Starting phenix.real_space_refine on Tue Jun 17 21:08:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_26107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_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/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_26107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_26107.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_26107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt1_26107/06_2025/7tt1_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.68, per 1000 atoms: 0.47 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: 4.83 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: 1.63 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: 7.75 Time building geometry restraints manager: 6.01 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: 0.990 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: 0.340 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 43.550 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- 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 10623 Z= 0.183 Angle : 0.818 6.619 14431 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 Details of bonding type rmsd hydrogen bonds : bond 0.24251 ( 469) hydrogen bonds : angle 8.18045 ( 1299) SS BOND : bond 0.00205 ( 2) SS BOND : angle 2.18001 ( 4) covalent geometry : bond 0.00363 (10621) covalent geometry : angle 0.81725 (14427) *********************** 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 to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.461 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: 0.5719 time to fit residues: 300.5593 Evaluate side-chains 231 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099883 restraints weight = 70008.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106397 restraints weight = 46493.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.105244 restraints weight = 37395.404| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 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 10623 Z= 0.226 Angle : 0.632 6.738 14431 Z= 0.362 Chirality : 0.045 0.177 1564 Planarity : 0.005 0.042 1896 Dihedral : 5.224 87.091 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 Details of bonding type rmsd hydrogen bonds : bond 0.06058 ( 469) hydrogen bonds : angle 6.64979 ( 1299) SS BOND : bond 0.00874 ( 2) SS BOND : angle 3.41865 ( 4) covalent geometry : bond 0.00466 (10621) covalent geometry : angle 0.62932 (14427) *********************** 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 to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.590 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: 0.8881 (m90) cc_final: 0.8575 (m90) REVERT: A 232 ASP cc_start: 0.8856 (m-30) cc_final: 0.8591 (m-30) REVERT: A 371 GLN cc_start: 0.7589 (tp40) cc_final: 0.7082 (tp-100) REVERT: A 372 MET cc_start: 0.8176 (mpp) cc_final: 0.6848 (mpp) REVERT: A 422 ASN cc_start: 0.8116 (m-40) cc_final: 0.7904 (m-40) REVERT: A 539 MET cc_start: 0.9051 (tpp) cc_final: 0.8689 (tpp) REVERT: B 76 ASP cc_start: 0.8319 (t0) cc_final: 0.7917 (t0) REVERT: B 278 MET cc_start: 0.7670 (mpp) cc_final: 0.7327 (mpp) REVERT: B 299 VAL cc_start: 0.8814 (t) cc_final: 0.8613 (t) REVERT: E 53 GLN cc_start: 0.9086 (mp10) cc_final: 0.8856 (mp10) REVERT: E 101 LEU cc_start: 0.9081 (tp) cc_final: 0.8832 (tt) REVERT: D 58 LEU cc_start: 0.8407 (mt) cc_final: 0.8103 (mt) REVERT: D 60 ASN cc_start: 0.8756 (m-40) cc_final: 0.8344 (m110) REVERT: D 79 TYR cc_start: 0.9142 (m-80) cc_final: 0.8616 (m-10) REVERT: D 89 GLN cc_start: 0.9198 (mt0) cc_final: 0.8561 (mm-40) REVERT: D 115 THR cc_start: 0.9180 (m) cc_final: 0.8871 (m) REVERT: D 116 ASN cc_start: 0.9246 (m-40) cc_final: 0.8871 (t0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.5149 time to fit residues: 191.4162 Evaluate side-chains 210 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101941 restraints weight = 70826.