Starting phenix.real_space_refine on Mon Mar 11 00:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/03_2024/7xoc_33344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/03_2024/7xoc_33344.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/7xoc_33344/03_2024/7xoc_33344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/03_2024/7xoc_33344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/03_2024/7xoc_33344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/03_2024/7xoc_33344.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= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4109 2.51 5 N 1074 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6432 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1551 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Time building chain proxies: 3.83, per 1000 atoms: 0.60 Number of scatterers: 6432 At special positions: 0 Unit cell: (97.232, 71.688, 121.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1211 8.00 N 1074 7.00 C 4109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.23 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 53 " " NAG D 902 " - " ASN D 546 " Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 53.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.809A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.805A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.754A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.176A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.742A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.604A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.347A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.235A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.510A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.614A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.183A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.734A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.567A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.735A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.516A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.665A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.531A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.511A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.691A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.199A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.595A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.698A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.511A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.519A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 798 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: 1.90 Time building geometry restraints manager: 2.60 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: 1669 1.33 - 1.45: 1458 1.45 - 1.58: 3426 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6611 Sorted by residual: bond pdb=" CA ALA A 376 " pdb=" CB ALA A 376 " ideal model delta sigma weight residual 1.533 1.487 0.046 1.69e-02 3.50e+03 7.37e+00 bond pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta sigma weight residual 1.468 1.442 0.026 1.20e-02 6.94e+03 4.58e+00 bond pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.41e-02 5.03e+03 4.38e+00 bond pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.23e-02 6.61e+03 4.28e+00 bond pdb=" N PHE A 371 " pdb=" CA PHE A 371 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.31e-02 5.83e+03 3.76e+00 ... (remaining 6606 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 247 107.23 - 113.92: 3517 113.92 - 120.61: 2776 120.61 - 127.30: 2345 127.30 - 133.99: 92 Bond angle restraints: 8977 Sorted by residual: angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 111.03 103.19 7.84 1.54e+00 4.22e-01 2.59e+01 angle pdb=" CA TYR A 369 " pdb=" C TYR A 369 " pdb=" O TYR A 369 " ideal model delta sigma weight residual 121.88 117.65 4.23 1.13e+00 7.83e-01 1.40e+01 angle pdb=" N PHE A 371 " pdb=" CA PHE A 371 " pdb=" CB PHE A 371 " ideal model delta sigma weight residual 110.25 115.65 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" CA PHE A 375 " pdb=" CB PHE A 375 " pdb=" CG PHE A 375 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" O PHE A 371 " ideal model delta sigma weight residual 121.53 115.87 5.66 1.74e+00 3.30e-01 1.06e+01 ... (remaining 8972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 3837 21.31 - 42.61: 91 42.61 - 63.92: 16 63.92 - 85.22: 6 85.22 - 106.53: 8 Dihedral angle restraints: 3958 sinusoidal: 1649 harmonic: 2309 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -169.86 83.86 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual 175.11 68.58 106.53 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual 53.78 -52.73 106.51 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 874 