Starting phenix.real_space_refine on Sat Sep 28 20:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt1_26107/09_2024/7tt1_26107.cif" } resolution = 4.3 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= 0.056 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6558 2.51 5 N 1773 2.21 5 O 2030 1.98 5 H 10005 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20398 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "A" Number of atoms: 9476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9476 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain breaks: 4 Chain: "B" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5187 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1382 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Time building chain proxies: 9.69, per 1000 atoms: 0.48 Number of scatterers: 20398 At special positions: 0 Unit cell: (113.825, 122.415, 137.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2030 8.00 N 1773 7.00 C 6558 6.00 H 10005 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 23.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.134A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.105A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.823A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.877A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.366A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.782A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.765A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.772A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.538A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'P' and resid 1272 through 1276 removed outlier: 3.784A pdb=" N ARG P1273 " --> pdb=" O ARG P1297 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY P1275 " --> pdb=" O ASN P1295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN P1295 " --> pdb=" O GLY P1275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 532 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 569 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 600 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.061A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.525A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.975A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.267A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.940A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.554A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 415 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.923A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.026A pdb=" N GLY B 385 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.707A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.268A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.646A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.732A pdb=" N THR B 201 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.566A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.860A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.738A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.893A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.825A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1299 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: 7.66 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10005 1.03 - 1.23: 361 1.23 - 1.43: 4284 1.43 - 1.63: 5916 1.63 - 1.83: 60 Bond restraints: 20626 Sorted by residual: bond pdb=" CA PRO C 84 " pdb=" C PRO C 84 " ideal model delta sigma weight residual 1.514 1.522 -0.007 5.50e-03 3.31e+04 1.82e+00 bond pdb=" C THR B 43 " pdb=" O THR B 43 " ideal model delta sigma weight residual 1.235 1.229 0.006 4.70e-03 4.53e+04 1.58e+00 bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.508 0.026 2.33e-02 1.84e+03 1.25e+00 bond pdb=" CB LEU E 63 " pdb=" CG LEU E 63 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C LEU A 365 " pdb=" N ARG A 366 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.38e-02 5.25e+03 1.13e+00 ... (remaining 20621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 34703 1.32 - 2.65: 2103 2.65 - 3.97: 208 3.97 - 5.30: 29 5.30 - 6.62: 7 Bond angle restraints: 37050 Sorted by residual: angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.76 103.34 6.42 1.64e+00 3.72e-01 1.53e+01 angle pdb=" N PHE A 738 " pdb=" CA PHE A 738 " pdb=" C PHE A 738 " ideal model delta sigma weight residual 109.07 114.32 -5.25 1.52e+00 4.33e-01 1.19e+01 angle pdb=" N PHE A 737 " pdb=" CA PHE A 737 " pdb=" C PHE A 737 " ideal model delta sigma weight residual 109.76 104.31 5.45 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ASP A 746 " pdb=" CA ASP A 746 " pdb=" C ASP A 746 " ideal model delta sigma weight residual 108.73 114.09 -5.36 1.63e+00 3.76e-01 1.08e+01 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 111.82 108.01 3.81 1.16e+00 7.43e-01 1.08e+01 ... (remaining 37045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9275 17.86 - 35.73: 303 35.73 - 53.59: 167 53.59 - 71.46: 49 71.46 - 89.32: 14 Dihedral angle restraints: 9808 sinusoidal: 5268 harmonic: 4540 Sorted by residual: dihedral pdb=" CA GLY A 482 " pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ILE A 519 " pdb=" C ILE A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -118.74 32.74 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 921 0.032 - 0.063: 374 0.063 - 0.095: 162 0.095 - 0.127: 86 0.127 - 0.158: 21 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA TYR A 585 " pdb=" N TYR A 585 " pdb=" C TYR A 585 " pdb=" CB TYR A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1561 not shown) Planarity restraints: 3157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C PRO D 86 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 33 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C ASN D 33 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN D 33 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU D 34 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 544 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C ALA A 544 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 544 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 545 " -0.012 2.00e-02 2.50e+03 ... (remaining 3154 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 441 2.09 - 2.72: 34873 2.72 - 3.35: 54979 3.35 - 3.97: 71350 3.97 - 4.60: 111354 Nonbonded interactions: 272997 Sorted by model distance: nonbonded pdb=" OD2 ASP A 624 " pdb=" HZ2 LYS A 626 " model vdw 1.466 2.450 nonbonded pdb=" OD1 ASP A 569 " pdb=" H ASP A 605 " model vdw 1.493 2.450 nonbonded pdb=" H ASN B 85 " pdb=" O LYS B 90 " model vdw 1.497 2.450 nonbonded pdb=" HG SER B 285 " pdb=" O VAL B 299 " model vdw 1.501 2.450 nonbonded pdb=" H ASN B 350 " pdb=" O ARG B 355 " model vdw 1.527 2.450 ... (remaining 272992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.790 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: 0.360 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 44.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 0.037 10621 Z= 0.237 Angle : 0.817 6.619 14427 Z= 0.507 Chirality : 0.047 0.158 1564 Planarity : 0.004 0.037 1896 Dihedral : 10.413 89.321 3826 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 0.92 (0.22), residues: 1303 helix: 0.36 (0.28), residues: 284 sheet: 1.13 (0.25), residues: 384 loop : 0.56 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 191 HIS 0.009 0.002 HIS B 165 PHE 0.026 0.002 PHE A 586 TYR 0.016 0.003 TYR A 432 ARG 0.030 0.003 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 HIS cc_start: 0.8289 (m-70) cc_final: 0.8029 (p90) REVERT: A 227 ARG cc_start: 0.8908 (mtp180) cc_final: 0.8527 (mtp85) REVERT: A 232 ASP cc_start: 0.8983 (m-30) cc_final: 0.8769 (m-30) REVERT: A 574 TYR cc_start: 0.8655 (p90) cc_final: 0.8411 (p90) REVERT: A 719 ILE cc_start: 0.8267 (mt) cc_final: 0.7832 (mt) REVERT: B 164 ILE cc_start: 0.9347 (mm) cc_final: 0.9141 (mp) REVERT: B 296 ILE cc_start: 0.9062 (mt) cc_final: 0.8764 (mt) REVERT: E 111 SER cc_start: 0.7751 (m) cc_final: 0.7516 (p) REVERT: D 58 LEU cc_start: 0.8090 (mt) cc_final: 0.7842 (mt) REVERT: D 60 ASN cc_start: 0.8521 (m-40) cc_final: 0.8157 (m110) REVERT: D 171 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8360 (ttmm) REVERT: D 180 SER cc_start: 0.8788 (m) cc_final: 0.8407 (t) REVERT: D 198 VAL cc_start: 0.9434 (t) cc_final: 0.9081 