Starting phenix.real_space_refine on Fri Mar 15 02:42:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kat_22783/03_2024/7kat_22783.pdb" } resolution = 4.4 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= 0.007 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 6813 2.51 5 N 1754 2.21 5 O 1825 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 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 "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 GLU 473": "OE1" <-> "OE2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10431 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3358 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 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: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 457} 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: 6.14, per 1000 atoms: 0.59 Number of scatterers: 10431 At special positions: 0 Unit cell: (109.48, 126.14, 136.85, 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 1825 8.00 N 1754 7.00 C 6813 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: 4.71 Conformation dependent library (CDL) restraints added in 2.1 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2526 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 68.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 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: 4.028A pdb=" N ARG A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.501A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.765A 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 226 removed outlier: 3.502A pdb=" N ARG A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.678A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.618A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 314 removed outlier: 4.189A pdb=" N ILE A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 347 removed outlier: 3.607A pdb=" N TYR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 347' Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.646A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) 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 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 4.276A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.041A 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 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.602A pdb=" N PHE D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 3.730A 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: 4.430A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.600A 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 113 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.922A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.772A pdb=" N TYR D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.639A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.963A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.400A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.803A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.991A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 removed outlier: 3.537A pdb=" N LEU D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.507A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.315A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 removed outlier: 3.528A pdb=" N LEU D 469 " --> pdb=" O PRO D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.121A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.667A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 3.661A 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: 3.617A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 182 removed outlier: 4.307A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.324A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.788A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.516A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.848A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.689A 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: 3.942A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.329A 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: 3.612A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (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 326 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.694A pdb=" N LYS D 454 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA D 433 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER D 