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107987 restraints weight = 45114.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107628 restraints weight = 31561.899| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10623 Z= 0.145 Angle : 0.540 4.663 14431 Z= 0.304 Chirality : 0.043 0.182 1564 Planarity : 0.004 0.068 1896 Dihedral : 5.074 88.162 1455 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 0.69 (0.22), residues: 1303 helix: 1.48 (0.30), residues: 286 sheet: 0.37 (0.23), residues: 405 loop : 0.16 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.010 0.001 HIS A 186 PHE 0.023 0.001 PHE A 426 TYR 0.019 0.001 TYR B 123 ARG 0.006 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 469) hydrogen bonds : angle 6.00223 ( 1299) SS BOND : bond 0.00376 ( 2) SS BOND : angle 1.84990 ( 4) covalent geometry : bond 0.00299 (10621) covalent geometry : angle 0.53911 (14427) *********************** 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 254 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.488 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: 0.8878 (t0) cc_final: 0.8372 (t0) REVERT: A 186 HIS cc_start: 0.8224 (p-80) cc_final: 0.7993 (p90) REVERT: A 232 ASP cc_start: 0.8892 (m-30) cc_final: 0.8546 (m-30) REVERT: A 371 GLN cc_start: 0.7401 (tp40) cc_final: 0.6811 (tp-100) REVERT: A 372 MET cc_start: 0.7712 (mpp) cc_final: 0.7178 (mpp) REVERT: A 539 MET cc_start: 0.8940 (tpp) cc_final: 0.8612 (tpp) REVERT: A 648 PHE cc_start: 0.8593 (p90) cc_final: 0.8237 (p90) REVERT: B 76 ASP cc_start: 0.8262 (t0) cc_final: 0.7943 (t0) REVERT: B 164 ILE cc_start: 0.9286 (mm) cc_final: 0.9034 (mp) REVERT: B 182 LYS cc_start: 0.9247 (tttm) cc_final: 0.8750 (tttt) REVERT: B 299 VAL cc_start: 0.8782 (t) cc_final: 0.8559 (t) REVERT: E 53 GLN cc_start: 0.8997 (mp10) cc_final: 0.8793 (mp10) REVERT: E 101 LEU cc_start: 0.9055 (tp) cc_final: 0.8817 (tt) REVERT: D 58 LEU cc_start: 0.8398 (mt) cc_final: 0.8103 (mt) REVERT: D 60 ASN cc_start: 0.8670 (m-40) cc_final: 0.8251 (m110) REVERT: D 89 GLN cc_start: 0.9177 (mt0) cc_final: 0.8530 (mm-40) REVERT: D 166 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8412 (mtt90) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.5103 time to fit residues: 182.1300 Evaluate side-chains 204 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 125 optimal weight: 0.0770 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101906 restraints weight = 73612.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106931 restraints weight = 48027.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106701 restraints weight = 36273.920| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10623 Z= 0.176 Angle : 0.525 4.321 14431 Z= 0.296 Chirality : 0.042 0.156 1564 Planarity : 0.004 0.040 1896 Dihedral : 5.043 87.560 1455 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % 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: 0.50 (0.23), residues: 1303 helix: 1.29 (0.30), residues: 291 sheet: 0.28 (0.24), residues: 419 loop : 0.02 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.004 0.001 HIS A 533 PHE 0.011 0.001 PHE E 77 TYR 0.012 0.002 TYR A 230 ARG 0.005 0.000 ARG D 132 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 469) hydrogen bonds : angle 5.69530 ( 1299) SS BOND : bond 0.00152 ( 2) SS BOND : angle 1.45347 ( 4) covalent geometry : bond 0.00370 (10621) covalent geometry : angle 0.52412 (14427) *********************** 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 243 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.546 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: P 1293 ASN cc_start: 0.8879 (t0) cc_final: 0.8173 (p0) REVERT: A 232 ASP cc_start: 0.8854 (m-30) cc_final: 0.8506 (m-30) REVERT: A 371 GLN cc_start: 0.7727 (tp40) cc_final: 0.7078 (tp-100) REVERT: A 372 MET cc_start: 0.8324 (mpp) cc_final: 0.7588 (mpp) REVERT: A 386 LYS cc_start: 0.9167 (tttp) cc_final: 