Starting phenix.real_space_refine on Thu Jul 24 19:45:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmb_22922/07_2025/7kmb_22922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmb_22922/07_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_22922/07_2025/7kmb_22922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmb_22922/07_2025/7kmb_22922.map" model { file = "/net/cci-nas-00/data/ceres_data/7kmb_22922/07_2025/7kmb_22922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmb_22922/07_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-5711/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: 5.12, per 1000 atoms: 0.79 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: 1.45 Conformation dependent library (CDL) restraints added in 914.1 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: 0.62 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: 1.57 Time building geometry restraints manager: 1.69 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: 4.780 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.510 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- 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 : 0.688 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: 0.1656 time to fit residues: 19.8175 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 : 0.637 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.093406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081883 restraints weight = 17427.821| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.95 r_work: 0.3294 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6705 Z= 0.164 Angle : 0.615 7.968 9132 Z= 0.314 Chirality : 0.043 0.145 977 Planarity : 0.004 0.030 1167 Dihedral : 5.028 45.957 1045 Min Nonbonded Distance : 2.425 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: -2.12 (0.27), residues: 784 helix: -1.23 (0.25), residues: 343 sheet: -0.44 (0.69), residues: 42 loop : -1.62 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 165 HIS 0.012 0.002 HIS F 540 PHE 0.010 0.001 PHE F 369 TYR 0.026 0.001 TYR F 183 ARG 0.002 0.000 ARG F 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 7) link_NAG-ASN : angle 1.93398 ( 21) link_BETA1-4 : bond 0.00529 ( 2) link_BETA1-4 : angle 0.87053 ( 6) hydrogen bonds : bond 0.05482 ( 236) hydrogen bonds : angle 5.29145 ( 675) SS BOND : bond 0.00224 ( 7) SS BOND : angle 1.16945 ( 14) covalent geometry : bond 0.00365 ( 6689) covalent geometry : angle 0.60720 ( 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 : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 441 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8467 (tmtt) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1786 time to fit residues: 18.0690 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 : 0.693 ------------------------------------------------------------------------------- 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: 0.2980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.092151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.080930 restraints weight = 17509.411| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.84 r_work: 0.3279 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2034 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= 0.158 Angle : 0.571 6.577 9132 Z= 0.290 Chirality : 0.043 0.151 977 Planarity : 0.004 0.030 1167 Dihedral : 4.737 40.277 1045 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.87 % Allowed : 13.89 % Favored : 85.24 % 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: -1.54 (0.28), residues: 784 helix: -0.48 (0.27), residues: 351 sheet: -0.72 (0.69), residues: 42 loop : -1.53 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 69 HIS 0.011 0.001 HIS F 540 PHE 0.011 0.001 PHE F 523 TYR 0.016 0.001 TYR F 183 ARG 0.004 0.000 ARG G 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 7) link_NAG-ASN : angle 1.97979 ( 21) link_BETA1-4 : bond 0.00329 ( 2) link_BETA1-4 : angle 0.86767 ( 6) hydrogen bonds : bond 0.05040 ( 236) hydrogen bonds : angle 4.79387 ( 675) SS BOND : bond 0.00301 ( 7) SS BOND : angle 1.16634 ( 14) covalent geometry : bond 0.00356 ( 6689) covalent geometry : angle 0.56159 ( 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 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: F 332 MET cc_start: 0.7106 (ppp) cc_final: 0.6835 (ptt) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.1507 time to fit residues: 15.7116 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 : 0.685 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.091136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079952 restraints weight = 17641.337| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.85 r_work: 0.3260 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2394 