Starting phenix.real_space_refine on Tue Mar 11 19:56:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmb_22922/03_2025/7kmb_22922.cif" } resolution = 3.39 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4159 2.51 5 N 1067 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6509 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.84, per 1000 atoms: 0.90 Number of scatterers: 6509 At special positions: 0 Unit cell: (99.452, 75.118, 111.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1246 8.00 N 1067 7.00 C 4159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 1 " - " ASN F 546 " " NAG B 1 " - " ASN G 343 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 861.9 milliseconds 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 52.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.788A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.796A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.714A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 4.551A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 4.223A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.751A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.608A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.607A pdb=" N GLU F 181 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.569A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 249 removed outlier: 3.707A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.778A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.967A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.543A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 4.140A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 365 through 383 removed outlier: 3.925A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 4.040A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.082A pdb=" N PHE F 438 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.703A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 523 removed outlier: 4.074A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.966A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.632A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 4.132A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 586' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.636A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 365 through 370 removed outlier: 3.675A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 365 through 370' Processing helix chain 'G' and resid 385 through 390 removed outlier: 3.978A pdb=" N ASP G 389 " --> pdb=" O THR G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.508A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 Processing helix chain 'G' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.664A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.023A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.604A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 510 " --> pdb=" O PHE G 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 452 through 454 236 hydrogen bonds defined for protein. 675 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: 1.85 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1771 1.47 - 1.59: 2792 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6689 Sorted by residual: bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" C1 NAG F 705 " pdb=" O5 NAG F 705 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG F 703 " pdb=" O5 NAG F 703 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 6684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 8914 2.29 - 4.57: 143 4.57 - 6.86: 19 6.86 - 9.14: 13 9.14 - 11.43: 2 Bond angle restraints: 9091 Sorted by residual: angle pdb=" CB MET F 152 " pdb=" CG MET F 152 " pdb=" SD MET F 152 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA MET F 557 " pdb=" CB MET F 557 " pdb=" CG MET F 557 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CB MET F 557 " pdb=" CG MET F 557 " pdb=" SD MET F 557 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N ASP F 499 " pdb=" CA ASP F 499 " pdb=" C ASP F 499 " ideal model delta sigma weight residual 109.81 117.51 -7.70 2.21e+00 2.05e-01 1.21e+01 angle pdb=" CB GLU F 238 " pdb=" CG GLU F 238 " pdb=" CD GLU F 238 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 9086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3596 17.56 - 35.12: 373 35.12 - 52.68: 70 52.68 - 70.24: 17 70.24 - 87.80: 5 Dihedral angle restraints: 4061 sinusoidal: 1750 harmonic: 2311 Sorted by residual: dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.69 66.31 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS F 530 " pdb=" SG CYS F 530 " pdb=" SG CYS F 542 " pdb=" CB CYS F 542 " ideal model delta sinusoidal sigma weight residual -86.00 -122.53 36.53 1 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" SG CYS G 391 " pdb=" CB CYS G 525 " pdb=" SG CYS G 525 " pdb=" CA CYS G 525 " ideal model delta sinusoidal sigma weight residual 79.00 16.22 62.78 1 2.00e+01 2.50e-03 1.30e+01 ... (remaining 