452 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.803A pdb=" N CYS D 514 " --> pdb=" O LYS D 593 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 592 " --> pdb=" O LEU D 602 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 602 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 652 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: 2.68 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3281 1.35 - 1.46: 2359 1.46 - 1.58: 4938 1.58 - 1.70: 0 1.70 - 1.81: 61 Bond restraints: 10639 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 9.23e-01 bond pdb=" N LEU D 235 " pdb=" CA LEU D 235 " ideal model delta sigma weight residual 1.462 1.454 0.008 8.50e-03 1.38e+04 8.92e-01 bond pdb=" CA LEU F 102 " pdb=" C LEU F 102 " ideal model delta sigma weight residual 1.521 1.530 -0.009 1.14e-02 7.69e+03 6.10e-01 bond pdb=" C TRP D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.30e-02 5.92e+03 5.75e-01 bond pdb=" C VAL D 215 " pdb=" O VAL D 215 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.19e-02 7.06e+03 5.71e-01 ... (remaining 10634 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.16: 305 107.16 - 113.86: 6261 113.86 - 120.57: 4223 120.57 - 127.28: 3528 127.28 - 133.99: 105 Bond angle restraints: 14422 Sorted by residual: angle pdb=" N ILE E 126 " pdb=" CA ILE E 126 " pdb=" C ILE E 126 " ideal model delta sigma weight residual 113.71 109.71 4.00 9.50e-01 1.11e+00 1.77e+01 angle pdb=" C GLU A 266 " pdb=" N LEU A 267 " pdb=" CA LEU A 267 " ideal model delta sigma weight residual 122.38 114.76 7.62 2.90e+00 1.19e-01 6.91e+00 angle pdb=" C LYS A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta sigma weight residual 123.16 120.70 2.46 1.06e+00 8.90e-01 5.41e+00 angle pdb=" CA ILE E 126 " pdb=" C ILE E 126 " pdb=" N GLY E 127 " ideal model delta sigma weight residual 119.87 116.76 3.11 1.34e+00 5.57e-01 5.37e+00 angle pdb=" CA VAL D 215 " pdb=" C VAL D 215 " pdb=" N ASP D 216 " ideal model delta sigma weight residual 116.60 119.92 -3.32 1.45e+00 4.76e-01 5.24e+00 ... (remaining 14417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6007 17.91 - 35.82: 348 35.82 - 53.73: 40 53.73 - 71.65: 5 71.65 - 89.56: 6 Dihedral angle restraints: 6406 sinusoidal: 2514 harmonic: 3892 Sorted by residual: dihedral pdb=" CB GLU E 142 " pdb=" CG GLU E 142 " pdb=" CD GLU E 142 " pdb=" OE1 GLU E 142 " ideal model delta sinusoidal sigma weight residual 0.00 89.56 -89.56 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 382 " pdb=" CG GLU A 382 " pdb=" CD GLU A 382 " pdb=" OE1 GLU A 382 " ideal model delta sinusoidal sigma weight residual 0.00 -85.22 85.22 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" CB GLU E 128 " pdb=" CG GLU E 128 " pdb=" CD GLU E 128 " pdb=" OE1 GLU E 128 " ideal model delta sinusoidal sigma weight residual 0.00 -82.63 82.63 1 3.00e+01 1.11e-03 9.30e+00 ... (remaining 6403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1258 0.035 - 0.071: 329 0.071 - 0.106: 108 0.106 - 0.142: 15 0.142 - 0.177: 2 Chirality restraints: 1712 Sorted by residual: chirality pdb=" CB VAL A 82 " pdb=" CA VAL A 82 " pdb=" CG1 VAL A 82 " pdb=" CG2 VAL A 82 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.85e-01 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 2.38 0.14 2.00e-01 2.50e+01 5.19e-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 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1709 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO F 48 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 27 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO D 28 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 28 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 28 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.17e-01 pdb=" N PRO D 463 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.013 5.00e-02 4.00e+02 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 552 2.73 - 3.27: 11272 3.27 - 3.81: 17200 3.81 - 4.36: 18541 4.36 - 4.90: 32319 Nonbonded interactions: 79884 Sorted by model distance: nonbonded pdb=" OG1 THR D 386 " pdb=" OD1 ASP D 388 " model vdw 2.185 2.440 nonbonded pdb=" OG1 THR A 201 " pdb=" OE1 GLU A 212 " model vdw 2.245 2.440 nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 66 " model vdw 2.251 2.440 nonbonded pdb=" O HIS D 282 " pdb=" OG SER D 285 " model vdw 2.269 2.440 nonbonded pdb=" O TRP A 380 " pdb=" OG SER A 384 " model vdw 2.273 2.440 ... (remaining 79879 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: 