Starting phenix.real_space_refine on Fri Feb 14 10:00:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.map" model { file = "/net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sz5_25561/02_2025/7sz5_25561.cif" } resolution = 3.6 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= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 847 atoms to isotropic. 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 114 5.16 5 C 5793 2.51 5 N 1668 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9367 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4723 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 30, 'TRANS': 583} Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 21, 'TRANS': 478} Chain: "D" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 386 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 7.83, per 1000 atoms: 0.84 Number of scatterers: 9367 At special positions: 0 Unit cell: (64.764, 145.719, 130.607, 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 114 16.00 O 1792 8.00 N 1668 7.00 C 5793 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 34 " distance=2.02 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.04 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 207 " distance=2.00 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 224 " distance=2.02 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 267 " distance=2.02 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 283 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 302 " distance=2.04 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 338 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 482 " - pdb=" SG CYS A 491 " distance=2.03 Simple disulfide: pdb=" SG CYS A 486 " - pdb=" SG CYS A 499 " distance=2.02 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 555 " distance=2.05 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.02 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 593 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 612 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 21 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 32 " distance=2.01 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 34 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.02 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 207 " distance=2.00 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 267 " distance=2.02 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 283 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 475 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.02 Simple disulfide: pdb=" SG CYS D 8 " - pdb=" SG CYS D 21 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 32 " distance=2.02 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 43 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 11.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 removed outlier: 3.654A pdb=" N PHE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 144 removed outlier: 4.083A pdb=" N ILE A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.636A pdb=" N LYS A 372 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.567A pdb=" N LEU A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.843A pdb=" N ASN A 554 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.650A pdb=" N GLU A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.704A pdb=" N PHE B 24 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.641A pdb=" N GLU B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 475 through 479 removed outlier: 4.180A pdb=" N GLY B 479 " --> pdb=" O LYS B 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 removed outlier: 7.334A pdb=" N ARG A 125 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 96 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 277 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.229A pdb=" N CYS A 313 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.502A pdb=" N LEU A 345 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE A 438 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA A 415 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N SER A 440 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 417 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 505 through 507 removed outlier: 4.162A pdb=" N GLU A 510 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 525 through 527 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.067A pdb=" N VAL A 575 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 586 through 587 removed outlier: 3.792A pdb=" N TYR A 586 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.559A pdb=" N LEU B 41 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ALA B 68 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 43 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 65 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 98 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 67 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TYR B 93 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ARG B 125 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 95 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 124 " --> pdb=" O SER B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB9, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AC2, first strand: chain 'B' and resid 291 through 295 Processing sheet with id=AC3, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC4, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.244A pdb=" N LEU B 381 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 414 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 5 through 7 103 hydrogen bonds defined for protein. 