4058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 594 0.036 - 0.072: 267 0.072 - 0.108: 84 0.108 - 0.144: 25 0.144 - 0.180: 7 Chirality restraints: 977 Sorted by residual: chirality pdb=" CB VAL F 364 " pdb=" CA VAL F 364 " pdb=" CG1 VAL F 364 " pdb=" CG2 VAL F 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ASP F 499 " pdb=" N ASP F 499 " pdb=" C ASP F 499 " pdb=" CB ASP F 499 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 974 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 395 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C VAL G 395 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL G 395 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR G 396 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 491 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C VAL F 491 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL F 491 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO F 492 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 491 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO F 492 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 492 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 492 " -0.022 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2005 2.82 - 3.34: 5801 3.34 - 3.86: 10775 3.86 - 4.38: 12487 4.38 - 4.90: 21006 Nonbonded interactions: 52074 Sorted by model distance: nonbonded pdb=" O ALA F 501 " pdb=" OG SER F 507 " model vdw 2.298 3.040 nonbonded pdb=" O ILE F 544 " pdb=" OG SER F 547 " model vdw 2.300 3.040 nonbonded pdb=" O THR F 118 " pdb=" OG1 THR F 122 " model vdw 2.303 3.040 nonbonded pdb=" OG SER G 438 " pdb=" O PRO G 507 " model vdw 2.305 3.040 nonbonded pdb=" O GLU F 406 " pdb=" OG SER F 409 " model vdw 2.342 3.040 ... (remaining 52069 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.041 6689 Z= 0.236 Angle : 0.741 11.430 9091 Z= 0.367 Chirality : 0.047 0.180 977 Planarity : 0.005 0.039 1167 Dihedral : 14.633 87.805 2558 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.24), residues: 784 helix: -3.19 (0.17), residues: 348 sheet: -0.40 (0.79), residues: 41 loop : -1.70 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 478 HIS 0.006 0.001 HIS F 540 PHE 0.009 0.001 PHE G 486 TYR 0.018 0.001 TYR G 396 ARG 0.006 0.001 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 121 ASN cc_start: 0.8004 (m110) cc_final: 0.7788 (m110) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1697 time to fit residues: 20.3316 Evaluate side-chains 67 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 overall best weight: 0.7368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 188 ASN F 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083078 restraints weight = 17394.260| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.94 r_work: 0.3314 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6689 Z= 0.201 Angle : 0.600 8.223 9091 Z= 0.308 Chirality : 0.043 0.148 977 Planarity : 0.004 0.031 1167 Dihedral : 4.914 45.717 1045 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.72 % Allowed : 10.27 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.27), residues: 784 helix: -1.21 (0.25), residues: 342 sheet: -0.33 (0.70), residues: 42 loop : -1.66 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 477 HIS 0.012 0.001 HIS F 540 PHE 0.011 0.001 PHE F 369 TYR 0.022 0.001 TYR F 183 ARG 0.003 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 441 LYS cc_start: 0.8694 (tmtt) cc_final: 0.8452 (tmtt) outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1754 time to fit residues: 18.1107 Evaluate side-chains 69 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.0000 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.094335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082820 restraints weight = 17550.157| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.96 r_work: 0.3308 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6689 Z= 0.166 Angle : 0.536 6.570 9091 Z= 0.272 Chirality : 0.041 0.145 977 Planarity : 0.003 0.029 1167 Dihedral : 4.475 38.751 1045 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.58 % Allowed : 13.46 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.28), residues: 784 helix: -0.42 (0.27), residues: 342 sheet: -0.54 (0.69), residues: 42 loop : -1.49 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 69 HIS 0.012 0.001 HIS F 540 PHE 0.010 0.001 PHE F 523 TYR 0.017 0.001 TYR F 183 ARG 0.003 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: F 332 MET cc_start: 0.6990 (ppp) cc_final: 0.6616 (ptt) REVERT: F 441 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8483 (tmtt) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1806 time to fit residues: 18.0917 Evaluate side-chains 65 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.094138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082574 restraints weight = 17653.753| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.97 r_work: 0.3310 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6689 