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= 0.161 Angle : 0.586 6.485 9132 Z= 0.296 Chirality : 0.043 0.150 977 Planarity : 0.003 0.032 1167 Dihedral : 4.618 31.275 1045 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.74 % Allowed : 14.91 % Favored : 83.36 % 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: -1.22 (0.29), residues: 784 helix: -0.11 (0.27), residues: 351 sheet: -0.81 (0.70), residues: 42 loop : -1.45 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.011 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 0.00282 ( 7) link_NAG-ASN : angle 2.08096 ( 21) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 0.86261 ( 6) hydrogen bonds : bond 0.04550 ( 236) hydrogen bonds : angle 4.58868 ( 675) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.14046 ( 14) covalent geometry : bond 0.00366 ( 6689) covalent geometry : angle 0.57649 ( 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 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.704 Fit side-chains REVERT: F 261 CYS cc_start: 0.7801 (m) cc_final: 0.7465 (m) REVERT: F 288 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6792 (ptpt) REVERT: G 355 ARG cc_start: 0.8287 (ttt90) cc_final: 0.7658 (ptm160) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.1752 time to fit residues: 18.1577 Evaluate side-chains 67 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 288 LYS Chi-restraints excluded: chain F residue 447 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** G 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.092590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081482 restraints weight = 17560.513| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.85 r_work: 0.3287 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2478 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= 0.116 Angle : 0.556 6.777 9132 Z= 0.280 Chirality : 0.042 0.152 977 Planarity : 0.003 0.031 1167 Dihedral : 4.326 22.612 1045 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.74 % Allowed : 16.21 % Favored : 82.05 % 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: -1.02 (0.29), residues: 784 helix: 0.13 (0.28), residues: 351 sheet: -0.62 (0.71), residues: 41 loop : -1.43 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 610 HIS 0.010 0.001 HIS F 540 PHE 0.012 0.001 PHE F 504 TYR 0.018 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 7) link_NAG-ASN : angle 2.02531 ( 21) link_BETA1-4 : bond 0.00397 ( 2) link_BETA1-4 : angle 0.79259 ( 6) hydrogen bonds : bond 0.04229 ( 236) hydrogen bonds : angle 4.36847 ( 675) SS BOND : bond 0.00517 ( 7) SS BOND : angle 1.43513 ( 14) covalent geometry : bond 0.00263 ( 6689) covalent geometry : angle 0.54518 ( 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 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.769 Fit side-chains REVERT: F 261 CYS cc_start: 0.7753 (m) cc_final: 0.7411 (m) REVERT: F 288 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6657 (ptpt) REVERT: F 332 MET cc_start: 0.7129 (ppp) cc_final: 0.6907 (ptt) REVERT: F 593 THR cc_start: 0.8600 (m) cc_final: 0.8359 (p) REVERT: G 355 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7623 (ptm160) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1655 time to fit residues: 17.6258 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 : 0.699 ------------------------------------------------------------------------------- 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 91 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.091894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.080871 restraints weight = 17320.054| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.82 r_work: 0.3277 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6705 Z= 0.139 Angle : 0.576 6.864 9132 Z= 0.288 Chirality : 0.043 0.151 977 Planarity : 0.003 0.032 1167 Dihedral : 4.291 20.285 1045 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.46 % Allowed : 15.92 % Favored : 81.62 % 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: -0.93 (0.29), residues: 784 helix: 0.23 (0.28), residues: 358 sheet: -0.70 (0.74), residues: 41 loop : -1.42 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.003 0.000 ARG F 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 7) link_NAG-ASN : angle 2.09516 ( 21) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 0.89348 ( 6) hydrogen bonds : bond 0.04115 ( 236) hydrogen bonds : angle 4.28915 ( 675) SS BOND : bond 0.00356 ( 7) SS BOND : angle 1.12906 ( 14) covalent geometry : bond 0.00319 ( 6689) covalent geometry : angle 0.56595 ( 9091) *********************** 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: 17 poor density : 62 time to evaluate : 0.701 Fit side-chains REVERT: F 23 GLU cc_start: 0.7768 (pt0) cc_final: 0.7547 (pt0) REVERT: F 116 LEU cc_start: 0.7951 (tt) cc_final: 0.7680 (mt) REVERT: F 261 CYS cc_start: 0.7829 (m) cc_final: 0.7492 (m) REVERT: F 288 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6794 (ptpt) REVERT: G 355 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7637 (ptm160) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1769 time to fit residues: 18.4437 Evaluate side-chains 73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 91 LEU 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 447 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 440 ASN Chi-restraints excluded: chain G residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 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 = 0.3579 r_free = 0.3579 target = 0.091170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080149 restraints weight = 17452.695| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.86 r_work: 0.3270 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6705 Z= 0.134 Angle : 0.579 6.439 9132 Z= 0.289 Chirality : 0.043 0.153 977 Planarity : 0.003 0.033 1167 Dihedral : 4.270 18.781 1045 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.46 % Allowed : 16.64 % 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: -0.84 (0.30), residues: 784 helix: 0.25 (0.28), residues: 358 sheet: -0.76 (0.75), residues: 41 loop : -1.29 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.00250 ( 7) link_NAG-ASN : angle 2.09761 ( 21) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 0.89333 ( 6) hydrogen bonds : bond 0.04063 ( 236) hydrogen bonds : angle 4.30575 ( 675) SS BOND : bond 0.00396 ( 7) SS BOND : angle 1.84974 ( 14) covalent geometry : bond 0.00311 ( 6689) covalent geometry : angle 0.56674 ( 9091) *********************** 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 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.715 Fit side-chains REVERT: F 23 GLU cc_start: 0.7776 (pt0) cc_final: 0.7565 (pt0) REVERT: F 116 LEU cc_start: 0.7945 (tt) cc_final: 0.7732 (mt) REVERT: F 261 CYS cc_start: 0.7798 (m) cc_final: 0.7492 (m) REVERT: F 288 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6696 (ptpt) REVERT: F 593 THR cc_start: 0.8639 (m) cc_final: 0.8361 (p) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.1638 time to fit residues: 16.6776 Evaluate side-chains 73 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 91 LEU 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 447 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.091413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080388 restraints weight = 17559.596| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.86 r_work: 0.3277 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6705 Z= 0.124 Angle : 0.579 7.400 9132 Z= 0.287 Chirality : 0.043 0.154 977 Planarity : 0.003 0.032 1167 Dihedral : 4.130 16.591 1045 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.03 % Allowed : 17.51 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.30), residues: 784 helix: 0.27 (0.28), residues: 358 sheet: -0.71 (0.76), residues: 41 loop : -1.28 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 610 HIS 0.011 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 7) link_NAG-ASN : angle 2.09578 ( 21) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 0.90576 ( 6) hydrogen bonds : bond 0.03968 ( 236) hydrogen bonds : angle 4.23555 ( 675) SS BOND : bond 0.00387 ( 7) SS BOND : angle 1.50907 ( 14) covalent geometry : bond 0.00290 ( 6689) covalent geometry : angle 0.56834 ( 9091) *********************** 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 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.718 Fit side-chains REVERT: F 23 GLU cc_start: 0.7740 (pt0) cc_final: 0.7535 (pt0) REVERT: F 116 LEU cc_start: 0.8011 (tt) cc_final: 0.7800 (mt) REVERT: F 261 CYS cc_start: 0.7810 (m) cc_final: 0.7457 (m) REVERT: F 288 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6829 (ptpt) REVERT: F 593 THR cc_start: 0.8635 (m) cc_final: 0.8352 (p) REVERT: G 355 ARG cc_start: 0.8297 (ttt90) cc_final: 0.7808 (ptm160) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1618 time to fit residues: 17.0231 Evaluate side-chains 72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 91 LEU 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 463 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.090754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079836 restraints weight = 17718.521| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.85 r_work: 0.3263 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6705 Z= 0.139 Angle : 0.608 12.240 9132 Z= 0.302 Chirality : 0.043 0.154 977 Planarity : 0.003 0.032 1167 Dihedral : 4.160 17.793 1045 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.32 % Allowed : 17.95 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 