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5750 time to fit residues: 300.3270 Evaluate side-chains 231 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 319 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10621 Z= 0.303 Angle : 0.629 5.752 14427 Z= 0.362 Chirality : 0.045 0.177 1564 Planarity : 0.005 0.042 1896 Dihedral : 5.224 87.090 1455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.77 (0.22), residues: 1303 helix: 1.23 (0.29), residues: 285 sheet: 0.56 (0.23), residues: 411 loop : 0.28 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 376 HIS 0.011 0.002 HIS A 533 PHE 0.022 0.002 PHE A 738 TYR 0.015 0.002 TYR D 154 ARG 0.005 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 HIS cc_start: 0.8853 (m90) cc_final: 0.8590 (m90) REVERT: A 232 ASP cc_start: 0.8851 (m-30) cc_final: 0.8551 (m-30) REVERT: A 371 GLN cc_start: 0.8352 (tp40) cc_final: 0.7839 (tp-100) REVERT: A 372 MET cc_start: 0.8788 (mpp) cc_final: 0.7773 (mpp) REVERT: A 408 SER cc_start: 0.8875 (t) cc_final: 0.8425 (m) REVERT: B 76 ASP cc_start: 0.8130 (t0) cc_final: 0.7767 (t0) REVERT: B 278 MET cc_start: 0.7620 (mpp) cc_final: 0.7295 (mpp) REVERT: E 101 LEU cc_start: 0.7947 (tp) cc_final: 0.7456 (tt) REVERT: D 58 LEU cc_start: 0.8112 (mt) cc_final: 0.7874 (mt) REVERT: D 60 ASN cc_start: 0.8571 (m-40) cc_final: 0.8154 (m110) REVERT: D 79 TYR cc_start: 0.8670 (m-80) cc_final: 0.8409 (m-10) REVERT: D 89 GLN cc_start: 0.8688 (mt0) cc_final: 0.8138 (mm-40) REVERT: D 116 ASN cc_start: 0.8716 (m-40) cc_final: 0.8136 (t0) REVERT: D 180 SER cc_start: 0.8903 (m) cc_final: 0.8537 (t) REVERT: D 198 VAL cc_start: 0.9363 (t) cc_final: 0.9067 (t) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.5214 time to fit residues: 192.8639 Evaluate side-chains 213 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10621 Z= 0.246 Angle : 0.562 4.708 14427 Z= 0.318 Chirality : 0.043 0.193 1564 Planarity : 0.004 0.065 1896 Dihedral : 5.143 87.945 1455 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1303 helix: 1.25 (0.30), residues: 292 sheet: 0.31 (0.24), residues: 404 loop : 0.10 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.009 0.001 HIS A 186 PHE 0.017 0.001 PHE A 426 TYR 0.020 0.002 TYR B 123 ARG 0.006 0.001 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7848 (t0) cc_final: 0.7462 (t0) REVERT: A 186 HIS cc_start: 0.8331 (p-80) cc_final: 0.8120 (p90) REVERT: A 232 ASP cc_start: 0.8884 (m-30) cc_final: 0.8494 (m-30) REVERT: A 371 GLN cc_start: 0.8305 (tp40) cc_final: 0.7693 (tp-100) REVERT: A 372 MET cc_start: 0.8473 (mpp) cc_final: 0.7904 (mpp) REVERT: A 648 PHE cc_start: 0.7976 (p90) cc_final: 0.7583 (p90) REVERT: B 76 ASP cc_start: 0.8023 (t0) cc_final: 0.7761 (t0) REVERT: E 101 LEU cc_start: 0.7988 (tp) cc_final: 0.7527 (tt) REVERT: D 58 LEU cc_start: 0.8165 (mt) cc_final: 0.7910 (mt) REVERT: D 60 ASN cc_start: 0.8534 (m-40) cc_final: 0.8098 (m110) REVERT: D 89 GLN cc_start: 0.8588 (mt0) cc_final: 0.7953 (mm-40) REVERT: D 116 ASN cc_start: 0.8751 (m-40) cc_final: 0.8221 (t0) REVERT: D 180 SER cc_start: 0.8875 (m) cc_final: 0.8527 (t) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.4942 time to fit residues: 166.9893 Evaluate side-chains 204 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10621 Z= 0.250 Angle : 0.526 4.567 14427 Z= 0.298 Chirality : 0.042 0.156 1564 Planarity : 0.004 0.042 1896 Dihedral : 5.095 85.854 1455 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.09 % Allowed : 0.81 % Favored : 99.10 % 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: 0.47 (0.23), residues: 1303 helix: 1.22 (0.30), residues: 297 sheet: 0.33 (0.24), residues: 422 loop : -0.04 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.005 0.001 HIS A 186 PHE 0.012 0.001 PHE E 77 TYR 0.012 0.002 TYR A 230 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7889 (t0) cc_final: 0.7469 (p0) REVERT: A 232 ASP cc_start: 0.8865 (m-30) cc_final: 0.8525 (m-30) REVERT: A 371 GLN cc_start: 0.8457 (tp40) cc_final: 0.7764 (tp-100) REVERT: A 372 MET cc_start: 0.8594 (mpp) cc_final: 0.8038 (mpp) REVERT: A 648 PHE cc_start: 0.7921 (p90) cc_final: 0.7592 (p90) REVERT: B 76 ASP cc_start: 0.8030 (t0) cc_final: 0.7770 (t0) REVERT: D 58 LEU cc_start: 