183 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: 2.59 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2984 1.33 - 1.46: 1962 1.46 - 1.58: 4474 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 9552 Sorted by residual: bond pdb=" CA SER A 196 " pdb=" CB SER A 196 " ideal model delta sigma weight residual 1.534 1.468 0.066 1.45e-02 4.76e+03 2.05e+01 bond pdb=" CA SER B 196 " pdb=" CB SER B 196 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.60e-02 3.91e+03 1.49e+01 bond pdb=" CA SER C 3 " pdb=" CB SER C 3 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.52e-02 4.33e+03 1.29e+01 bond pdb=" N CYS A 538 " pdb=" CA CYS A 538 " ideal model delta sigma weight residual 1.453 1.494 -0.042 1.31e-02 5.83e+03 1.01e+01 bond pdb=" N ASN A 134 " pdb=" CA ASN A 134 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 ... (remaining 9547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 12079 1.73 - 3.47: 735 3.47 - 5.20: 88 5.20 - 6.94: 13 6.94 - 8.67: 2 Bond angle restraints: 12917 Sorted by residual: angle pdb=" CA PHE B 156 " pdb=" CB PHE B 156 " pdb=" CG PHE B 156 " ideal model delta sigma weight residual 113.80 119.25 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" C LYS B 430 " pdb=" N GLU B 431 " pdb=" CA GLU B 431 " ideal model delta sigma weight residual 122.87 116.59 6.28 1.44e+00 4.82e-01 1.90e+01 angle pdb=" N VAL A 500 " pdb=" CA VAL A 500 " pdb=" C VAL A 500 " ideal model delta sigma weight residual 113.53 109.28 4.25 9.80e-01 1.04e+00 1.88e+01 angle pdb=" N PRO B 171 " pdb=" CA PRO B 171 " pdb=" C PRO B 171 " ideal model delta sigma weight residual 112.47 121.14 -8.67 2.06e+00 2.36e-01 1.77e+01 angle pdb=" N ILE B 432 " pdb=" CA ILE B 432 " pdb=" C ILE B 432 " ideal model delta sigma weight residual 109.58 104.48 5.10 1.29e+00 6.01e-01 1.57e+01 ... (remaining 12912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5228 17.97 - 35.95: 562 35.95 - 53.92: 107 53.92 - 71.90: 26 71.90 - 89.87: 11 Dihedral angle restraints: 5934 sinusoidal: 2453 harmonic: 3481 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual 93.00 7.81 85.19 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual 93.00 175.50 -82.50 1 1.00e+01 1.00e-02 8.35e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 555 " pdb=" CB CYS A 555 " ideal model delta sinusoidal sigma weight residual -86.00 -16.01 -69.99 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 5931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1023 0.057 - 0.114: 327 0.114 - 0.170: 53 0.170 - 0.227: 12 0.227 - 0.284: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ILE A 43 " pdb=" N ILE A 43 " pdb=" C ILE A 43 " pdb=" CB ILE A 43 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE B 432 " pdb=" N ILE B 432 " pdb=" C ILE B 432 " pdb=" CB ILE B 432 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1415 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 158 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C ASN B 158 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN B 158 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 159 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 192 " 0.011 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C ALA B 192 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA B 192 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN B 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 168 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PRO B 168 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO B 168 " -0.014 2.00e-02 2.50e+03 pdb=" N SER B 169 " -0.012 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 140 2.54 - 3.13: 7929 3.13 - 3.72: 13565 3.72 - 4.31: 19045 4.31 - 4.90: 31401 Nonbonded interactions: 72080 Sorted by model distance: nonbonded pdb=" CB MET B 154 " pdb=" CE1 PHE B 156 " model vdw 1.947 3.740 nonbonded pdb=" O ARG A 403 " pdb=" OG SER A 433 " model vdw 2.029 3.040 nonbonded pdb=" OH TYR B 101 " pdb=" OE1 GLN D 26 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR A 391 " pdb=" OG1 THR A 422 " model vdw 2.154 3.040 nonbonded pdb=" O VAL B 437 " pdb=" OG1 THR B 464 " model vdw 2.163 3.040 ... (remaining 72075 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.007 0.066 9552 Z= 0.485 Angle : 0.902 8.671 12917 Z= 0.558 Chirality : 0.057 0.284 1418 Planarity : 0.005 0.043 1709 Dihedral : 14.971 89.870 3550 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.83 % Favored : 83.00 % Rotamer: Outliers : 2.83 % Allowed : 10.84 % Favored : 86.33 % 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: -5.33 (0.18), residues: 1206 helix: -5.02 (0.18), residues: 91 sheet: -3.65 (0.39), residues: 127 loop : -3.75 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 176 HIS 0.006 0.001 HIS B 409 PHE 0.020 0.002 PHE B 156 TYR 0.017 