Starting phenix.real_space_refine on Fri Mar 15 04:35:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kas_22782/03_2024/7kas_22782.pdb" } resolution = 3.9 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= 0.003 sd= 0.052 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 41 5.16 5 C 6915 2.51 5 N 1791 2.21 5 O 1869 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 ARG 196": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 128": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3268 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 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: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3804 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 27, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 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 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 6.01, per 1000 atoms: 0.57 Number of scatterers: 10616 At special positions: 0 Unit cell: (110.67, 126.14, 135.66, 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 41 16.00 O 1869 8.00 N 1791 7.00 C 6915 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 70.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.564A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.577A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.106A 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 214 through 224 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.130A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.858A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.563A pdb=" N MET 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 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.574A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.604A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 367 " --> pdb=" O ILE A 363 " (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 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.991A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.548A pdb=" N VAL C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.863A 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: 4.484A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 4.103A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.678A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.592A pdb=" N ALA D 259 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.913A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.651A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.131A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 362 Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.571A 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: 3.988A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.220A 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 486 removed outlier: 3.593A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.311A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.493A pdb=" N ASN D 539 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.789A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 4.155A pdb=" N LEU E 92 " --> pdb=" O HIS E 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.642A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.041A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.793A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.640A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.699A 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: 3.564A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.989A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.874A 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 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 4.008A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.101A 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 174 through 192 removed outlier: 3.923A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 Processing helix chain 'G' and resid 175 through 205 removed outlier: 3.573A pdb=" N UNK G 205 " --> pdb=" O UNK G 201 " (cutoff:3.500A) 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 278 through 284 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 450 through 453 removed outlier: 3.662A pdb=" N ILE D 571 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.522A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.804A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 6 689 hydrogen bonds defined for protein. 