0.8179 (mt) cc_final: 0.7956 (mt) REVERT: D 60 ASN cc_start: 0.8514 (m-40) cc_final: 0.8132 (m110) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.5062 time to fit residues: 166.0412 Evaluate side-chains 192 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 324 HIS B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 10621 Z= 0.451 Angle : 0.651 7.061 14427 Z= 0.373 Chirality : 0.044 0.170 1564 Planarity : 0.005 0.050 1896 Dihedral : 5.457 80.446 1455 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % 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: -0.28 (0.22), residues: 1303 helix: 0.33 (0.29), residues: 299 sheet: -0.01 (0.24), residues: 417 loop : -0.45 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 376 HIS 0.004 0.001 HIS A 533 PHE 0.016 0.002 PHE E 77 TYR 0.032 0.002 TYR B 123 ARG 0.007 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.8002 (t0) cc_final: 0.7553 (p0) REVERT: A 181 ASN cc_start: 0.7999 (t0) cc_final: 0.7682 (t0) REVERT: A 305 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 666 ASN cc_start: 0.7029 (m-40) cc_final: 0.6784 (p0) REVERT: B 76 ASP cc_start: 0.7875 (t0) cc_final: 0.7650 (t0) REVERT: D 110 TYR cc_start: 0.8433 (t80) cc_final: 0.8214 (t80) REVERT: D 198 VAL cc_start: 0.9388 (t) cc_final: 0.9113 (t) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.5209 time to fit residues: 160.3232 Evaluate side-chains 184 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.0570 chunk 112 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10621 Z= 0.147 Angle : 0.513 5.235 14427 Z= 0.284 Chirality : 0.043 0.158 1564 Planarity : 0.004 0.076 1896 Dihedral : 5.058 80.825 1455 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.09 % Allowed : 0.81 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1303 helix: 1.09 (0.30), residues: 291 sheet: 0.09 (0.24), residues: 422 loop : -0.36 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 810 HIS 0.003 0.001 HIS B 324 PHE 0.015 0.001 PHE A 785 TYR 0.023 0.001 TYR A 618 ARG 0.005 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7933 (t0) cc_final: 0.7516 (p0) REVERT: A 232 ASP cc_start: 0.8836 (m-30) cc_final: 0.8493 (m-30) REVERT: A 305 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 648 PHE cc_start: 0.7989 (p90) cc_final: 0.7693 (p90) REVERT: B 76 ASP cc_start: 0.8007 (t0) cc_final: 0.7781 (t0) REVERT: D 60 ASN cc_start: 0.8550 (m-40) cc_final: 0.8182 (m110) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.5351 time to fit residues: 169.8261 Evaluate side-chains 191 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 534 ASN E 36 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10621 Z= 0.263 Angle : 0.533 7.142 14427 Z= 0.301 Chirality : 0.043 0.191 1564 Planarity : 0.004 0.051 1896 Dihedral : 5.070 80.999 1455 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.28 % 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: -0.05 (0.23), residues: 1303 helix: 0.97 (0.30), residues: 296 sheet: 0.02 (0.24), residues: 415 loop : -0.48 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.005 0.001 HIS A 280 PHE 0.012 0.001 PHE E 77 TYR 0.018 0.002 TYR A 315 ARG 0.005 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7954 (t0) cc_final: 0.7543 (p0) REVERT: A 181 ASN cc_start: 0.7771 (t0) cc_final: 0.7395 (t0) REVERT: A 232 ASP cc_start: 0.8881 (m-30) cc_final: 0.8533 (m-30) REVERT: A 648 PHE cc_start: 0.8093 (p90) cc_final: 0.7732 (p90) REVERT: B 76 ASP cc_start: 0.7834 (t0) cc_final: 0.7592 (t0) REVERT: D 60 ASN cc_start: 0.8571 (m-40) cc_final: 0.8205 (m110) outliers start: 2 outliers final: 1 residues processed: 214 average time/residue: 0.5335 time to fit residues: 157.3493 Evaluate side-chains 182 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10621 Z= 0.166 Angle : 0.492 4.872 14427 Z= 0.274 Chirality : 0.043 0.168 1564 Planarity : 0.004 0.049 1896 Dihedral : 4.911 80.541 1455 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % 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: 0.18 (0.23), residues: 1303 helix: 1.23 (0.30), residues: 292 sheet: 0.11 (0.24), residues: 403 loop : -0.32 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.003 0.001 HIS A 280 PHE 