0.8953 (tttp) REVERT: A 539 MET cc_start: 0.8945 (tpp) cc_final: 0.8622 (tpp) REVERT: A 648 PHE cc_start: 0.8576 (p90) cc_final: 0.8301 (p90) REVERT: B 76 ASP cc_start: 0.8214 (t0) cc_final: 0.7903 (t0) REVERT: B 299 VAL cc_start: 0.8827 (t) cc_final: 0.8621 (t) REVERT: E 53 GLN cc_start: 0.9019 (mp10) cc_final: 0.8807 (mp10) REVERT: D 58 LEU cc_start: 0.8439 (mt) cc_final: 0.8163 (mt) REVERT: D 60 ASN cc_start: 0.8665 (m-40) cc_final: 0.8259 (m110) REVERT: D 74 ASP cc_start: 0.8906 (m-30) cc_final: 0.8697 (m-30) REVERT: D 79 TYR cc_start: 0.9189 (m-80) cc_final: 0.8589 (m-10) REVERT: D 114 LEU cc_start: 0.9683 (mt) cc_final: 0.9469 (mt) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.5161 time to fit residues: 176.7288 Evaluate side-chains 190 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.131974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092305 restraints weight = 74559.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094525 restraints weight = 36320.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.096382 restraints weight = 23206.349| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10623 Z= 0.289 Angle : 0.608 5.894 14431 Z= 0.347 Chirality : 0.043 0.219 1564 Planarity : 0.005 0.045 1896 Dihedral : 5.300 85.124 1455 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: -0.05 (0.22), residues: 1303 helix: 0.70 (0.29), residues: 290 sheet: 0.02 (0.24), residues: 413 loop : -0.32 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 376 HIS 0.004 0.001 HIS A 533 PHE 0.027 0.002 PHE A 738 TYR 0.039 0.002 TYR B 123 ARG 0.006 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 469) hydrogen bonds : angle 5.94525 ( 1299) SS BOND : bond 0.00736 ( 2) SS BOND : angle 2.82426 ( 4) covalent geometry : bond 0.00607 (10621) covalent geometry : angle 0.60631 (14427) *********************** 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 219 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.574 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: 0.9047 (t0) cc_final: 0.8323 (p0) REVERT: A 196 HIS cc_start: 0.8774 (m90) cc_final: 0.8558 (m90) REVERT: A 232 ASP cc_start: 0.8844 (m-30) cc_final: 0.8523 (m-30) REVERT: A 305 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8404 (mt-10) REVERT: A 306 ASP cc_start: 0.9150 (m-30) cc_final: 0.8903 (m-30) REVERT: A 422 ASN cc_start: 0.8409 (m-40) cc_final: 0.8176 (m-40) REVERT: A 539 MET cc_start: 0.9172 (tpp) cc_final: 0.8835 (tpp) REVERT: A 576 TRP cc_start: 0.8532 (t60) cc_final: 0.8329 (t60) REVERT: A 648 PHE cc_start: 0.8791 (p90) cc_final: 0.8455 (p90) REVERT: B 76 ASP cc_start: 0.8166 (t0) cc_final: 0.7837 (t0) REVERT: B 123 TYR cc_start: 0.8171 (m-80) cc_final: 0.7939 (m-80) REVERT: E 53 GLN cc_start: 0.9152 (mp10) cc_final: 0.8922 (mp10) REVERT: D 58 LEU cc_start: 0.8551 (mt) cc_final: 0.8324 (mt) REVERT: D 60 ASN cc_start: 0.8820 (m-40) cc_final: 0.8434 (m110) REVERT: D 110 TYR cc_start: 0.8943 (t80) cc_final: 0.8676 (t80) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.5140 time to fit residues: 154.8903 Evaluate side-chains 183 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.135366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102939 restraints weight = 73871.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106757 restraints weight = 53665.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.107352 restraints weight = 38056.784| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10623 Z= 0.105 Angle : 0.495 4.607 14431 Z= 0.274 Chirality : 0.043 0.162 1564 Planarity : 0.004 0.046 1896 Dihedral : 4.933 83.584 1455 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % 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: 0.34 (0.23), residues: 1303 helix: 1.34 (0.30), residues: 285 sheet: 0.18 (0.24), residues: 420 loop : -0.18 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 810 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE E 77 TYR 0.017 0.001 TYR D 36 ARG 0.003 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 469) hydrogen bonds : angle 5.26212 ( 1299) SS BOND : bond 0.00457 ( 2) SS BOND : angle 2.05233 ( 4) covalent geometry : bond 0.00227 (10621) covalent geometry : angle 0.49379 (14427) *********************** 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 229 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.439 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: P 1293 ASN cc_start: 0.8881 (t0) cc_final: 0.8180 (p0) REVERT: A 232 ASP cc_start: 0.8855 (m-30) cc_final: 0.8654 (m-30) REVERT: A 284 ILE cc_start: 0.7842 (mm) cc_final: 0.6746 (tp) REVERT: A 305 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 306 ASP cc_start: 0.9051 (m-30) cc_final: 0.8803 (m-30) REVERT: A 371 GLN cc_start: 0.7697 (tp40) cc_final: 0.7439 (tp-100) REVERT: A 372 MET cc_start: 0.8331 (mpp) cc_final: 0.7813 (mpp) REVERT: A 386 LYS cc_start: 0.9035 (tttp) cc_final: 0.8532 (tppt) REVERT: A 422 ASN cc_start: 0.8404 (m-40) cc_final: 0.8204 (m-40) REVERT: A 539 MET cc_start: 0.8949 (tpp) cc_final: 0.8684 (tpp) REVERT: A 648 PHE cc_start: 0.8578 (p90) cc_final: 0.8304 (p90) REVERT: B 76 ASP cc_start: 0.8122 (t0) cc_final: 0.7814 (t0) REVERT: B 164 ILE cc_start: 0.9312 (mm) cc_final: 0.9105 (mp) REVERT: E 53 GLN cc_start: 0.9041 (mp10) cc_final: 0.8811 (pm20) REVERT: D 60 ASN cc_start: 0.8704 (m-40) cc_final: 0.8327 (m110) REVERT: D 110 TYR cc_start: 0.8641 (t80) cc_final: 0.8407 (t80) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.5110 time to fit residues: 161.6789 Evaluate side-chains 190 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN E 36 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 = 0.3998 r_free = 0.3998 target = 0.133266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094353 restraints weight = 73540.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097921 restraints weight = 37570.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098778 restraints weight = 23316.839| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10623 Z= 0.172 Angle : 0.507 4.892 14431 Z= 0.286 Chirality : 0.042 0.170 1564 Planarity : 0.004 0.048 1896 Dihedral : 4.952 84.195 1455 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.09 % Allowed : 0.63 % 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: 0.09 (0.23), residues: 1303 helix: 1.10 (0.30), residues: 290 sheet: 0.08 (0.24), residues: 415 loop : -0.37 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 546 HIS 0.002 0.001 HIS A 533 PHE 0.012 0.001 PHE E 77 TYR 0.015 0.001 TYR D 36 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 469) hydrogen bonds : angle 5.38184 ( 1299) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.45252 ( 4) covalent geometry : bond 0.00360 (10621) covalent geometry : angle 0.50650 (14427) *********************** 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 218 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.697 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: 0.9008 (t0) cc_final: 0.8322 (p0) REVERT: A 305 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 306 ASP cc_start: 0.9091 (m-30) cc_final: 0.8839 (m-30) REVERT: A 372 MET cc_start: 0.8758 (mpp) cc_final: 0.8544 (mpp) REVERT: A 386 LYS cc_start: 0.9140 (tttp) cc_final: 0.8930 (tttp) REVERT: A 539 MET cc_start: 0.9101 (tpp) cc_final: 0.8758 (tpp) REVERT: A 648 PHE cc_start: 0.8753 (p90) cc_final: 0.8453 (p90) REVERT: A 785 PHE cc_start: 0.8816 (p90) cc_final: 0.8603 (p90) REVERT: B 76 ASP cc_start: 0.8185 (t0) cc_final: 0.7843 (t0) REVERT: B 164 ILE cc_start: 0.9228 (mm) cc_final: 0.8998 (mp) REVERT: E 53 GLN cc_start: 0.9111 (mp10) cc_final: 0.8846 (pm20) REVERT: D 60 ASN cc_start: 0.8712 (m-40) cc_final: 0.8430 (m110) REVERT: D 110 TYR cc_start: 0.8886 (t80) cc_final: 0.8614 (t80) REVERT: D 111 MET cc_start: 0.8913 (tpp) cc_final: 0.8490 (tpp) outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.5077 time to fit residues: 153.0156 Evaluate side-chains 189 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101450 restraints weight = 73380.