 0.276 Chirality : 0.040 0.246 1724 Planarity : 0.003 0.038 1806 Dihedral : 3.322 16.235 1429 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.16 % Allowed : 19.88 % Favored : 78.97 % 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: 1.86 (0.24), residues: 1325 helix: 2.18 (0.18), residues: 843 sheet: -0.47 (0.62), residues: 73 loop : -0.42 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.025 0.001 PHE A 304 TYR 0.012 0.001 TYR E 75 ARG 0.007 0.000 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7660 (ttt) cc_final: 0.6689 (ptm) REVERT: A 400 MET cc_start: 0.8931 (tpp) cc_final: 0.8480 (tpp) REVERT: C 66 TYR cc_start: 0.8472 (t80) cc_final: 0.8024 (t80) REVERT: B 59 PHE cc_start: 0.8519 (m-10) cc_final: 0.8032 (t80) REVERT: D 14 TRP cc_start: 0.9061 (p-90) cc_final: 0.8475 (p-90) REVERT: D 19 LEU cc_start: 0.9438 (mt) cc_final: 0.9149 (mt) REVERT: E 76 PHE cc_start: 0.9095 (m-80) cc_final: 0.8552 (m-10) REVERT: F 114 ASP cc_start: 0.9135 (t0) cc_final: 0.8772 (p0) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1766 time to fit residues: 20.7132 Evaluate side-chains 70 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain F residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 0.0370 chunk 105 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10713 Z= 0.148 Angle : 0.612 17.016 14526 Z= 0.276 Chirality : 0.040 0.365 1724 Planarity : 0.003 0.034 1806 Dihedral : 3.238 15.727 1429 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.07 % Allowed : 19.79 % Favored : 79.14 % 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: 1.98 (0.24), residues: 1325 helix: 2.27 (0.18), residues: 842 sheet: -0.73 (0.54), residues: 89 loop : -0.28 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.003 0.001 HIS C 72 PHE 0.025 0.001 PHE A 304 TYR 0.010 0.001 TYR F 190 ARG 0.008 0.000 ARG F 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.7556 (ttt) cc_final: 0.6501 (ptm) REVERT: A 400 MET cc_start: 0.8922 (tpp) cc_final: 0.8486 (tpp) REVERT: C 66 TYR cc_start: 0.8452 (t80) cc_final: 0.8080 (t80) REVERT: B 59 PHE cc_start: 0.8508 (m-10) cc_final: 0.8027 (t80) REVERT: D 14 TRP cc_start: 0.9055 (p-90) cc_final: 0.8482 (p-90) REVERT: D 19 LEU cc_start: 0.9432 (mt) cc_final: 0.9126 (mt) REVERT: E 76 PHE cc_start: 0.9139 (m-80) cc_final: 0.8671 (m-80) outliers start: 12 outliers final: 11 residues processed: 72 average time/residue: 0.1781 time to fit residues: 20.9540 Evaluate side-chains 70 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 381 HIS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain F residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 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 = 0.3121 r_free = 0.3121 target = 0.046162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.035528 restraints weight = 76540.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.036525 restraints weight = 38007.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037015 restraints weight = 23993.367| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10713 Z= 0.362 Angle : 0.721 15.629 14526 Z= 0.341 Chirality : 0.043 0.347 1724 Planarity : 0.004 0.040 1806 Dihedral : 3.685 17.956 1429 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.34 % Allowed : 19.96 % Favored : 78.70 % 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: 1.67 (0.24), residues: 1325 helix: 2.02 (0.18), residues: 849 sheet: -0.83 (0.59), residues: 81 loop : -0.42 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 513 HIS 0.009 0.001 HIS C 72 PHE 0.024 0.001 PHE A 304 TYR 0.018 0.001 TYR F 190 ARG 0.018 0.001 ARG F 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.30 seconds wall clock time: 33 minutes 8.86 seconds (1988.86 seconds total)