0.680 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: 4.030 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.900 Find NCS groups from input model: 0.320 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.002 0.024 10639 Z= 0.147 Angle : 0.513 7.624 14422 Z= 0.291 Chirality : 0.037 0.177 1712 Planarity : 0.003 0.041 1791 Dihedral : 11.321 89.557 3880 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: -0.63 (0.22), residues: 1316 helix: 0.62 (0.18), residues: 816 sheet: -1.99 (0.51), residues: 84 loop : -2.11 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.003 0.001 HIS D 334 PHE 0.009 0.001 PHE A 92 TYR 0.008 0.001 TYR F 190 ARG 0.002 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.9450 (mtp) cc_final: 0.9149 (mmm) REVERT: A 400 MET cc_start: 0.9512 (mmm) cc_final: 0.9285 (mmm) REVERT: D 24 MET cc_start: 0.9260 (mmp) cc_final: 0.9040 (mmm) REVERT: D 608 MET cc_start: 0.8604 (ptm) cc_final: 0.8386 (ppp) REVERT: E 81 MET cc_start: 0.9058 (ttm) cc_final: 0.8829 (ptp) REVERT: F 108 MET cc_start: 0.9642 (mtm) cc_final: 0.9264 (ttt) REVERT: F 128 ASP cc_start: 0.9433 (m-30) cc_final: 0.9212 (m-30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2040 time to fit residues: 24.9095 Evaluate side-chains 46 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 0.0570 chunk 53 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN D 113 ASN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 123 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10639 Z= 0.304 Angle : 0.605 6.856 14422 Z= 0.308 Chirality : 0.039 0.144 1712 Planarity : 0.004 0.039 1791 Dihedral : 3.543 17.227 1421 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 5.12 % Favored : 94.79 % 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: 0.70 (0.23), residues: 1316 helix: 1.58 (0.18), residues: 837 sheet: -1.23 (0.54), residues: 86 loop : -1.58 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 513 HIS 0.004 0.001 HIS D 334 PHE 0.016 0.002 PHE D 343 TYR 0.011 0.001 TYR A 456 ARG 0.004 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9222 (mtm) cc_final: 0.8723 (mtp) REVERT: A 158 MET cc_start: 0.9445 (mtp) cc_final: 0.9126 (mmm) REVERT: A 400 MET cc_start: 0.9520 (mmm) cc_final: 0.9272 (mmm) REVERT: D 24 MET cc_start: 0.9261 (mmp) cc_final: 0.9050 (mmm) REVERT: D 608 MET cc_start: 0.8534 (ptm) cc_final: 0.8284 (ppp) REVERT: F 108 MET cc_start: 0.9558 (mtm) cc_final: 0.9187 (ttt) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1680 time to fit residues: 15.2698 Evaluate side-chains 43 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 40.0000 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 188 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10639 Z= 0.253 Angle : 0.567 10.240 14422 Z= 0.283 Chirality : 0.039 0.143 1712 Planarity : 0.003 0.046 1791 Dihedral : 3.567 18.543 1421 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % 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: 1.25 (0.24), residues: 1316 helix: 1.99 (0.18), residues: 832 sheet: -1.09 (0.53), residues: 88 loop : -1.28 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 513 HIS 0.004 0.001 HIS D 334 PHE 0.014 0.001 PHE A 92 TYR 0.011 0.001 TYR A 456 ARG 0.003 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9247 (mtm) cc_final: 0.8760 (mtp) REVERT: A 158 MET cc_start: 0.9405 (mtp) cc_final: 0.9073 (mmm) REVERT: A 188 ASN cc_start: 0.9690 (t160) cc_final: 0.9483 (t0) REVERT: A 400 MET cc_start: 0.9534 (mmm) cc_final: 0.9256 (mmm) REVERT: D 608 MET cc_start: 0.8596 (ptm) cc_final: 0.8246 (ppp) REVERT: F 108 MET cc_start: 0.9544 (mtm) cc_final: 0.9218 (mtp) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1707 time to fit residues: 16.0740 Evaluate side-chains 45 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 ASN ** D 558 HIS ** 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10639 Z= 0.132 Angle : 0.494 8.943 14422 Z= 0.239 Chirality : 0.037 0.145 1712 Planarity : 0.003 0.046 1791 Dihedral : 3.333 17.476 1421 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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 (0.24), residues: 1316 helix: 2.34 (0.18), residues: 844 sheet: -0.79 (0.53), residues: 88 loop : -1.07 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.004 0.001 HIS D 334 PHE 0.013 0.001 PHE D 17 TYR 0.009 0.001 TYR A 456 ARG 0.001 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.9284 (mtm) cc_final: 0.8794 (mtt) REVERT: A 158 MET cc_start: 0.9427 (mtp) cc_final: 0.9121 (mmm) REVERT: A 188 ASN cc_start: 0.9667 (t160) cc_final: 0.9427 (t0) REVERT: A 400 MET cc_start: 0.9581 (mmm) cc_final: 0.9371 (mmm) REVERT: C 68 ILE cc_start: 0.9926 (mm) cc_final: 0.9671 (tt) REVERT: D 608 MET cc_start: 0.8515 (ptm) cc_final: 0.8295 (ppp) REVERT: F 108 MET cc_start: 0.9561 (mtm) cc_final: 0.9123 (ttt) REVERT: F 128 ASP cc_start: 0.9475 (m-30) cc_final: 0.9255 (m-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1856 time to fit residues: 18.3214 Evaluate side-chains 48 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 381 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 HIS ** 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10639 Z= 0.281 Angle : 0.593 8.335 14422 Z= 0.297 Chirality : 0.039 0.144 1712 Planarity : 0.003 0.046 1791 Dihedral : 3.704 19.699 1421 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 1316 helix: 2.21 (0.18), residues: 832 sheet: -0.94 (0.52), residues: 88 loop : -0.96 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 513 HIS 0.004 0.001 HIS D 255 PHE 0.036 0.002 PHE A 245 TYR 0.013 0.001 TYR A 456 ARG 0.003 0.000 ARG D 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.9326 (mtm) cc_final: 0.8814 (mtt) REVERT: A 158 MET cc_start: 0.9393 (mtp) cc_final: 0.9062 (mmm) REVERT: A 188 ASN cc_start: 0.9671 (t160) cc_final: 0.9462 (t0) REVERT: A 400 MET cc_start: 0.9576 (mmm) cc_final: 0.9365 (mmm) REVERT: D 606 MET cc_start: 0.8618 (ptm) cc_final: 0.8241 (ptt) REVERT: F 108 MET cc_start: 0.9548 (mtm) cc_final: 0.9167 (ttt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1597 time to fit residues: 14.3269 Evaluate side-chains 45 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN D 381 HIS D 412 GLN D 416 ASN ** D 558 HIS ** 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10639 Z= 0.128 Angle : 0.497 9.150 14422 Z= 0.239 Chirality : 0.037 0.142 1712 Planarity : 0.003 0.049 1791 Dihedral : 3.378 17.147 1421 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.24), residues: 1316 helix: 2.47 (0.18), residues: 845 sheet: -0.58 (0.51), residues: 86 loop : -0.89 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 283 HIS 0.002 0.001 HIS D 309 PHE 0.008 0.001 PHE A 92 TYR 0.013 0.001 TYR D 237 ARG 0.001 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 69 MET cc_start: 0.9319 (mtm) cc_final: 0.8803 (mtt) REVERT: A 158 MET cc_start: 0.9371 (mtp) cc_final: 0.9069 (mmm) REVERT: A 188 ASN cc_start: 0.9659 (t160) cc_final: 0.9416 (t0) REVERT: A 400 MET cc_start: 0.9576 (mmm) cc_final: 0.9340 (mmm) REVERT: C 68 ILE cc_start: 0.9928 (mm) cc_final: 0.9686 (tt) REVERT: D 606 MET cc_start: 0.8624 (ptm) cc_final: 0.8420 (ptt) REVERT: D 608 MET cc_start: 0.8718 (ptt) cc_final: 0.8426 (ppp) REVERT: F 108 MET cc_start: 0.9557 (mtm) cc_final: 0.9105 (ttt) REVERT: F 128 ASP cc_start: 0.9489 (m-30) cc_final: 0.9253 (m-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1755 time to fit residues: 17.5331 Evaluate side-chains 49 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 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 188 ASN ** 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 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 HIS ** 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10639 Z= 0.272 Angle : 0.587 8.377 14422 Z= 0.295 Chirality : 0.039 0.160 1712 Planarity : 0.003 0.047 1791 Dihedral : 3.693 19.726 1421 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.75 (0.24), residues: 1316 helix: 2.25 (0.18), residues: 843 sheet: -0.65 (0.52), residues: 86 loop : -0.88 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 513 HIS 0.004 0.001 HIS D 390 PHE 0.038 0.001 PHE A 245 TYR 0.014 0.001 TYR A 456 ARG 0.002 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.361 Fit side-chains REVERT: A 69 MET cc_start: 0.9345 (mtm) cc_final: 0.8877 (mtt) REVERT: A 158 MET cc_start: 0.9387 (mtp) cc_final: 0.9085 (mmm) REVERT: A 188 ASN cc_start: 0.9651 (t0) cc_final: 0.9412 (t0) REVERT: A 400 MET cc_start: 0.9533 (mmm) cc_final: 0.9316 (mmm) REVERT: D 608 MET cc_start: 0.8719 (ptt) cc_final: 0.8444 (ppp) REVERT: F 108 MET cc_start: 0.9566 (mtm) cc_final: 0.9146 (ttt) REVERT: F 128 ASP cc_start: 0.9463 (m-30) cc_final: 0.9254 (m-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1653 time to fit residues: 15.5453 Evaluate side-chains 46 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** D 558 HIS ** 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10639 