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107559 restraints weight = 48162.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107636 restraints weight = 31042.640| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10623 Z= 0.111 Angle : 0.478 4.977 14431 Z= 0.266 Chirality : 0.043 0.261 1564 Planarity : 0.003 0.048 1896 Dihedral : 4.802 83.142 1455 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.34 (0.23), residues: 1303 helix: 1.37 (0.30), residues: 292 sheet: 0.19 (0.24), residues: 409 loop : -0.21 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.004 0.001 HIS A 280 PHE 0.011 0.001 PHE E 77 TYR 0.015 0.001 TYR D 36 ARG 0.004 0.000 ARG B 195 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 469) hydrogen bonds : angle 5.11474 ( 1299) SS BOND : bond 0.00306 ( 2) SS BOND : angle 1.47646 ( 4) covalent geometry : bond 0.00237 (10621) covalent geometry : angle 0.47751 (14427) *********************** 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 to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.626 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: P 1293 ASN cc_start: 0.8908 (t0) cc_final: 0.8282 (p0) REVERT: A 224 GLU cc_start: 0.8577 (mp0) cc_final: 0.8144 (mp0) REVERT: A 232 ASP cc_start: 0.8911 (m-30) cc_final: 0.8680 (m-30) REVERT: A 305 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 306 ASP cc_start: 0.9096 (m-30) cc_final: 0.8849 (m-30) REVERT: A 422 ASN cc_start: 0.8446 (m-40) cc_final: 0.8242 (m-40) REVERT: A 539 MET cc_start: 0.9071 (tpp) cc_final: 0.8733 (tpp) REVERT: A 648 PHE cc_start: 0.8656 (p90) cc_final: 0.8347 (p90) REVERT: A 785 PHE cc_start: 0.8755 (p90) cc_final: 0.8551 (p90) REVERT: B 76 ASP cc_start: 0.8092 (t0) cc_final: 0.7807 (t0) REVERT: B 164 ILE cc_start: 0.9327 (mm) cc_final: 0.9124 (mp) REVERT: E 53 GLN cc_start: 0.9073 (mp10) cc_final: 0.8834 (pm20) REVERT: D 60 ASN cc_start: 0.8611 (m-40) cc_final: 0.8331 (m110) REVERT: D 110 TYR cc_start: 0.8768 (t80) cc_final: 0.8536 (t80) REVERT: D 111 MET cc_start: 0.8758 (tpp) cc_final: 0.8311 (tpp) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.5136 time to fit residues: 158.5646 Evaluate side-chains 187 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090975 restraints weight = 72994.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095786 restraints weight = 33341.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.098848 restraints weight = 21159.708| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10623 Z= 0.176 Angle : 0.515 6.694 14431 Z= 0.286 Chirality : 0.042 0.196 1564 Planarity : 0.004 0.049 1896 Dihedral : 4.886 83.288 1455 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 0.11 (0.23), residues: 1303 helix: 1.08 (0.30), residues: 295 sheet: 0.10 (0.24), residues: 402 loop : -0.36 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.004 0.001 HIS A 280 PHE 0.012 0.001 PHE E 77 TYR 0.014 0.001 TYR D 36 ARG 0.003 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 469) hydrogen bonds : angle 5.26644 ( 1299) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.32927 ( 4) covalent geometry : bond 0.00371 (10621) covalent geometry : angle 0.51470 (14427) *********************** 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 216 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 1.657 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: P 1293 ASN cc_start: 0.9029 (t0) cc_final: 0.8370 (p0) REVERT: A 232 ASP cc_start: 0.8950 (m-30) cc_final: 0.8701 (m-30) REVERT: A 305 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 306 ASP cc_start: 0.9101 (m-30) cc_final: 0.8852 (m-30) REVERT: A 539 MET cc_start: 0.9125 (tpp) cc_final: 0.8741 (tpp) REVERT: A 648 PHE cc_start: 0.8775 (p90) cc_final: 0.8400 (p90) REVERT: B 76 ASP cc_start: 0.8202 (t0) cc_final: 0.7901 (t0) REVERT: B 164 ILE cc_start: 0.9135 (mm) cc_final: 0.8889 (mp) REVERT: E 53 GLN cc_start: 0.9097 (mp10) cc_final: 0.8838 (pm20) REVERT: D 60 ASN cc_start: 0.8673 (m-40) cc_final: 0.8389 (m110) REVERT: D 110 TYR cc_start: 0.8922 (t80) cc_final: 0.8665 (t80) REVERT: D 111 MET cc_start: 0.8940 (tpp) cc_final: 0.8525 (tpp) outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.5065 time to fit residues: 151.9397 Evaluate side-chains 189 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100375 restraints weight = 73819.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106861 restraints weight = 48764.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.106712 restraints weight = 30253.806| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10623 Z= 0.153 Angle : 0.519 12.783 14431 Z= 0.283 Chirality : 0.042 0.185 1564 Planarity : 0.004 0.048 1896 Dihedral : 4.866 82.993 1455 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 0.04 (0.23), residues: 1303 helix: 1.10 (0.30), residues: 295 sheet: -0.08 (0.24), residues: 414 loop : -0.34 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.002 0.001 HIS B 324 PHE 0.020 0.001 PHE E 68 TYR 0.026 0.001 TYR A 618 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 469) hydrogen bonds : angle 5.21596 ( 1299) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.50390 ( 4) covalent geometry : bond 0.00328 (10621) covalent geometry : angle 0.51798 (14427) ********************** 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 217 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.472 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: 0.8884 (t0) cc_final: 0.8227 (p0) REVERT: A 232 ASP cc_start: 0.8852 (m-30) cc_final: 0.8623 (m-30) REVERT: A 305 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 306 ASP cc_start: 0.9099 (m-30) cc_final: 0.8860 (m-30) REVERT: A 371 GLN cc_start: 0.7621 (tp40) cc_final: 0.7345 (tp-100) REVERT: A 372 MET cc_start: 0.7979 (mpp) cc_final: 0.7624 (mpp) REVERT: A 539 MET cc_start: 0.9061 (tpp) cc_final: 0.8727 (tpp) REVERT: A 648 PHE cc_start: 0.8694 (p90) cc_final: 0.8383 (p90) REVERT: A 777 MET cc_start: 0.7058 (mmt) cc_final: 0.6593 (mmt) REVERT: A 785 PHE cc_start: 0.8750 (p90) cc_final: 0.8531 (p90) REVERT: B 76 ASP cc_start: 0.8011 (t0) cc_final: 0.7744 (t0) REVERT: E 53 GLN cc_start: 0.9107 (mp10) cc_final: 0.8890 (pm20) REVERT: D 60 ASN cc_start: 0.8634 (m-40) cc_final: 0.8353 (m110) REVERT: D 110 TYR cc_start: 0.8860 (t80) cc_final: 0.8586 (t80) REVERT: D 111 MET cc_start: 0.8786 (tpp) cc_final: 0.8332 (tpp) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.5284 time to fit residues: 158.7448 Evaluate side-chains 186 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.133075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090811 restraints weight = 74066.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095612 restraints weight = 34315.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098571 restraints weight = 22116.977| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10623 Z= 0.153 Angle : 0.508 7.764 14431 Z= 0.280 Chirality : 0.042 0.187 1564 Planarity : 0.004 0.048 1896 Dihedral : 4.871 82.573 1455 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: 0.03 (0.23), residues: 1303 helix: 1.18 (0.30), residues: 298 sheet: -0.10 (0.24), residues: 414 loop : -0.38 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.004 0.001 HIS A 280 PHE 0.012 0.001 PHE E 77 TYR 0.018 0.001 TYR A 618 ARG 0.003 0.000 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 469) hydrogen bonds : angle 5.17410 ( 1299) SS BOND : bond 0.00208 ( 2) SS BOND : angle 1.30526 ( 4) covalent geometry : bond 0.00326 (10621) covalent geometry : angle 0.50766 (14427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6791.52 seconds wall clock time: 116 minutes 17.37 seconds (6977.37 seconds total)