2025 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: 3.03 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: 1.23 - 1.34: 3355 1.34 - 1.46: 1582 1.46 - 1.57: 5818 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 10820 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.41e-02 5.03e+03 1.36e+00 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.27e+00 bond pdb=" CB TRP D 513 " pdb=" CG TRP D 513 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.01e+00 bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.62e-01 bond pdb=" N LEU F 102 " pdb=" CA LEU F 102 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 8.92e-01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 295 106.80 - 113.61: 6204 113.61 - 120.43: 4297 120.43 - 127.24: 3778 127.24 - 134.05: 102 Bond angle restraints: 14676 Sorted by residual: angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 111.88 106.81 5.07 1.06e+00 8.90e-01 2.28e+01 angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 111.90 108.73 3.17 8.10e-01 1.52e+00 1.54e+01 angle pdb=" C GLU D 12 " pdb=" N THR D 13 " pdb=" CA THR D 13 " ideal model delta sigma weight residual 122.08 117.55 4.53 1.53e+00 4.27e-01 8.76e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.21 114.91 -4.70 1.64e+00 3.72e-01 8.21e+00 angle pdb=" C THR D 595 " pdb=" N ASP D 596 " pdb=" CA ASP D 596 " ideal model delta sigma weight residual 121.52 117.30 4.22 1.74e+00 3.30e-01 5.89e+00 ... (remaining 14671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5908 17.76 - 35.51: 506 35.51 - 53.27: 80 53.27 - 71.03: 14 71.03 - 88.78: 7 Dihedral angle restraints: 6515 sinusoidal: 2489 harmonic: 4026 Sorted by residual: dihedral pdb=" CA ARG F 154 " pdb=" C ARG F 154 " pdb=" N GLN F 155 " pdb=" CA GLN F 155 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG D 509 " pdb=" C ARG D 509 " pdb=" N ARG D 510 " pdb=" CA ARG D 510 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 986 0.028 - 0.056: 507 0.056 - 0.084: 160 0.084 - 0.112: 77 0.112 - 0.140: 21 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CB ILE E 170 " pdb=" CA ILE E 170 " pdb=" CG1 ILE E 170 " pdb=" CG2 ILE E 170 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB VAL E 205 " pdb=" CA VAL E 205 " pdb=" CG1 VAL E 205 " pdb=" CG2 VAL E 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-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 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1748 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 53 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 54 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 366 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 367 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO F 94 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.020 5.00e-02 4.00e+02 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 299 2.71 - 3.26: 11030 3.26 - 3.80: 16319 3.80 - 4.35: 18560 4.35 - 4.90: 32083 Nonbonded interactions: 78291 Sorted by model distance: nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.162 2.440 nonbonded pdb=" ND2 ASN D 55 " pdb=" O LEU D 496 " model vdw 2.250 2.520 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.269 2.520 nonbonded pdb=" O SER D 423 " pdb=" OG SER D 423 " model vdw 2.293 2.440 nonbonded pdb=" O PRO F 171 " pdb=" NH2 ARG F 177 " model vdw 2.293 2.520 ... (remaining 78286 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: 1.450 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: 4.050 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.830 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.036 10820 Z= 0.246 Angle : 0.619 7.450 14676 Z= 0.349 Chirality : 0.040 0.140 1751 Planarity : 0.004 0.037 1831 Dihedral : 13.683 88.782 3899 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % 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 (0.22), residues: 1305 helix: 0.09 (0.17), residues: 809 sheet: -2.52 (0.51), residues: 84 loop : -2.44 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 14 HIS 0.006 0.001 HIS B 72 PHE 0.010 0.001 PHE F 46 TYR 0.021 0.001 TYR F 190 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8717 (mmm) cc_final: 0.8412 (tpp) REVERT: E 73 ASP cc_start: 0.8497 (p0) cc_final: 0.8200 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2462 time to fit residues: 41.5241 Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 311 ASN D 427 ASN D 539 ASN D 558 HIS E 88 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 155 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10820 Z= 0.154 Angle : 0.528 9.263 14676 Z= 0.264 Chirality : 0.038 0.159 1751 Planarity : 0.004 0.034 1831 Dihedral : 3.587 17.992 1463 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.09 % Allowed : 13.24 % Favored : 85.68 % 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: 0.34 (0.24), residues: 1305 helix: 1.54 (0.18), residues: 817 sheet: -2.32 (0.49), residues: 94 loop : -1.97 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 195 HIS 0.007 0.001 HIS D 309 PHE 0.016 0.001 PHE A 256 TYR 0.013 0.001 TYR A 139 ARG 0.004 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8745 (mmm) cc_final: 0.8419 (tpp) REVERT: E 73 ASP cc_start: 0.8488 (p0) cc_final: 0.8187 (p0) REVERT: E 165 MET cc_start: 0.7756 (ttp) cc_final: 0.7402 (tmm) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.2006 time to fit residues: 28.2942 Evaluate side-chains 74 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain E residue 84 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 0.0010 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 40.0000 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10820 