Z= 0.140 Angle : 0.511 9.272 14422 Z= 0.248 Chirality : 0.038 0.171 1712 Planarity : 0.003 0.050 1791 Dihedral : 3.450 17.129 1421 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 2.10 (0.24), residues: 1316 helix: 2.51 (0.18), residues: 843 sheet: -0.53 (0.51), residues: 90 loop : -0.73 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 513 HIS 0.005 0.001 HIS C 72 PHE 0.026 0.001 PHE A 245 TYR 0.012 0.001 TYR D 237 ARG 0.001 0.000 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.313 Fit side-chains REVERT: A 69 MET cc_start: 0.9351 (mtm) cc_final: 0.8877 (mtt) REVERT: A 158 MET cc_start: 0.9372 (mtp) cc_final: 0.9076 (mmm) REVERT: A 188 ASN cc_start: 0.9654 (t160) cc_final: 0.9433 (t0) REVERT: C 68 ILE cc_start: 0.9885 (mm) cc_final: 0.9588 (tt) REVERT: D 608 MET cc_start: 0.8643 (ptt) cc_final: 0.8429 (ppp) REVERT: F 108 MET cc_start: 0.9558 (mtm) cc_final: 0.9109 (ttt) REVERT: F 128 ASP cc_start: 0.9479 (m-30) cc_final: 0.9259 (m-30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1736 time to fit residues: 16.6969 Evaluate side-chains 48 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** 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 558 HIS ** 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10639 Z= 0.194 Angle : 0.529 8.878 14422 Z= 0.260 Chirality : 0.038 0.152 1712 Planarity : 0.003 0.048 1791 Dihedral : 3.523 18.828 1421 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 2.10 (0.24), residues: 1316 helix: 2.48 (0.18), residues: 844 sheet: -0.32 (0.52), residues: 86 loop : -0.72 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.002 0.001 HIS D 288 PHE 0.019 0.001 PHE A 245 TYR 0.011 0.001 TYR A 456 ARG 0.002 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.387 Fit side-chains REVERT: A 69 MET cc_start: 0.9358 (mtm) cc_final: 0.8897 (mtt) REVERT: A 158 MET cc_start: 0.9393 (mtp) cc_final: 0.9105 (mmm) REVERT: A 188 ASN cc_start: 0.9646 (t0) cc_final: 0.9410 (t0) REVERT: D 608 MET cc_start: 0.8705 (ptt) cc_final: 0.8444 (ppp) REVERT: F 108 MET cc_start: 0.9578 (mtm) cc_final: 0.9137 (ttt) REVERT: F 128 ASP cc_start: 0.9462 (m-30) cc_final: 0.9251 (m-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1631 time to fit residues: 15.1341 Evaluate side-chains 45 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** 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 558 HIS ** 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 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10639 Z= 0.202 Angle : 0.537 9.310 14422 Z= 0.266 Chirality : 0.038 0.150 1712 Planarity : 0.003 0.048 1791 Dihedral : 3.565 17.820 1421 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 2.08 (0.24), residues: 1316 helix: 2.45 (0.18), residues: 844 sheet: -0.46 (0.52), residues: 90 loop : -0.63 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 513 HIS 0.002 0.001 HIS F 122 PHE 0.025 0.001 PHE A 245 TYR 0.011 0.001 TYR A 456 ARG 0.002 0.000 ARG E 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.267 Fit side-chains REVERT: A 69 MET cc_start: 0.9344 (mtm) cc_final: 0.8875 (mtt) REVERT: A 158 MET cc_start: 0.9406 (mtp) cc_final: 0.9126 (mmm) REVERT: F 108 MET cc_start: 0.9575 (mtm) cc_final: 0.9146 (ttt) REVERT: F 128 ASP cc_start: 0.9455 (m-30) cc_final: 0.9246 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1650 time to fit residues: 15.1679 Evaluate side-chains 44 residues out of total 1172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 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 = 0.3015 r_free = 0.3015 target = 0.036463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.027058 restraints weight = 123299.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027761 restraints weight = 71694.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028220 restraints weight = 49311.699| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10639 Z= 0.133 Angle : 0.512 9.632 14422 Z= 0.248 Chirality : 0.038 0.154 1712 Planarity : 0.003 0.049 1791 Dihedral : 3.360 17.300 1421 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 2.29 (0.24), residues: 1316 helix: 2.61 (0.18), residues: 844 sheet: -0.32 (0.52), residues: 90 loop : -0.54 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 14 HIS 0.003 0.001 HIS D 330 PHE 0.015 0.001 PHE A 245 TYR 0.011 0.001 TYR D 237 ARG 0.001 0.000 ARG E 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.68 seconds wall clock time: 30 minutes 44.88 seconds (1844.88 seconds total)