Starting phenix.real_space_refine on Mon Mar 11 02:27:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v84_31789/03_2024/7v84_31789.pdb" } resolution = 3.0 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= -0.002 sd= 0.033 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 4238 2.51 5 N 1083 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6636 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} 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: "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: "C" 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: "D" 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: "E" 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: "G" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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 Time building chain proxies: 4.05, per 1000 atoms: 0.61 Number of scatterers: 6636 At special positions: 0 Unit cell: (102.3, 74.8, 126.5, 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 1278 8.00 N 1083 7.00 C 4238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 103 " " NAG E 1 " - " ASN F 322 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 432 " " NAG G 1 " - " ASN F 546 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 52.7% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.507A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.367A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.722A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 53 removed outlier: 4.030A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.342A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.648A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 Processing helix chain 'F' and resid 147 through 152 removed outlier: 4.084A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 175 through 193 removed outlier: 4.252A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.901A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.887A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.728A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.683A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.580A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.904A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.716A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.542A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 removed outlier: 3.517A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.590A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.637A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.864A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.532A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.606A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.552A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.782A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.598A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.663A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.981A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 735 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: 1.64 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2101 1.34 - 1.46: 1769 1.46 - 1.58: 2891 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6819 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.84e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6814 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.63: 215 106.63 - 113.47: 3613 113.47 - 120.30: 2520 120.30 - 127.14: 2820 127.14 - 133.98: 100 Bond angle restraints: 9268 Sorted by residual: angle pdb=" N GLY F 326 " pdb=" CA GLY F 326 " pdb=" C GLY F 326 " ideal model delta sigma weight residual 113.58 110.08 3.50 1.07e+00 8.73e-01 1.07e+01 angle pdb=" CA MET F 557 " pdb=" CB MET F 557 " pdb=" CG MET F 557 " ideal model delta sigma weight residual 114.10 119.57 -5.47 2.00e+00 2.50e-01 7.48e+00 angle pdb=" CB MET F 557 " pdb=" CG MET F 557 " pdb=" SD MET F 557 " ideal model delta sigma weight residual 112.70 120.39 -7.69 3.00e+00 1.11e-01 6.58e+00 angle pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sigma weight residual 113.21 118.73 -5.52 3.00e+00 1.11e-01 3.39e+00 angle pdb=" N ASP F 335 " pdb=" CA ASP F 335 " pdb=" C ASP F 335 " ideal model delta sigma weight residual 109.81 113.87 -4.06 2.21e+00 2.05e-01 3.37e+00 ... (remaining 9263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 3897 23.59 - 47.17: 245 47.17 - 70.76: 26 70.76 - 94.35: 10 94.35 - 117.94: 15 Dihedral angle restraints: 4193 sinusoidal: 1854 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 43.92 49.08 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS F 133 " pdb=" SG CYS F 133 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual -86.00 -120.26 34.26 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA PRO F 146 " pdb=" C PRO F 146 " pdb=" N GLY F 147 " pdb=" CA GLY F 147 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 988 0.106 - 0.212: 19 0.212 - 0.318: 1 0.318 - 0.424: 0 0.424 - 0.530: 1 Chirality restraints: 1009 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.27 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 1006 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 72 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.68e+00 pdb=" C PHE F 72 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE F 72 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU F 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 283 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO F 284 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 234 " -0.019 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO F 235 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " -0.017 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 462 2.74 - 3.28: 6514 3.28 - 3.82: 10579 3.82 - 4.36: 12110 4.36 - 4.90: 21228 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" OG1 THR F 20 " pdb=" OE1 GLU F 23 " model vdw 2.199 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.256 2.440 nonbonded pdb=" NE1 TRP F 271 " pdb=" O SER F 502 " model vdw 2.324 2.520 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.335 2.440 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.335 2.520 ... (remaining 50888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 2.430 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: 0.000 Extract box with map and model: 11.750 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.300 Find NCS groups from input model: 0.180 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.003 0.065 6819 Z= 0.197 Angle : 0.538 7.693 9268 Z= 0.266 Chirality : 0.045 0.530 1009 Planarity : 0.003 0.031 1182 Dihedral : 16.314 117.936 2672 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.29), residues: 793 helix: 0.79 (0.29), residues: 343 sheet: 1.04 (0.79), residues: 47 loop : -1.35 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 165 HIS 0.005 0.001 HIS F 378 PHE 0.008 0.001 PHE F 369 TYR 0.006 0.001 TYR F 50 ARG 0.007 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.700 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.2568 time to fit residues: 66.4572 Evaluate side-chains 38 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS F 81 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN F 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6819 Z= 0.186 Angle : 0.573 9.656 9268 Z= 0.269 Chirality : 0.045 0.407 1009 Planarity : 0.003 0.031 1182 Dihedral : 10.972 104.442 1139 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.71 % Allowed : 6.86 % Favored : 92.43 % 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: -0.13 (0.29), residues: 793 helix: 0.90 (0.29), residues: 356 sheet: 1.05 (0.80), residues: 47 loop : -1.18 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 69 HIS 0.004 0.001 HIS F 378 PHE 0.009 0.001 PHE F 327 TYR 0.010 0.001 TYR A 369 ARG 0.001 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.893 