Starting phenix.real_space_refine on Sat May 10 16:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmb_22922/05_2025/7kmb_22922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmb_22922/05_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_22922/05_2025/7kmb_22922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmb_22922/05_2025/7kmb_22922.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmb_22922/05_2025/7kmb_22922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmb_22922/05_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-5687/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: 4.70, per 1000 atoms: 0.72 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: 1.65 Conformation dependent library (CDL) restraints added in 892.0 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: 0.67 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: 1.61 Time building geometry restraints manager: 1.88 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.830 Find NCS groups from input model: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- 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 6705 Z= 0.174 Angle : 0.751 11.430 9132 Z= 0.370 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 7) link_NAG-ASN : angle 2.22106 ( 21) link_BETA1-4 : bond 0.00548 ( 2) link_BETA1-4 : angle 0.75241 ( 6) hydrogen bonds : bond 0.30483 ( 236) hydrogen bonds : angle 9.17138 ( 675) SS BOND : bond 0.00214 ( 7) SS BOND : angle 1.70651 ( 14) covalent geometry : bond 0.00371 ( 6689) covalent geometry : angle 0.74145 ( 9091) *********************** 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 : 0.672 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: 0.1599 time to fit residues: 19.1670 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 : 0.664 ------------------------------------------------------------------------------- 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: 4.9990 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: 6.9990 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: 0.9370 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.093383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081845 restraints weight = 17456.400| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.95 r_work: 0.3293 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6705 Z= 0.163 Angle : 0.614 7.895 9132 Z= 0.313 Chirality : 0.043 0.144 977 Planarity : 0.004 0.030 1167 Dihedral : 5.022 45.834 1045 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.01 % Allowed : 10.85 % Favored : 88.13 % 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: -1.23 (0.25), residues: 343 sheet: -0.43 (0.69), residues: 42 loop : -1.62 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 477 HIS 0.011 0.002 HIS F 540 PHE 0.010 0.001 PHE F 369 TYR 0.025 0.001 TYR F 183 ARG 0.002 0.000 ARG F 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 7) link_NAG-ASN : angle 1.91960 ( 21) link_BETA1-4 : bond 0.00585 ( 2) link_BETA1-4 : angle 0.80680 ( 6) hydrogen bonds : bond 0.05480 ( 236) hydrogen bonds : angle 5.28325 ( 675) SS BOND : bond 0.00422 ( 7) SS BOND : angle 1.17750 ( 14) covalent geometry : bond 0.00363 ( 6689) covalent geometry : angle 0.60610 ( 9091) *********************** 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 75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 441 LYS cc_start: 0.8695 (tmtt) cc_final: 0.8464 (tmtt) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1754 time to fit residues: 17.6559 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 276 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082143 restraints weight = 17472.781| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.87 r_work: 0.3297 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6705 Z= 0.142 Angle : 0.559 6.535 9132 Z= 0.282 Chirality : 0.042 0.148 977 Planarity : 0.003 0.029 1167 Dihedral : 4.636 39.255 1045 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.87 % Allowed : 14.18 % Favored : 84.95 % 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: -1.50 (0.28), residues: 784 helix: -0.44 (0.27), residues: 351 sheet: -0.69 (0.69), residues: 42 loop : -1.52 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 69 HIS 0.009 0.001 HIS F 540 PHE 0.012 0.001 PHE F 523 TYR 0.016 0.001 TYR F 183 ARG 0.006 0.001 ARG G 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 7) link_NAG-ASN : angle 1.94022 ( 21) link_BETA1-4 : bond 0.00267 ( 2) link_BETA1-4 : angle 0.79999 ( 6) hydrogen bonds : bond 0.04923 ( 236) hydrogen bonds : angle 4.75353 ( 675) SS BOND : bond 0.00256 ( 7) SS BOND : angle 1.09938 ( 14) covalent geometry : bond 0.00320 ( 6689) covalent geometry : angle 0.55030 ( 9091) *********************** 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 73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 332 MET cc_start: 0.7121 (ppp) cc_final: 0.6819 (ptt) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.1438 time to fit residues: 14.8468 Evaluate side-chains 65 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 91 LEU 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: 3.