0.002 TYR A 447 ARG 0.004 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4767 (mm-30) outliers start: 30 outliers final: 5 residues processed: 87 average time/residue: 0.1904 time to fit residues: 24.4885 Evaluate side-chains 41 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 537 GLU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 419 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 0.0010 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 40 ASN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN A 597 HIS B 23 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 134 ASN B 193 GLN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN D 4 HIS D 14 GLN D 18 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.047368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032921 restraints weight = 64955.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.033587 restraints weight = 40888.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034117 restraints weight = 30123.488| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9552 Z= 0.256 Angle : 0.672 12.181 12917 Z= 0.348 Chirality : 0.047 0.202 1418 Planarity : 0.005 0.041 1709 Dihedral : 6.399 53.568 1306 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 2.64 % Allowed : 13.20 % Favored : 84.17 % 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: -4.37 (0.21), residues: 1206 helix: -4.41 (0.30), residues: 74 sheet: -3.29 (0.40), residues: 130 loop : -3.02 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 386 HIS 0.005 0.001 HIS D 18 PHE 0.010 0.001 PHE B 396 TYR 0.007 0.001 TYR A 586 ARG 0.006 0.001 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 253 MET cc_start: 0.9292 (mmt) cc_final: 0.8869 (mmm) REVERT: A 521 GLU cc_start: 0.9656 (mp0) cc_final: 0.9260 (tm-30) REVERT: B 229 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8866 (ttmt) REVERT: B 498 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7282 (p0) outliers start: 28 outliers final: 12 residues processed: 68 average time/residue: 0.1710 time to fit residues: 18.6835 Evaluate side-chains 52 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 498 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.047109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032515 restraints weight = 66493.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.033262 restraints weight = 40874.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033764 restraints weight = 29655.943| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9552 Z= 0.233 Angle : 0.627 13.238 12917 Z= 0.322 Chirality : 0.046 0.173 1418 Planarity : 0.004 0.041 1709 Dihedral : 5.793 47.944 1298 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 2.36 % Allowed : 16.02 % 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: -3.83 (0.22), residues: 1206 helix: -3.84 (0.37), residues: 72 sheet: -2.91 (0.42), residues: 130 loop : -2.65 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.011 0.001 HIS A 597 PHE 0.012 0.001 PHE B 31 TYR 0.011 0.001 TYR A 292 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 40 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 184 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: A 253 MET cc_start: 0.9289 (mmt) cc_final: 0.8911 (mmm) REVERT: B 152 MET cc_start: 0.8717 (tmm) cc_final: 0.8493 (tmm) REVERT: B 229 LYS cc_start: 0.9266 (ttmm) cc_final: 0.8812 (ttmt) outliers start: 25 outliers final: 14 residues processed: 63 average time/residue: 0.1591 time to fit residues: 16.3029 Evaluate side-chains 51 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 100 ASN A 483 HIS A 528 ASN A 597 HIS B 40 ASN B 252 GLN ** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.047011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.032827 restraints weight = 66105.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033555 restraints weight = 41101.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033949 restraints weight = 29965.234| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9552 Z= 0.191 Angle : 0.592 13.328 12917 Z= 0.304 Chirality : 0.045 0.172 1418 Planarity : 0.004 0.043 1709 Dihedral : 5.615 51.729 1298 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.92 % Allowed : 16.97 % Favored : 80.11 % 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: -3.38 (0.22), residues: 1206 helix: -3.08 (0.49), residues: 66 sheet: -2.71 (0.41), residues: 140 loop : -2.34 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 386 HIS 0.011 0.001 HIS A 597 PHE 0.009 0.001 PHE D 23 TYR 0.006 0.001 TYR A 586 ARG 0.003 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 71 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9122 (p) REVERT: A 98 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 253 MET cc_start: 0.9295 (mmt) cc_final: 0.8934 (mmm) REVERT: B 152 MET cc_start: 0.8807 (tmm) cc_final: 0.8600 (tmm) REVERT: B 229 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8799 (ttmt) REVERT: B 498 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7401 (p0) outliers start: 31 outliers final: 18 residues processed: 65 average time/residue: 0.1720 time to fit residues: 17.5393 Evaluate side-chains 56 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 60 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 chunk 59 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS B 442 ASN ** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.047270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032925 restraints weight = 65181.