Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:34:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/02_2023/7xoc_33344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/02_2023/7xoc_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_33344/02_2023/7xoc_33344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/02_2023/7xoc_33344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/02_2023/7xoc_33344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoc_33344/02_2023/7xoc_33344.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 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 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 chiralities: 1 Time building chain proxies: 4.31, per 1000 atoms: 0.67 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 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: 0.33 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: 1.71 Time building geometry restraints manager: 2.51 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 - 20.55: 3790 20.55 - 41.09: 90 41.09 - 61.64: 11 61.64 - 82.18: 3 82.18 - 102.73: 4 Dihedral angle restraints: 3898 sinusoidal: 1589 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=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual 50.00 -52.73 102.73 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" C1 NAG B 2 " pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " ideal model delta sinusoidal sigma weight residual -50.00 39.14 -89.14 1 2.00e+01 2.50e-03 2.36e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 878 0.077 - 0.154: 58 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 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. 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: 6.610 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: 21.770 Check model and map are aligned: 0.110 Process input model: 20.980 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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= 0.128 Angle : 0.478 7.843 8977 Z= 0.290 Chirality : 0.042 0.384 942 Planarity : 0.004 0.058 1160 Dihedral : 9.173 102.729 2395 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.00 % 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: -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 *********************** 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 : 0.713 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 249 average time/residue: 1.0209 time to fit residues: 268.9707 Evaluate side-chains 189 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2135 time to fit residues: 1.4812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 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: 0.4980 chunk 70 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7318 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 6611 Z= 0.324 Angle : 0.616 6.956 8977 Z= 0.314 Chirality : 0.047 0.474 942 Planarity : 0.005 0.062 1160 Dihedral : 6.334 102.788 884 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 3.96 % 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: -0.74 (0.30), residues: 780 helix: 0.58 (0.28), residues: 380 sheet: 0.03 (0.60), residues: 43 loop : -1.78 (0.32), residues: 357 *********************** 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 221 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 0.758 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 209 average time/residue: 1.0979 time to fit residues: 241.8065 Evaluate side-chains 194 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.6410 time to fit residues: 4.5207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 ASN D 562 ASN D 578 ASN D 586 ASN A 414 GLN A 450 ASN A 505 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 6611 Z= 0.322 Angle : 0.592 8.219 8977 Z= 0.298 Chirality : 0.044 0.157 942 Planarity : 0.004 0.060 1160 Dihedral : 7.953 102.143 884 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 780 helix: 0.91 (0.28), residues: 376 sheet: 0.77 (0.66), residues: 43 loop : -1.41 (0.33), residues: 361 *********************** 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 201 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 0.854 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 191 average time/residue: 1.1646 time to fit residues: 234.8475 Evaluate side-chains 177 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.3529 time to fit residues: 3.1260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 0.0020 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS D 578 ASN A 417 ASN A 450 ASN A 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 6611 Z= 0.261 Angle : 0.567 7.694 8977 Z= 0.283 Chirality : 0.043 0.259 942 Planarity : 0.004 0.060 1160 Dihedral : 8.211 108.424 884 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 3.52 % 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: 0.10 (0.31), residues: 780 helix: 1.17 (0.29), residues: 381 sheet: 1.10 (0.69), residues: 43 loop : -1.33 (0.33), residues: 356 *********************** 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 199 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 190 average time/residue: 1.0708 time to fit residues: 214.9541 Evaluate side-chains 183 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 8 average time/residue: 0.6535 time to fit residues: 6.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.1980 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.0870 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 ASN D 373 HIS D 536 ASN D 562 ASN D 578 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 6611 Z= 0.294 Angle : 0.582 6.464 8977 Z= 0.290 Chirality : 0.043 0.144 942 Planarity : 0.004 0.058 1160 Dihedral : 8.262 108.708 884 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 2.93 % 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: 0.26 (0.31), residues: 780 helix: 1.31 (0.28), residues: 378 sheet: 1.23 (0.70), residues: 43 loop : -1.24 (0.33), residues: 359 *********************** 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 186 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 0.826 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 179 average time/residue: 1.0962 time to fit residues: 207.0937 Evaluate side-chains 171 