Z= 0.164 Angle : 0.526 6.603 9091 Z= 0.267 Chirality : 0.042 0.148 977 Planarity : 0.003 0.029 1167 Dihedral : 4.185 28.168 1045 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.72 % Allowed : 14.91 % Favored : 84.37 % 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: -1.15 (0.29), residues: 784 helix: -0.03 (0.28), residues: 344 sheet: -0.61 (0.70), residues: 42 loop : -1.43 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.009 0.001 HIS F 540 PHE 0.010 0.001 PHE F 523 TYR 0.017 0.001 TYR F 183 ARG 0.004 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 332 MET cc_start: 0.7080 (ppp) cc_final: 0.6723 (ptt) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1582 time to fit residues: 15.3899 Evaluate side-chains 64 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN F 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.092954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081689 restraints weight = 17565.617| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.85 r_work: 0.3304 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6689 Z= 0.194 Angle : 0.545 6.440 9091 Z= 0.277 Chirality : 0.042 0.146 977 Planarity : 0.003 0.030 1167 Dihedral : 4.208 23.382 1045 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.30 % Allowed : 15.92 % Favored : 82.78 % 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: -0.96 (0.29), residues: 784 helix: 0.13 (0.28), residues: 353 sheet: -0.46 (0.71), residues: 41 loop : -1.36 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 610 HIS 0.009 0.001 HIS F 540 PHE 0.011 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.003 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: F 332 MET cc_start: 0.7228 (ppp) cc_final: 0.6990 (ptt) REVERT: G 355 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7782 (ptm160) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1730 time to fit residues: 17.2035 Evaluate side-chains 66 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 48 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.094099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082817 restraints weight = 17241.210| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.86 r_work: 0.3306 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6689 Z= 0.158 Angle : 0.531 6.926 9091 Z= 0.268 Chirality : 0.041 0.147 977 Planarity : 0.003 0.031 1167 Dihedral : 3.981 17.879 1045 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.59 % Allowed : 16.64 % Favored : 81.77 % 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: -0.83 (0.29), residues: 784 helix: 0.32 (0.28), residues: 352 sheet: -0.47 (0.73), residues: 41 loop : -1.38 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 610 HIS 0.008 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.001 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: F 116 LEU cc_start: 0.7952 (tt) cc_final: 0.7701 (mt) REVERT: F 261 CYS cc_start: 0.7704 (m) cc_final: 0.7400 (m) REVERT: F 332 MET cc_start: 0.7121 (ppp) cc_final: 0.6830 (ptt) REVERT: F 593 THR cc_start: 0.8531 (m) cc_final: 0.8315 (p) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.1487 time to fit residues: 16.4684 Evaluate side-chains 68 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 402 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.092724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081580 restraints weight = 17301.611| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.81 r_work: 0.3295 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6689 Z= 0.191 Angle : 0.564 6.917 9091 Z= 0.283 Chirality : 0.043 0.149 977 Planarity : 0.003 0.031 1167 Dihedral : 4.040 17.805 1045 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.59 % Allowed : 16.64 % Favored : 81.77 % 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: -0.80 (0.29), residues: 784 helix: 0.31 (0.28), residues: 357 sheet: -0.47 (0.74), residues: 41 loop : -1.34 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.008 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.002 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: F 116 LEU cc_start: 0.7924 (tt) cc_final: 0.7715 (mt) REVERT: F 261 CYS cc_start: 0.7654 (m) cc_final: 0.7365 (m) REVERT: F 332 MET cc_start: 0.7153 (ppp) cc_final: 0.6887 (ptt) REVERT: F 366 MET cc_start: 0.8281 (mmm) cc_final: 0.7938 (tpp) REVERT: F 593 THR cc_start: 0.8611 (m) cc_final: 0.8381 (p) REVERT: G 355 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7776 (ptm160) outliers start: 11 outliers final: 11 residues processed: 71 average time/residue: 0.1670 time to fit residues: 16.9013 Evaluate side-chains 73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** 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 = 0.3602 r_free = 0.3602 target = 0.092394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081274 restraints weight = 17395.911| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.80 r_work: 0.3282 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6689 Z= 0.200 Angle : 0.576 7.057 9091 