0.011 0.001 PHE E 77 TYR 0.023 0.001 TYR A 618 ARG 0.013 0.001 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7931 (t0) cc_final: 0.7522 (p0) REVERT: A 181 ASN cc_start: 0.7711 (t0) cc_final: 0.7351 (t0) REVERT: A 232 ASP cc_start: 0.8855 (m-30) cc_final: 0.8523 (m-30) REVERT: A 305 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 386 LYS cc_start: 0.8691 (tttp) cc_final: 0.8435 (tptt) REVERT: A 648 PHE cc_start: 0.8028 (p90) cc_final: 0.7698 (p90) REVERT: A 777 MET cc_start: 0.6378 (mmt) cc_final: 0.6157 (mmt) REVERT: B 76 ASP cc_start: 0.7883 (t0) cc_final: 0.7662 (t0) REVERT: D 60 ASN cc_start: 0.8502 (m-40) cc_final: 0.8198 (m110) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.5245 time to fit residues: 162.9489 Evaluate side-chains 184 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10621 Z= 0.291 Angle : 0.554 6.096 14427 Z= 0.310 Chirality : 0.043 0.244 1564 Planarity : 0.004 0.051 1896 Dihedral : 5.064 80.966 1455 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % 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: -0.17 (0.23), residues: 1303 helix: 0.87 (0.30), residues: 294 sheet: -0.08 (0.24), residues: 409 loop : -0.54 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE E 77 TYR 0.024 0.002 TYR A 618 ARG 0.004 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7920 (t0) cc_final: 0.7532 (p0) REVERT: A 181 ASN cc_start: 0.7946 (t0) cc_final: 0.7625 (t0) REVERT: A 232 ASP cc_start: 0.8868 (m-30) cc_final: 0.8492 (m-30) REVERT: A 648 PHE cc_start: 0.8081 (p90) cc_final: 0.7653 (p90) REVERT: A 666 ASN cc_start: 0.7101 (m-40) cc_final: 0.6799 (p0) REVERT: A 777 MET cc_start: 0.6596 (mmt) cc_final: 0.6360 (mmt) REVERT: B 226 MET cc_start: 0.8292 (tpp) cc_final: 0.7831 (tmm) REVERT: D 60 ASN cc_start: 0.8548 (m-40) cc_final: 0.8258 (m110) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.5082 time to fit residues: 146.7749 Evaluate side-chains 177 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 0.0570 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10621 Z= 0.183 Angle : 0.512 11.441 14427 Z= 0.281 Chirality : 0.043 0.198 1564 Planarity : 0.004 0.050 1896 Dihedral : 4.942 80.942 1455 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % 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: -0.02 (0.23), residues: 1303 helix: 1.08 (0.30), residues: 292 sheet: 0.01 (0.24), residues: 408 loop : -0.47 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.003 0.001 HIS B 324 PHE 0.016 0.001 PHE E 68 TYR 0.020 0.001 TYR D 36 ARG 0.003 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.7885 (t0) cc_final: 0.7467 (p0) REVERT: A 181 ASN cc_start: 0.7825 (t0) cc_final: 0.7440 (t0) REVERT: A 232 ASP cc_start: 0.8900 (m-30) cc_final: 0.8549 (m-30) REVERT: A 305 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8018 (mt-10) REVERT: A 648 PHE cc_start: 0.8009 (p90) cc_final: 0.7690 (p90) REVERT: B 226 MET cc_start: 0.8282 (tpp) cc_final: 0.7765 (tmm) REVERT: D 60 ASN cc_start: 0.8510 (m-40) cc_final: 0.8226 (m110) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.4953 time to fit residues: 144.8817 Evaluate side-chains 183 residues out of total 1107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 534 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.101236 restraints weight = 73792.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104463 restraints weight = 55350.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105618 restraints weight = 38900.306| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10621 Z= 0.188 Angle : 0.509 7.420 14427 Z= 0.280 Chirality : 0.043 0.212 1564 Planarity : 0.004 0.067 1896 Dihedral : 4.909 80.867 1455 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.18 % Allowed : 0.27 % 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: 0.02 (0.23), residues: 1303 helix: 1.18 (0.31), residues: 292 sheet: 0.02 (0.24), residues: 406 loop : -0.48 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.004 0.001 HIS B 324 PHE 0.011 0.001 PHE E 77 TYR 0.020 0.001 TYR D 36 ARG 0.004 0.000 ARG B 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4751.47 seconds wall clock time: 83 minutes 35.09 seconds (5015.09 seconds total)