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.1038 time to fit residues: 1.1970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.0020 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS ** D 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN A 409 GLN A 450 ASN A 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 6611 Z= 0.246 Angle : 0.562 5.664 8977 Z= 0.285 Chirality : 0.042 0.147 942 Planarity : 0.004 0.058 1160 Dihedral : 8.267 109.135 884 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.64 % 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: 0.39 (0.31), residues: 780 helix: 1.42 (0.28), residues: 378 sheet: 1.21 (0.70), residues: 43 loop : -1.16 (0.34), residues: 359 *********************** 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 188 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 179 average time/residue: 1.2099 time to fit residues: 229.1043 Evaluate side-chains 181 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 6 average time/residue: 0.6077 time to fit residues: 5.2229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 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: 0.7411 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 6611 Z= 0.264 Angle : 0.572 6.499 8977 Z= 0.286 Chirality : 0.042 0.150 942 Planarity : 0.004 0.057 1160 Dihedral : 8.281 108.944 884 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 3.08 % 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: 0.47 (0.31), residues: 780 helix: 1.50 (0.28), residues: 377 sheet: 1.26 (0.72), residues: 43 loop : -1.14 (0.33), residues: 360 *********************** 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: 21 poor density : 177 time to evaluate : 0.775 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 188 average time/residue: 1.0441 time to fit residues: 207.6821 Evaluate side-chains 185 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 8 average time/residue: 0.2755 time to fit residues: 3.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.0000 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 42 optimal weight: 0.3980 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 ASN D 322 HIS D 378 HIS D 562 ASN D 578 ASN A 409 GLN A 450 ASN A 460 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 6611 Z= 0.210 Angle : 0.550 8.312 8977 Z= 0.275 Chirality : 0.041 0.206 942 Planarity : 0.004 0.059 1160 Dihedral : 8.260 109.379 884 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 2.20 % 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: 0.61 (0.31), residues: 780 helix: 1.65 (0.28), residues: 377 sheet: 1.25 (0.73), residues: 43 loop : -1.09 (0.33), residues: 360 *********************** 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 185 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 0.690 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 179 average time/residue: 0.9876 time to fit residues: 187.1394 Evaluate side-chains 180 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 6 average time/residue: 0.4635 time to fit residues: 3.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.0030 chunk 21 optimal weight: 0.0870 chunk 63 optimal weight: 0.0980 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 0.1980 chunk 46 optimal weight: 0.0970 chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.0966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 HIS D 522 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: 0.7347 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 6611 Z= 0.168 Angle : 0.538 6.574 8977 Z= 0.270 Chirality : 0.040 0.204 942 Planarity : 0.004 0.059 1160 Dihedral : 8.216 110.020 884 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.61 % 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: 0.85 (0.31), residues: 780 helix: 1.90 (0.29), residues: 371 sheet: 1.20 (0.71), residues: 43 loop : -0.97 (0.33), residues: 366 *********************** 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 185 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 183 average time/residue: 1.0214 time to fit residues: 197.6295 Evaluate side-chains 183 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 0.705 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1415 time to fit residues: 1.4047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0040 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 6 optimal weight: 0.0370 chunk 47 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.0050 chunk 9 optimal weight: 0.3980 overall best weight: 0.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 6611 Z= 0.162 Angle : 0.545 8.148 8977 Z= 0.270 Chirality : 0.040 0.188 942 Planarity : 0.004 0.061 1160 Dihedral : 8.183 110.181 884 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.31), residues: 780 helix: 1.93 (0.28), residues: 371 sheet: 1.27 (0.73), residues: 43 loop : -0.92 (0.33), residues: 366 ********************** 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 188 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 187 average time/residue: 1.1306 time to fit residues: 223.8266 Evaluate side-chains 186 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 4 average time/residue: 0.1292 time to fit residues: 1.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.2980 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.0020 chunk 63 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 overall best weight: 0.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 572 ASN 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 = 0.3581 r_free = 0.3581 target = 0.121435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109562 restraints weight = 9107.859| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.99 r_work: 0.3295 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 6611 Z= 0.174 Angle : 0.554 10.076 8977 Z= 0.277 Chirality : 0.041 0.208 942 Planarity : 0.004 0.058 1160 Dihedral : 8.190 109.931 884 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 780 helix: 1.89 (0.28), residues: 377 sheet: 1.29 (0.71), residues: 43 loop : -0.80 (0.34), residues: 360 =============================================================================== Job complete usr+sys time: 3887.83 seconds wall clock time: 69 minutes 41.48 seconds (4181.48 seconds total)