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033658 restraints weight = 40683.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.034165 restraints weight = 29492.986| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9552 Z= 0.152 Angle : 0.567 13.034 12917 Z= 0.289 Chirality : 0.044 0.156 1418 Planarity : 0.004 0.043 1709 Dihedral : 5.442 54.654 1298 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.64 % Allowed : 18.00 % Favored : 79.36 % 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: -3.13 (0.23), residues: 1206 helix: -2.88 (0.51), residues: 72 sheet: -2.55 (0.41), residues: 138 loop : -2.14 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 386 HIS 0.008 0.001 HIS A 597 PHE 0.010 0.001 PHE A 380 TYR 0.005 0.001 TYR B 292 ARG 0.008 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 253 MET cc_start: 0.9272 (mmt) cc_final: 0.8929 (mmm) REVERT: B 229 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8863 (ttmt) REVERT: B 498 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7602 (p0) outliers start: 28 outliers final: 17 residues processed: 65 average time/residue: 0.1635 time to fit residues: 17.5950 Evaluate side-chains 55 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 597 HIS B 134 ASN B 252 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 45 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.031334 restraints weight = 69009.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.032009 restraints weight = 43112.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.032544 restraints weight = 31686.828| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 9552 Z= 0.439 Angle : 0.754 14.894 12917 Z= 0.377 Chirality : 0.046 0.174 1418 Planarity : 0.005 0.041 1709 Dihedral : 6.139 57.043 1298 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 3.58 % Allowed : 18.94 % Favored : 77.47 % 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: -3.23 (0.22), residues: 1206 helix: -2.60 (0.51), residues: 72 sheet: -2.76 (0.40), residues: 140 loop : -2.21 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 386 HIS 0.006 0.001 HIS A 121 PHE 0.012 0.002 PHE C 17 TYR 0.011 0.001 TYR A 586 ARG 0.005 0.001 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 33 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8848 (pp) REVERT: A 253 MET cc_start: 0.9290 (mmt) cc_final: 0.8965 (mmm) REVERT: A 331 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7915 (p0) REVERT: B 229 LYS cc_start: 0.9282 (ttmm) cc_final: 0.8767 (ttmt) REVERT: B 244 MET cc_start: 0.9405 (mmm) cc_final: 0.9140 (mmm) REVERT: B 498 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7402 (p0) outliers start: 38 outliers final: 25 residues processed: 67 average time/residue: 0.1711 time to fit residues: 19.2136 Evaluate side-chains 60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS B 366 GLN B 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030883 restraints weight = 70223.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.031660 restraints weight = 44105.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.032107 restraints weight = 32233.178| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9552 Z= 0.407 Angle : 0.728 15.009 12917 Z= 0.364 Chirality : 0.046 0.174 1418 Planarity : 0.004 0.038 1709 Dihedral : 5.999 59.122 1298 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.18 % Favored : 86.82 % Rotamer: Outliers : 3.58 % Allowed : 19.04 % Favored : 77.38 % 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: -3.11 (0.23), residues: 1206 helix: -2.03 (0.58), residues: 66 sheet: -2.82 (0.40), residues: 140 loop : -2.15 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 140 HIS 0.006 0.001 HIS A 121 PHE 0.012 0.002 PHE B 412 TYR 0.009 0.001 TYR A 586 ARG 0.005 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 32 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8846 (pp) REVERT: A 253 MET cc_start: 0.9301 (mmt) cc_final: 0.8948 (mmm) REVERT: A 293 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: A 331 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 229 LYS cc_start: 0.9304 (ttmm) cc_final: 0.8782 (ttmt) REVERT: B 244 MET cc_start: 0.9382 (mmm) cc_final: 0.9137 (mmm) REVERT: B 498 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7313 (p0) outliers start: 38 outliers final: 27 residues processed: 66 average time/residue: 0.1558 time to fit residues: 17.1660 Evaluate side-chains 63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 597 HIS B 40 ASN B 134 ASN B 252 GLN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.046503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.032147 restraints weight = 67408.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032796 restraints weight = 41669.