784 helix: 0.31 (0.29), residues: 360 sheet: -0.70 (0.75), residues: 41 loop : -1.27 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.007 0.001 HIS F 540 PHE 0.014 0.001 PHE F 504 TYR 0.016 0.001 TYR F 183 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 7) link_NAG-ASN : angle 2.14586 ( 21) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 0.93570 ( 6) hydrogen bonds : bond 0.03932 ( 236) hydrogen bonds : angle 4.22284 ( 675) SS BOND : bond 0.00365 ( 7) SS BOND : angle 1.19589 ( 14) covalent geometry : bond 0.00323 ( 6689) covalent geometry : angle 0.59860 ( 9091) *********************** 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 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.697 Fit side-chains REVERT: F 23 GLU cc_start: 0.7783 (pt0) cc_final: 0.7577 (pt0) REVERT: F 261 CYS cc_start: 0.7838 (m) cc_final: 0.7508 (m) REVERT: F 288 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6820 (ptpt) REVERT: F 366 MET cc_start: 0.8135 (mmm) cc_final: 0.7058 (tmm) REVERT: F 593 THR cc_start: 0.8643 (m) cc_final: 0.8357 (p) REVERT: G 355 ARG cc_start: 0.8405 (ttt90) cc_final: 0.7866 (ptm160) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1582 time to fit residues: 16.5511 Evaluate side-chains 75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 91 LEU 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 447 VAL Chi-restraints excluded: chain F residue 463 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.090628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079461 restraints weight = 17879.566| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.92 r_work: 0.3256 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6705 Z= 0.142 Angle : 0.606 7.426 9132 Z= 0.305 Chirality : 0.043 0.154 977 Planarity : 0.003 0.033 1167 Dihedral : 4.194 17.968 1045 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.03 % Allowed : 17.95 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 784 helix: 0.27 (0.28), residues: 361 sheet: -0.71 (0.75), residues: 41 loop : -1.23 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.007 0.001 HIS F 540 PHE 0.013 0.001 PHE F 504 TYR 0.022 0.001 TYR G 365 ARG 0.003 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 7) link_NAG-ASN : angle 2.16408 ( 21) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 0.98859 ( 6) hydrogen bonds : bond 0.03978 ( 236) hydrogen bonds : angle 4.23273 ( 675) SS BOND : bond 0.00395 ( 7) SS BOND : angle 1.41282 ( 14) covalent geometry : bond 0.00331 ( 6689) covalent geometry : angle 0.59571 ( 9091) ********************** 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 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.713 Fit side-chains REVERT: F 23 GLU cc_start: 0.7785 (pt0) cc_final: 0.7582 (pt0) REVERT: F 116 LEU cc_start: 0.7912 (mt) cc_final: 0.7669 (tt) REVERT: F 261 CYS cc_start: 0.7877 (m) cc_final: 0.7550 (m) REVERT: F 288 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6802 (ptpt) REVERT: F 366 MET cc_start: 0.8272 (mmm) cc_final: 0.7994 (tmm) REVERT: F 593 THR cc_start: 0.8649 (m) cc_final: 0.8355 (p) REVERT: G 355 ARG cc_start: 0.8412 (ttt90) cc_final: 0.7856 (ptm160) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.1591 time to fit residues: 16.4683 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 91 LEU 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 447 VAL Chi-restraints excluded: chain F residue 463 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 23 optimal weight: 0.0010 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.092109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080898 restraints weight = 18006.824| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.93 r_work: 0.3283 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6705 Z= 0.114 Angle : 0.591 7.400 9132 Z= 0.295 Chirality : 0.042 0.157 977 Planarity : 0.003 0.032 1167 Dihedral : 3.974 16.809 1045 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.88 % Allowed : 18.23 % Favored : 79.88 % 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: -0.72 (0.30), residues: 784 helix: 0.30 (0.28), residues: 361 sheet: -0.74 (0.74), residues: 41 loop : -1.18 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 610 HIS 0.002 0.001 HIS F 417 PHE 0.013 0.001 PHE F 504 TYR 0.020 0.001 TYR G 365 ARG 0.002 0.000 ARG F 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 2.09870 ( 21) link_BETA1-4 : bond 0.00522 ( 2) link_BETA1-4 : angle 0.95007 ( 6) hydrogen bonds : bond 0.03893 ( 236) hydrogen bonds : angle 4.16442 ( 675) SS BOND : bond 0.00436 ( 7) SS BOND : angle 0.87933 ( 14) covalent geometry : bond 0.00270 ( 6689) covalent geometry : angle 0.58260 ( 9091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.59 seconds wall clock time: 66 minutes 42.53 seconds (4002.53 seconds total)