0.077 - 0.154: 62 0.154 - 0.231: 3 0.231 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN D 53 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 939 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO D 500 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 368 " 0.009 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C LEU A 368 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 368 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 369 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 372 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C ALA A 372 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA A 372 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO A 373 " -0.010 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 147 2.70 - 3.25: 6238 3.25 - 3.80: 10006 3.80 - 4.35: 13444 4.35 - 4.90: 22297 Nonbonded interactions: 52132 Sorted by model distance: nonbonded pdb=" CA CYS D 344 " pdb=" SG CYS D 361 " model vdw 2.149 3.064 nonbonded pdb=" O TYR D 279 " pdb=" CG2 VAL D 283 " model vdw 2.232 3.460 nonbonded pdb=" OG SER D 84 " pdb=" OE1 GLU D 87 " model vdw 2.241 2.440 nonbonded pdb=" OH TYR D 41 " pdb=" OG1 THR A 500 " model vdw 2.252 2.440 nonbonded pdb=" OD2 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.269 2.440 ... (remaining 52127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 13.450 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: 0.020 Extract box with map and model: 21.860 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 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 : 0.002 0.046 6611 Z= 0.149 Angle : 0.494 7.843 8977 Z= 0.293 Chirality : 0.042 0.384 942 Planarity : 0.004 0.058 1160 Dihedral : 10.956 106.527 2455 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: -2.11 (0.27), residues: 780 helix: -0.53 (0.26), residues: 382 sheet: -1.52 (0.52), residues: 47 loop : -2.37 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 165 HIS 0.001 0.000 HIS D 322 PHE 0.014 0.001 PHE A 371 TYR 0.009 0.001 TYR A 369 ARG 0.001 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: D 302 TRP cc_start: 0.7000 (m-10) cc_final: 0.6668 (m-10) REVERT: D 477 TRP cc_start: 0.7441 (t-100) cc_final: 0.7223 (t-100) REVERT: A 489 TYR cc_start: 0.7850 (m-80) cc_final: 0.7618 (m-80) outliers start: 0 outliers final: 1 residues processed: 249 average time/residue: 1.0100 time to fit residues: 266.1143 Evaluate side-chains 189 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 ASN D 51 ASN D 60 GLN D 76 GLN D 86 GLN D 89 GLN D 96 GLN D 101 GLN D 188 ASN D 322 HIS D 394 ASN D 417 HIS D 472 GLN D 493 HIS D 562 ASN D 572 ASN D 586 ASN D 599 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6611 Z= 0.313 Angle : 0.614 7.604 8977 Z= 0.306 Chirality : 0.047 0.436 942 Planarity : 0.004 0.062 1160 Dihedral : 6.970 54.837 946 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.96 % Allowed : 15.98 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 780 helix: 0.52 (0.28), residues: 381 sheet: 0.04 (0.60), residues: 43 loop : -1.80 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.007 0.002 HIS D 373 PHE 0.028 0.002 PHE D 308 TYR 0.022 0.002 TYR A 453 ARG 0.004 0.001 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: D 325 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6650 (mm110) REVERT: D 364 VAL cc_start: 0.7478 (m) cc_final: 0.7268 (t) REVERT: D 366 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7232 (ttp) REVERT: D 406 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6437 (mm-30) REVERT: D 471 GLU cc_start: 0.6719 (mp0) cc_final: 0.6463 (mp0) REVERT: D 517 THR cc_start: 0.7464 (p) cc_final: 0.6983 (t) outliers start: 27 outliers final: 9 residues processed: 212 average time/residue: 1.1222 time to fit residues: 250.7962 Evaluate side-chains 201 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 53 optimal weight: 0.0040 overall best weight: 0.2230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 ASN D 522 GLN D 562 ASN D 578 ASN D 586 ASN A 414 GLN A 450 ASN A 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6611 Z= 0.196 Angle : 0.567 8.949 8977 Z= 0.273 Chirality : 0.042 0.217 942 Planarity : 0.004 0.061 1160 Dihedral : 5.881 67.605 944 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.25 % Allowed : 18.91 % Favored : 76.83 % 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: -0.12 (0.31), residues: 780 helix: 1.03 (0.28), residues: 378 sheet: 0.59 (0.64), residues: 43 loop : -1.41 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 PHE 0.023 0.002 PHE D 428 TYR 0.015 0.002 TYR D 516 ARG 0.004 0.000 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: D 95 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7039 (ttp-170) REVERT: D 98 GLN cc_start: 0.6721 (tt0) cc_final: 0.6481 (mt0) REVERT: D 152 MET cc_start: 0.7437 (mmm) cc_final: 0.7205 (mmp) REVERT: D 169 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6034 (mtm-85) REVERT: D 325 GLN cc_start: 0.6996 (mm-40) cc_final: 0.6780 (tp40) REVERT: D 366 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7238 (ttp) REVERT: D 517 THR cc_start: 0.7302 (p) cc_final: 0.6815 (t) outliers start: 29 outliers final: 11 residues processed: 208 average time/residue: 1.0107 time to fit residues: 222.2405 Evaluate side-chains 201 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 562 ASN D 578 ASN A 414 GLN A 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6611 Z= 0.215 Angle : 0.572 8.782 8977 Z= 0.277 Chirality : 0.042 0.261 942 Planarity : 0.004 0.061 1160 Dihedral : 5.242 55.350 944 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 20.53 % Favored : 76.25 % 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: 0.12 (0.31), residues: 780 helix: 1.24 (0.28), residues: 380 sheet: 0.90 (0.67), residues: 43 loop : -1.36 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 PHE 0.024 0.001 PHE D 428 TYR 0.018 0.001 TYR D 516 ARG 0.004 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: D 366 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7198 (ttp) REVERT: D 517 THR cc_start: 0.7386 (p) cc_final: 0.6758 (t) REVERT: D 585 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7460 (mp) REVERT: A 350 VAL cc_start: 0.7897 (p) cc_final: 0.7598 (t) REVERT: A 421 TYR cc_start: 0.8204 (m-10) cc_final: 0.7956 (m-80) outliers start: 22 outliers final: 10 residues processed: 202 average time/residue: 1.0825 time to fit residues: 230.7413 Evaluate side-chains 197 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 0.0070 chunk 52 optimal weight: 0.0060 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 25 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 overall best weight: 0.1310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6611 Z= 0.162 Angle : 0.543 8.950 8977 Z= 0.263 Chirality : 0.041 0.254 942 Planarity : 0.003 0.029 1160 Dihedral : 5.024 52.968 944 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.23 % Allowed : 21.85 % Favored : 74.93 % 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: 0.42 (0.31), residues: 780 helix: 1.54 (0.29), residues: 377 sheet: 1.05 (0.68), residues: 43 loop : -1.24 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 163 HIS 0.002 0.001 HIS D 265 PHE 0.025 0.001 PHE D 428 TYR 0.014 0.001 TYR D 516 ARG 0.004 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: D 517 THR cc_start: 0.7225 (p) cc_final: 0.6652 (t) REVERT: A 350 VAL cc_start: 0.7896 (p) cc_final: 0.7577 (t) outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 1.0763 time to fit residues: 230.7316 Evaluate side-chains 193 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 39 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 42 optimal weight: 0.7980 overall best weight: 0.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 562 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6611 Z= 0.219 Angle : 0.574 7.122 8977 Z= 0.279 Chirality : 0.041 0.172 942 Planarity : 0.003 0.038 1160 Dihedral : 4.972 48.554 944 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.81 % Allowed : 21.26 % Favored : 74.93 % 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: 0.54 (0.31), residues: 780 helix: 1.60 (0.29), residues: 377 sheet: 1.17 (0.70), residues: 43 loop : -1.13 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 PHE 0.027 0.001 PHE D 428 TYR 0.017 0.001 TYR D 516 ARG 0.005 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.7452 (mmm) cc_final: 0.7224 (mmp) REVERT: D 517 THR cc_start: 0.7343 (p) cc_final: 0.6699 (t) REVERT: A 350 VAL cc_start: 0.7873 (p) cc_final: 0.7589 (t) REVERT: A 421 TYR cc_start: 0.8159 (m-10) cc_final: 0.7917 (m-80) outliers start: 26 outliers final: 15 residues processed: 193 average time/residue: 1.0053 time to fit residues: 205.3501 Evaluate side-chains 189 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 75 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.1556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN D 552 GLN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6611 Z= 0.177 Angle : 0.565 6.972 8977 Z= 0.273 Chirality : 0.041 0.170 942 Planarity : 0.003 0.043 1160 Dihedral : 4.926 46.346 944 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.37 % Allowed : 22.43 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.31), residues: 780 helix: 1.67 (0.28), residues: 377 sheet: 1.26 (0.70), residues: 43 loop : -1.03 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.003 0.001 HIS D 353 PHE 0.027 0.001 PHE D 428 TYR 0.014 0.001 TYR D 516 ARG 0.006 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: D 517 THR cc_start: 0.7268 (p) cc_final: 0.6623 (t) REVERT: D 548 THR cc_start: 0.7766 (t) cc_final: 0.7551 (m) REVERT: A 350 VAL cc_start: 0.7859 (p) cc_final: 