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033292 restraints weight = 30509.270| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9552 Z= 0.156 Angle : 0.611 13.772 12917 Z= 0.304 Chirality : 0.045 0.161 1418 Planarity : 0.004 0.040 1709 Dihedral : 5.413 55.107 1297 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 2.54 % Allowed : 19.89 % Favored : 77.57 % 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: -2.79 (0.23), residues: 1206 helix: -2.00 (0.58), residues: 73 sheet: -2.37 (0.44), residues: 125 loop : -1.95 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 386 HIS 0.004 0.001 HIS A 597 PHE 0.009 0.001 PHE A 380 TYR 0.006 0.001 TYR A 292 ARG 0.006 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 37 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.9332 (mmt) cc_final: 0.8913 (mmm) REVERT: B 244 MET cc_start: 0.9308 (mmm) cc_final: 0.9094 (mmm) REVERT: B 498 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7524 (p0) outliers start: 27 outliers final: 21 residues processed: 60 average time/residue: 0.1630 time to fit residues: 16.0152 Evaluate side-chains 55 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 597 HIS Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 0.0070 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 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 = 0.3347 r_free = 0.3347 target = 0.046887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032584 restraints weight = 66101.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033297 restraints weight = 41256.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.033873 restraints weight = 30064.903| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9552 Z= 0.145 Angle : 0.606 12.273 12917 Z= 0.300 Chirality : 0.045 0.175 1418 Planarity : 0.004 0.040 1709 Dihedral : 4.954 19.982 1296 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 2.07 % Allowed : 20.55 % Favored : 77.38 % 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: -2.59 (0.23), residues: 1206 helix: -1.75 (0.60), residues: 73 sheet: -2.09 (0.44), residues: 133 loop : -1.83 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.004 0.001 HIS A 594 PHE 0.009 0.001 PHE D 23 TYR 0.005 0.001 TYR A 275 ARG 0.005 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.9338 (tpt) cc_final: 0.8974 (tpt) REVERT: A 253 MET cc_start: 0.9330 (mmt) cc_final: 0.8940 (mmm) REVERT: B 229 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8886 (ttmt) REVERT: B 244 MET cc_start: 0.9289 (mmm) cc_final: 0.9075 (mmm) REVERT: B 498 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7544 (p0) outliers start: 22 outliers final: 16 residues processed: 55 average time/residue: 0.1682 time to fit residues: 15.4771 Evaluate side-chains 51 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 33 optimal weight: 0.0170 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS ** B 442 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 = 0.3334 r_free = 0.3334 target = 0.046369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.032172 restraints weight = 67950.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.032881 restraints weight = 42107.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033355 restraints weight = 30498.776| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9552 Z= 0.189 Angle : 0.617 11.256 12917 Z= 0.304 Chirality : 0.045 0.205 1418 Planarity : 0.004 0.039 1709 Dihedral : 4.961 19.346 1296 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 1.98 % Allowed : 20.83 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.23), residues: 1206 helix: -1.78 (0.58), residues: 78 sheet: -2.25 (0.43), residues: 140 loop : -1.77 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.005 0.001 HIS A 597 PHE 0.008 0.001 PHE B 412 TYR 0.005 0.001 TYR A 586 ARG 0.005 0.000 ARG A 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 30 MET cc_start: 0.9380 (tpt) cc_final: 0.8975 (tpt) REVERT: A 253 MET cc_start: 0.9337 (mmt) cc_final: 0.8984 (mmm) REVERT: B 229 LYS cc_start: 0.9297 (ttmm) cc_final: 0.8827 (ttmt) REVERT: B 498 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7552 (p0) outliers start: 21 outliers final: 18 residues processed: 53 average time/residue: 0.1556 time to fit residues: 13.9484 Evaluate side-chains 53 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 442 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 = 0.3331 r_free = 0.3331 target = 0.046305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.032107 restraints weight = 67553.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032757 restraints weight = 41179.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033239 restraints weight = 29714.678| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9552 Z= 0.202 Angle : 0.622 10.905 12917 Z= 0.306 Chirality : 0.045 0.202 1418 Planarity : 0.004 0.038 1709 Dihedral : 4.989 19.151 1296 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.17 % Allowed : 20.55 % Favored : 77.29 % 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: -2.54 (0.23), residues: 1206 helix: -1.65 (0.59), residues: 79 sheet: -2.23 (0.43), residues: 138 loop : -1.75 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 386 HIS 0.002 0.001 HIS A 121 PHE 0.007 0.001 PHE C 17 TYR 0.006 0.001 TYR A 586 ARG 0.005 0.000 ARG A 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.83 seconds wall clock time: 54 minutes 43.12 seconds (3283.12 seconds total)