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 1.4869 time to fit residues: 65.9826 Evaluate side-chains 39 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 522 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6819 Z= 0.329 Angle : 0.616 9.661 9268 Z= 0.299 Chirality : 0.045 0.436 1009 Planarity : 0.004 0.032 1182 Dihedral : 8.897 105.962 1139 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.57 % Allowed : 11.43 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 793 helix: 0.66 (0.28), residues: 368 sheet: 0.91 (0.77), residues: 49 loop : -1.28 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 477 HIS 0.006 0.001 HIS F 505 PHE 0.015 0.001 PHE A 347 TYR 0.014 0.001 TYR F 385 ARG 0.004 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.708 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 43 average time/residue: 1.5852 time to fit residues: 71.7004 Evaluate side-chains 40 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS F 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6819 Z= 0.169 Angle : 0.542 9.621 9268 Z= 0.258 Chirality : 0.042 0.399 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.676 97.806 1139 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.00 % Allowed : 13.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 793 helix: 0.96 (0.28), residues: 359 sheet: 1.16 (0.80), residues: 47 loop : -1.28 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 PHE 0.009 0.001 PHE F 369 TYR 0.008 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.796 Fit side-chains REVERT: F 175 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8110 (pm20) outliers start: 7 outliers final: 1 residues processed: 44 average time/residue: 1.4228 time to fit residues: 66.0222 Evaluate side-chains 40 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6819 Z= 0.192 Angle : 0.544 9.672 9268 Z= 0.259 Chirality : 0.043 0.400 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.404 91.424 1139 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.43 % Allowed : 13.57 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 793 helix: 1.01 (0.28), residues: 360 sheet: 1.22 (0.81), residues: 47 loop : -1.24 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 401 PHE 0.010 0.001 PHE F 523 TYR 0.008 0.001 TYR F 50 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.712 Fit side-chains REVERT: F 175 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8154 (pm20) outliers start: 10 outliers final: 2 residues processed: 48 average time/residue: 1.3502 time to fit residues: 68.5903 Evaluate side-chains 40 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6819 Z= 0.252 Angle : 0.575 9.705 9268 Z= 0.276 Chirality : 0.044 0.406 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.374 88.743 1139 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.29 % Allowed : 14.57 % Favored : 84.14 % 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: -0.16 (0.29), residues: 793 helix: 0.94 (0.28), residues: 360 sheet: 0.99 (0.77), residues: 51 loop : -1.32 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.005 0.001 HIS F 505 PHE 0.011 0.001 PHE F 369 TYR 0.010 0.001 TYR A 453 ARG 0.003 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.805 Fit side-chains REVERT: F 81 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: F 175 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8172 (pm20) outliers start: 9 outliers final: 2 residues processed: 47 average time/residue: 1.4642 time to fit residues: 72.4873 Evaluate side-chains 42 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6819 Z= 0.178 Angle : 0.552 10.313 9268 Z= 0.263 Chirality : 0.043 0.385 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.215 85.787 1139 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.43 % Allowed : 15.29 % Favored : 83.29 % 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: -0.06 (0.29), residues: 793 helix: 1.01 (0.28), residues: 360 sheet: 1.18 (0.80), residues: 49 loop : -1.26 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 505 PHE 0.009 0.001 PHE F 369 TYR 0.008 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8891 (pt) cc_final: 0.8453 (pp) REVERT: F 81 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: F 175 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8114 (pm20) outliers start: 10 outliers final: 3 residues processed: 49 average time/residue: 1.3644 time to fit residues: 70.6250 Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 432 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6819 Z= 0.186 Angle : 0.565 10.234 9268 Z= 0.267 Chirality : 0.043 0.382 1009 Planarity : 0.003 0.026 1182 Dihedral : 7.145 83.732 1139 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.29 % Allowed : 15.29 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 793 helix: 1.04 (0.28), residues: 360 sheet: 1.19 (0.80), residues: 49 loop : -1.24 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 505 PHE 0.009 0.001 PHE F 369 TYR 0.008 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: F 81 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: F 175 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8101 (pm20) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 1.3931 time to fit residues: 69.1461 Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 432 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6819 Z= 0.160 Angle : 0.557 10.990 9268 Z= 0.262 Chirality : 0.042 0.371 1009 Planarity : 0.003 0.026 1182 Dihedral : 6.996 80.328 1139 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.00 % Allowed : 15.57 % Favored : 83.43 % 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: 0.02 (0.30), residues: 793 helix: 1.08 (0.28), residues: 360 sheet: 1.25 (0.80), residues: 49 loop : -1.22 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS A 519 PHE 0.008 0.001 PHE F 369 TYR 0.009 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: F 175 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8031 (pm20) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.3845 time to fit residues: 65.7636 Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 432 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS F 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6819 Z= 0.178 Angle : 0.573 10.263 9268 Z= 0.268 Chirality : 0.043 0.374 1009 Planarity : 0.003 0.026 1182 Dihedral : 6.995 77.305 1139 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.00 % Allowed : 15.43 % Favored : 83.57 % 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: 0.03 (0.30), residues: 793 helix: 1.12 (0.28), residues: 360 sheet: 1.28 (0.80), residues: 49 loop : -1.26 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS A 519 PHE 0.008 0.001 PHE F 369 TYR 0.009 0.001 TYR F 50 ARG 0.003 0.000 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: F 175 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8106 (pm20) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.3635 time to fit residues: 63.6186 Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 175 GLN Chi-restraints excluded: chain F residue 432 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.046153 restraints weight = 19937.849| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.61 r_work: 0.2563 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6819 Z= 0.190 Angle : 0.579 10.830 9268 Z= 0.272 Chirality : 0.043 0.376 1009 Planarity : 0.003 0.048 1182 Dihedral : 6.946 75.150 1139 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.86 % Allowed : 15.43 % Favored : 83.71 % 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: 0.03 (0.29), residues: 793 helix: 1.10 (0.28), residues: 360 sheet: 1.28 (0.80), residues: 49 loop : -1.24 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 505 PHE 0.009 0.001 PHE F 369 TYR 0.009 0.001 TYR F 50 ARG 0.003 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.28 seconds wall clock time: 38 minutes 31.32 seconds (2311.32 seconds total)