0.7583 (t) REVERT: A 421 TYR cc_start: 0.8150 (m-10) cc_final: 0.7890 (m-80) outliers start: 23 outliers final: 14 residues processed: 184 average time/residue: 1.1173 time to fit residues: 216.6977 Evaluate side-chains 188 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6611 Z= 0.223 Angle : 0.590 7.685 8977 Z= 0.287 Chirality : 0.042 0.155 942 Planarity : 0.004 0.064 1160 Dihedral : 4.955 42.675 944 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.37 % Allowed : 22.29 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.31), residues: 780 helix: 1.65 (0.28), residues: 377 sheet: 1.38 (0.72), residues: 43 loop : -0.96 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 322 PHE 0.028 0.002 PHE D 428 TYR 0.019 0.001 TYR D 516 ARG 0.010 0.001 ARG D 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: D 249 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6373 (mtt) REVERT: D 517 THR cc_start: 0.7286 (p) cc_final: 0.6698 (t) REVERT: D 548 THR cc_start: 0.7732 (t) cc_final: 0.7439 (m) REVERT: A 350 VAL cc_start: 0.7875 (p) cc_final: 0.7625 (t) REVERT: A 421 TYR cc_start: 0.8179 (m-10) cc_final: 0.7962 (m-80) REVERT: A 477 ASN cc_start: 0.8113 (m110) cc_final: 0.7886 (m110) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 1.0683 time to fit residues: 205.7125 Evaluate side-chains 183 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0030 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 63 optimal weight: 0.0970 chunk 66 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.1026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6611 Z= 0.166 Angle : 0.569 7.000 8977 Z= 0.278 Chirality : 0.040 0.167 942 Planarity : 0.004 0.050 1160 Dihedral : 4.904 41.890 944 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 23.90 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.32), residues: 780 helix: 1.83 (0.29), residues: 373 sheet: 1.41 (0.71), residues: 43 loop : -0.83 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 566 HIS 0.002 0.001 HIS D 373 PHE 0.029 0.001 PHE D 428 TYR 0.013 0.001 TYR A 380 ARG 0.008 0.000 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: D 517 THR cc_start: 0.7253 (p) cc_final: 0.6627 (t) REVERT: D 577 ARG cc_start: 0.6970 (ptp90) cc_final: 0.6631 (ptp90) REVERT: A 350 VAL cc_start: 0.7894 (p) cc_final: 0.7605 (t) REVERT: A 477 ASN cc_start: 0.8098 (m110) cc_final: 0.7861 (m110) outliers start: 18 outliers final: 10 residues processed: 181 average time/residue: 1.0921 time to fit residues: 208.4322 Evaluate side-chains 187 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 177 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 117 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN D 578 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6611 Z= 0.290 Angle : 0.641 11.065 8977 Z= 0.314 Chirality : 0.044 0.196 942 Planarity : 0.004 0.039 1160 Dihedral : 5.034 39.507 944 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.91 % Allowed : 25.07 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.31), residues: 780 helix: 1.71 (0.28), residues: 377 sheet: 1.47 (0.71), residues: 43 loop : -0.82 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 163 HIS 0.004 0.001 HIS D 373 PHE 0.030 0.002 PHE D 428 TYR 0.022 0.002 TYR A 421 ARG 0.005 0.000 ARG D 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: D 249 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6312 (mtt) REVERT: D 517 THR cc_start: 0.7388 (p) cc_final: 0.6814 (t) REVERT: A 350 VAL cc_start: 0.7940 (p) cc_final: 0.7649 (t) REVERT: A 477 ASN cc_start: 0.8120 (m110) cc_final: 0.7881 (m110) outliers start: 13 outliers final: 8 residues processed: 173 average time/residue: 1.0488 time to fit residues: 191.5558 Evaluate side-chains 174 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 chunk 63 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.1980 overall best weight: 0.1316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN A 409 GLN A 450 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108179 restraints weight = 9167.653| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.01 r_work: 0.3273 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6611 Z= 0.183 Angle : 0.605 11.620 8977 Z= 0.293 Chirality : 0.041 0.179 942 Planarity : 0.003 0.039 1160 Dihedral : 4.940 38.782 944 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.91 % Allowed : 25.51 % Favored : 72.58 % 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: 0.97 (0.31), residues: 780 helix: 1.89 (0.28), residues: 373 sheet: 1.41 (0.71), residues: 43 loop : -0.79 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 163 HIS 0.003 0.001 HIS D 373 PHE 0.029 0.001 PHE D 428 TYR 0.014 0.001 TYR A 421 ARG 0.004 0.000 ARG D 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.32 seconds wall clock time: 75 minutes 9.95 seconds (4509.95 seconds total)