Z= 0.217 Angle : 0.543 9.520 14676 Z= 0.271 Chirality : 0.038 0.141 1751 Planarity : 0.004 0.038 1831 Dihedral : 3.550 17.944 1463 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.45 % Allowed : 16.23 % Favored : 81.32 % 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: 0.91 (0.24), residues: 1305 helix: 1.97 (0.19), residues: 816 sheet: -2.09 (0.49), residues: 94 loop : -1.69 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.005 0.001 HIS D 309 PHE 0.015 0.001 PHE A 256 TYR 0.016 0.001 TYR F 190 ARG 0.003 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7108 (tpt) cc_final: 0.6783 (tpt) REVERT: A 256 PHE cc_start: 0.8238 (t80) cc_final: 0.8029 (t80) REVERT: B 64 PHE cc_start: 0.8357 (t80) cc_final: 0.8121 (t80) REVERT: D 24 MET cc_start: 0.8801 (mmm) cc_final: 0.8486 (tpp) REVERT: E 73 ASP cc_start: 0.8496 (p0) cc_final: 0.8210 (p0) outliers start: 27 outliers final: 15 residues processed: 94 average time/residue: 0.1928 time to fit residues: 27.9492 Evaluate side-chains 79 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 87 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 50.0000 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10820 Z= 0.269 Angle : 0.576 9.950 14676 Z= 0.288 Chirality : 0.039 0.148 1751 Planarity : 0.004 0.034 1831 Dihedral : 3.689 19.032 1463 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.26 % Allowed : 17.14 % Favored : 79.60 % 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: 1.11 (0.24), residues: 1305 helix: 2.07 (0.18), residues: 816 sheet: -1.82 (0.51), residues: 94 loop : -1.51 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.004 0.001 HIS D 309 PHE 0.015 0.001 PHE D 356 TYR 0.020 0.001 TYR F 190 ARG 0.003 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 65 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: B 64 PHE cc_start: 0.8412 (t80) cc_final: 0.8200 (t80) REVERT: D 24 MET cc_start: 0.8823 (mmm) cc_final: 0.8517 (tpp) REVERT: D 526 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7837 (pp) REVERT: E 73 ASP cc_start: 0.8456 (p0) cc_final: 0.8210 (p0) outliers start: 36 outliers final: 20 residues processed: 97 average time/residue: 0.1831 time to fit residues: 27.2696 Evaluate side-chains 79 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10820 Z= 0.198 Angle : 0.540 10.407 14676 Z= 0.268 Chirality : 0.039 0.201 1751 Planarity : 0.003 0.034 1831 Dihedral : 3.555 17.913 1463 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 19.13 % Favored : 77.97 % 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: 1.37 (0.25), residues: 1305 helix: 2.23 (0.19), residues: 815 sheet: -1.55 (0.54), residues: 94 loop : -1.34 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 95 HIS 0.005 0.001 HIS D 309 PHE 0.016 0.001 PHE A 92 TYR 0.015 0.001 TYR F 190 ARG 0.002 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6951 (tpt) REVERT: B 64 PHE cc_start: 0.8328 (t80) cc_final: 0.7895 (t80) REVERT: D 24 MET cc_start: 0.8833 (mmm) cc_final: 0.8497 (tpp) REVERT: D 526 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7815 (pp) REVERT: E 73 ASP cc_start: 0.8429 (p0) cc_final: 0.8181 (p0) outliers start: 32 outliers final: 23 residues processed: 92 average time/residue: 0.1862 time to fit residues: 26.8349 Evaluate side-chains 81 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 56 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 50.0000 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10820 Z= 0.287 Angle : 0.599 11.190 14676 Z= 0.299 Chirality : 0.041 0.180 1751 Planarity : 0.004 0.032 1831 Dihedral : 3.712 16.930 1463 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.90 % Allowed : 19.95 % Favored : 76.16 % 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: 1.26 (0.25), residues: 1305 helix: 2.10 (0.18), residues: 817 sheet: -1.55 (0.53), residues: 94 loop : -1.31 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 95 HIS 0.003 0.001 HIS F 122 PHE 0.019 0.001 PHE A 395 TYR 0.020 0.001 TYR F 190 ARG 0.003 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 56 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.7013 (tpt) REVERT: B 64 PHE cc_start: 0.8473 (t80) cc_final: 0.8223 (t80) REVERT: D 24 MET cc_start: 0.8865 (mmm) cc_final: 0.8440 (tpp) REVERT: D 526 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7905 (pp) REVERT: E 73 ASP cc_start: 0.8498 (p0) cc_final: 0.8258 (p0) outliers start: 43 outliers final: 31 residues processed: 93 average time/residue: 0.1683 time to fit residues: 25.1585 Evaluate side-chains 88 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 55 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 50.0000 chunk 82 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10820 Z= 0.140 Angle : 0.532 10.438 14676 Z= 0.257 Chirality : 0.038 0.163 1751 Planarity : 0.003 0.036 1831 Dihedral : 3.417 16.744 1463 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.18 % Allowed : 22.03 % Favored : 75.79 % 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 (0.25), residues: 1305 helix: 2.35 (0.19), residues: 822 sheet: -1.24 (0.55), residues: 94 loop : -1.13 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 159 HIS 0.007 0.001 HIS D 309 PHE 0.017 0.001 PHE A 395 TYR 0.012 0.001 TYR E 121 ARG 0.002 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 67 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6988 (tpt) REVERT: B 64 PHE cc_start: 0.8252 (t80) cc_final: 0.7768 (t80) REVERT: D 24 MET cc_start: 0.8772 (mmm) cc_final: 0.8532 (tpp) REVERT: E 73 ASP cc_start: 0.8410 (p0) cc_final: 0.8166 (p0) outliers start: 24 outliers final: 18 residues processed: 87 average time/residue: 0.1688 time to fit residues: 23.5548 Evaluate side-chains 81 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10820 Z= 0.138 Angle : 0.520 11.099 14676 Z= 0.252 Chirality : 0.038 0.250 1751 Planarity : 0.003 0.038 1831 Dihedral : 3.292 16.126 1463 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 22.39 % Favored : 75.43 % 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: 1.76 (0.25), residues: 1305 helix: 2.38 (0.18), residues: 823 sheet: -1.10 (0.55), residues: 94 loop : -0.95 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.006 0.001 HIS D 309 PHE 0.014 0.001 PHE A 395 TYR 0.013 0.001 TYR F 190 ARG 0.001 0.000 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.7009 (tpt) REVERT: B 64 PHE cc_start: 0.8198 (t80) cc_final: 0.7735 (t80) REVERT: D 24 MET cc_start: 0.8798 (mmm) cc_final: 0.8566 (tpp) REVERT: E 73 ASP cc_start: 0.8409 (p0) cc_final: 0.8164 (p0) outliers start: 24 outliers final: 19 residues processed: 85 average time/residue: 0.1829 time to fit residues: 24.5057 Evaluate side-chains 77 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain F residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10820 Z= 0.183 Angle : 0.565 10.485 14676 Z= 0.273 Chirality : 0.039 0.248 1751 Planarity : 0.003 0.038 1831 Dihedral : 3.344 16.252 1463 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.27 % Allowed : 22.76 % Favored : 74.98 % 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: 1.73 (0.25), residues: 1305 helix: 2.31 (0.18), residues: 818 sheet: -1.13 (0.55), residues: 94 loop : -0.81 (0.34), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 159 HIS 0.005 0.001 HIS D 309 PHE 0.012 0.001 PHE A 395 TYR 0.015 0.001 TYR F 190 ARG 0.004 0.000 ARG F 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7027 (tpt) REVERT: B 64 PHE cc_start: 0.8318 (t80) cc_final: 0.7817 (t80) REVERT: D 24 MET cc_start: 0.8776 (mmm) cc_final: 0.8525 (tpp) REVERT: E 73 ASP cc_start: 0.8451 (p0) cc_final: 0.8204 (p0) outliers start: 25 outliers final: 21 residues processed: 82 average time/residue: 0.1779 time to fit residues: 23.7407 Evaluate side-chains 81 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 135 optimal weight: 60.0000 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10820 Z= 0.162 Angle : 0.557 10.744 14676 Z= 0.268 Chirality : 0.039 0.246 1751 Planarity : 0.003 0.036 1831 Dihedral : 3.305 15.988 1463 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.18 % Allowed : 23.03 % Favored : 74.80 % 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: 1.80 (0.25), residues: 1305 helix: 2.34 (0.18), residues: 818 sheet: -1.08 (0.55), residues: 94 loop : -0.70 (0.34), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 159 HIS 0.005 0.001 HIS D 309 PHE 0.012 0.001 PHE A 395 TYR 0.013 0.001 TYR F 190 ARG 0.001 0.000 ARG F 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.7007 (tpt) REVERT: C 28 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: B 64 PHE cc_start: 0.8243 (t80) cc_final: 0.7766 (t80) REVERT: D 24 MET cc_start: 0.8796 (mmm) cc_final: 0.8556 (tpp) REVERT: E 73 ASP cc_start: 0.8519 (p0) cc_final: 0.8244 (p0) outliers start: 24 outliers final: 20 residues processed: 78 average time/residue: 0.1610 time to fit residues: 20.4912 Evaluate side-chains 80 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 376 ASN Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 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 = 0.3724 r_free = 0.3724 target = 0.080650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060811 restraints weight = 44940.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061665 restraints weight = 25707.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061891 restraints weight = 18059.218| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10820 Z= 0.313 Angle : 0.642 10.891 14676 Z= 0.316 Chirality : 0.041 0.257 1751 Planarity : 0.004 0.033 1831 Dihedral : 3.655 16.624 1463 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.45 % Allowed : 22.85 % Favored : 74.71 % 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: 1305 helix: 2.12 (0.18), residues: 819 sheet: -1.24 (0.54), residues: 94 loop : -0.88 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 156 HIS 0.003 0.001 HIS D 330 PHE 0.018 0.001 PHE D 356 TYR 0.019 0.002 TYR F 190 ARG 0.004 0.000 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.55 seconds wall clock time: 31 minutes 5.31 seconds (1865.31 seconds total)