Z= 0.288 Chirality : 0.043 0.150 977 Planarity : 0.003 0.032 1167 Dihedral : 4.063 17.576 1045 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.88 % Allowed : 16.93 % Favored : 81.19 % 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: -0.70 (0.30), residues: 784 helix: 0.35 (0.28), residues: 357 sheet: -0.56 (0.74), residues: 41 loop : -1.23 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 610 HIS 0.008 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: F 261 CYS cc_start: 0.7708 (m) cc_final: 0.7420 (m) REVERT: F 332 MET cc_start: 0.7145 (ppp) cc_final: 0.6828 (ptt) REVERT: F 366 MET cc_start: 0.8208 (mmm) cc_final: 0.7869 (tpp) REVERT: F 593 THR cc_start: 0.8614 (m) cc_final: 0.8386 (p) REVERT: G 355 ARG cc_start: 0.8284 (ttt90) cc_final: 0.7849 (ptm160) outliers start: 13 outliers final: 12 residues processed: 73 average time/residue: 0.1794 time to fit residues: 18.1946 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.094112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082836 restraints weight = 17494.047| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.93 r_work: 0.3276 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6689 Z= 0.190 Angle : 0.571 7.182 9091 Z= 0.288 Chirality : 0.042 0.151 977 Planarity : 0.003 0.033 1167 Dihedral : 4.022 16.209 1045 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 17.08 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.30), residues: 784 helix: 0.39 (0.28), residues: 358 sheet: -0.55 (0.75), residues: 41 loop : -1.21 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 610 HIS 0.008 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.017 0.001 TYR F 183 ARG 0.002 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: F 116 LEU cc_start: 0.7944 (mt) cc_final: 0.7679 (tt) REVERT: F 261 CYS cc_start: 0.7858 (m) cc_final: 0.7510 (m) REVERT: F 332 MET cc_start: 0.7304 (ppp) cc_final: 0.7087 (ptt) REVERT: F 593 THR cc_start: 0.8713 (m) cc_final: 0.8439 (p) REVERT: G 355 ARG cc_start: 0.8442 (ttt90) cc_final: 0.7970 (ptm160) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.1716 time to fit residues: 17.5130 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 22 optimal weight: 0.4980 chunk 55 optimal weight: 0.0770 chunk 76 optimal weight: 0.5980 chunk 32 optimal weight: 0.0070 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.0050 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** 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 = 0.3652 r_free = 0.3652 target = 0.095274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084055 restraints weight = 17422.135| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.83 r_work: 0.3343 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 6689 Z= 0.168 Angle : 0.572 7.903 9091 Z= 0.284 Chirality : 0.041 0.157 977 Planarity : 0.003 0.031 1167 Dihedral : 3.713 16.719 1045 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.45 % Allowed : 17.66 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 784 helix: 0.40 (0.29), residues: 358 sheet: -0.52 (0.72), residues: 41 loop : -1.17 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 168 HIS 0.006 0.001 HIS F 540 PHE 0.011 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.001 0.000 ARG F 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1568 Ramachandran restraints generated. 784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 116 LEU cc_start: 0.7906 (mt) cc_final: 0.7685 (tt) REVERT: F 261 CYS cc_start: 0.7681 (m) cc_final: 0.7295 (m) REVERT: F 332 MET cc_start: 0.6997 (ppp) cc_final: 0.6765 (ptt) REVERT: F 366 MET cc_start: 0.8226 (mmm) cc_final: 0.7797 (tpp) REVERT: F 593 THR cc_start: 0.8556 (m) cc_final: 0.8318 (p) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.1945 time to fit residues: 20.0067 Evaluate side-chains 72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 271 TRP Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 570 LEU Chi-restraints excluded: chain G residue 392 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 194 ASN ** G 422 ASN ** 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 = 0.3633 r_free = 0.3633 target = 0.093842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082638 restraints weight = 17882.237| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.92 r_work: 0.3274 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6689 Z= 0.227 Angle : 0.601 7.658 9091 Z= 0.303 Chirality : 0.043 0.151 977 Planarity : 0.003 0.032 1167 Dihedral : 3.984 16.361 1045 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.30 % Allowed : 18.09 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 784 helix: 0.37 (0.28), residues: 360 sheet: -0.47 (0.75), residues: 41 loop : -1.14 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 168 HIS 0.010 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.037 0.001 TYR F 50 ARG 0.006 0.000 ARG G 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.18 seconds wall clock time: 49 minutes 2.61 seconds (2942.61 seconds total)