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080603 restraints weight = 17632.613| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.83 r_work: 0.3274 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6705 Z= 0.148 Angle : 0.568 6.472 9132 Z= 0.287 Chirality : 0.043 0.149 977 Planarity : 0.003 0.031 1167 Dihedral : 4.488 30.366 1045 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.45 % Allowed : 15.63 % Favored : 82.92 % 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: -1.17 (0.29), residues: 784 helix: -0.06 (0.28), residues: 345 sheet: -0.67 (0.70), residues: 41 loop : -1.42 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.010 0.001 HIS F 540 PHE 0.011 0.001 PHE F 523 TYR 0.017 0.001 TYR F 183 ARG 0.005 0.000 ARG G 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 2.02007 ( 21) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 0.81511 ( 6) hydrogen bonds : bond 0.04490 ( 236) hydrogen bonds : angle 4.53465 ( 675) SS BOND : bond 0.00424 ( 7) SS BOND : angle 1.03071 ( 14) covalent geometry : bond 0.00338 ( 6689) covalent geometry : angle 0.55875 ( 9091) *********************** 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 73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.670 Fit side-chains REVERT: F 332 MET cc_start: 0.7220 (ppp) cc_final: 0.6963 (ptt) REVERT: G 355 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7623 (ptm160) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.1625 time to fit residues: 16.3901 Evaluate side-chains 64 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 570 LEU 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: 0.2980 chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 134 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 = 0.3638 r_free = 0.3638 target = 0.094250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083102 restraints weight = 17626.320| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.92 r_work: 0.3284 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6705 Z= 0.113 Angle : 0.554 6.795 9132 Z= 0.278 Chirality : 0.042 0.151 977 Planarity : 0.003 0.030 1167 Dihedral : 4.212 21.064 1045 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.74 % Allowed : 15.92 % Favored : 82.34 % 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: -0.99 (0.29), residues: 784 helix: 0.16 (0.28), residues: 351 sheet: -0.60 (0.72), residues: 41 loop : -1.41 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 610 HIS 0.009 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 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.97296 ( 21) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 0.79575 ( 6) hydrogen bonds : bond 0.04167 ( 236) hydrogen bonds : angle 4.34648 ( 675) SS BOND : bond 0.00557 ( 7) SS BOND : angle 1.41436 ( 14) covalent geometry : bond 0.00256 ( 6689) covalent geometry : angle 0.54388 ( 9091) *********************** 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 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.754 Fit side-chains REVERT: F 261 CYS cc_start: 0.7903 (m) cc_final: 0.7543 (m) REVERT: F 593 THR cc_start: 0.8612 (m) cc_final: 0.8350 (p) REVERT: G 355 ARG cc_start: 0.8289 (ttt90) cc_final: 0.7836 (ptm160) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.1714 time to fit residues: 18.2425 Evaluate side-chains 69 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1065 > 50: distance: 77 - 81: 20.586 distance: 81 - 82: 45.733 distance: 81 - 87: 27.812 distance: 82 - 83: 31.862 distance: 82 - 85: 42.680 distance: 83 - 84: 27.213 distance: 83 - 88: 42.778 distance: 85 - 86: 19.309 distance: 86 - 87: 22.056 distance: 88 - 89: 20.620 distance: 89 - 90: 4.382 distance: 89 - 92: 15.997 distance: 90 - 91: 13.889 distance: 90 - 96: 8.415 distance: 92 - 93: 3.599 distance: 92 - 94: 3.640 distance: 93 - 95: 7.207 distance: 96 - 97: 13.027 distance: 97 - 98: 24.059 distance: 98 - 99: 26.116 distance: 98 - 100: 34.413 distance: 100 - 101: 31.939 distance: 101 - 102: 9.848 distance: 101 - 104: 27.552 distance: 102 - 103: 54.766 distance: 102 - 106: 15.427 distance: 104 - 105: 26.262 distance: 106 - 107: 20.691 distance: 107 - 108: 38.704 distance: 107 - 110: 49.354 distance: 108 - 109: 42.841 distance: 108 - 114: 35.491 distance: 110 - 111: 40.487 distance: 111 - 112: 15.067 distance: 111 - 113: 25.725 distance: 114 - 115: 14.756 distance: 114 - 120: 27.657 distance: 115 - 116: 21.805 distance: 115 - 118: 13.689 distance: 116 - 117: 17.208 distance: 116 - 121: 43.918 distance: 118 - 119: 20.712 distance: 119 - 120: 10.723 distance: 121 - 122: 15.191 distance: 122 - 123: 15.162 distance: 122 - 125: 28.014 distance: 123 - 124: 22.442 distance: 123 - 126: 30.499 distance: 126 - 127: 16.542 distance: 127 - 128: 14.228 distance: 127 - 130: 14.523 distance: 128 - 129: 44.993 distance: 128 - 136: 13.934 distance: 130 - 131: 10.388 distance: 131 - 132: 4.523 distance: 131 - 133: 3.944 distance: 132 - 134: 6.229 distance: 133 - 135: 6.961 distance: 134 - 135: 3.844 distance: 136 - 137: 10.643 distance: 137 - 138: 40.143 distance: 137 - 140: 34.928 distance: 138 - 139: 12.998 distance: 138 - 144: 34.374 distance: 140 - 141: 26.785 distance: 141 - 142: 11.865 distance: 141 - 143: 27.606 distance: 144 - 145: 15.717 distance: 145 - 146: 20.062 distance: 145 - 148: 26.546 distance: 146 - 147: 26.818 distance: 146 - 152: 5.923 distance: 148 - 149: 28.808 distance: 149 - 150: 3.167 distance: 149 - 151: 21.339