Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:13:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ddo_30655/02_2023/7ddo_30655.pdb" } resolution = 3.4 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= 0.005 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 "A ASP 30": "OD1" <-> "OD2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" 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: 6468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1534 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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: 6.32, per 1000 atoms: 0.98 Number of scatterers: 6468 At special positions: 0 Unit cell: (101.362, 96.3937, 106.331, 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 1230 8.00 N 1067 7.00 C 4133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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 NAG-ASN " NAG A 902 " - " ASN A 546 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 55.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.599A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.737A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.621A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.564A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 143 through 155 removed outlier: 4.233A pdb=" N ASN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.192A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.720A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.643A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.666A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.619A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.780A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.929A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.715A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.815A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.174A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.815A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 875 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: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2077 1.34 - 1.46: 1660 1.46 - 1.58: 2854 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6649 Sorted by residual: bond pdb=" CA VAL C 524 " pdb=" CB VAL C 524 " ideal model delta sigma weight residual 1.531 1.545 -0.014 1.11e-02 8.12e+03 1.61e+00 bond pdb=" N PRO C 337 " pdb=" CA PRO C 337 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 8.72e-01 bond pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 1.463 1.455 0.008 9.30e-03 1.16e+04 6.59e-01 bond pdb=" CA VAL A 283 " pdb=" CB VAL A 283 " ideal model delta sigma weight residual 1.531 1.543 -0.012 1.48e-02 4.57e+03 6.36e-01 bond pdb=" C GLU A 35 " pdb=" O GLU A 35 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.23e-02 6.61e+03 6.24e-01 ... (remaining 6644 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 218 106.89 - 113.67: 3507 113.67 - 120.45: 2693 120.45 - 127.22: 2528 127.22 - 134.00: 96 Bond angle restraints: 9042 Sorted by residual: angle pdb=" N VAL C 524 " pdb=" CA VAL C 524 " pdb=" C VAL C 524 " ideal model delta sigma weight residual 106.53 110.71 -4.18 1.41e+00 5.03e-01 8.81e+00 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.22 109.75 3.47 1.23e+00 6.61e-01 7.95e+00 angle pdb=" N GLU A 589 " pdb=" CA GLU A 589 " pdb=" C GLU A 589 " ideal model delta sigma weight residual 109.81 115.20 -5.39 2.21e+00 2.05e-01 5.95e+00 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 120.97 124.12 -3.15 1.48e+00 4.57e-01 4.53e+00 angle pdb=" N VAL A 506 " pdb=" CA VAL A 506 " pdb=" C VAL A 506 " ideal model delta sigma weight residual 111.45 109.52 1.93 9.30e-01 1.16e+00 4.30e+00 ... (remaining 9037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3510 17.31 - 34.63: 314 34.63 - 51.94: 61 51.94 - 69.25: 15 69.25 - 86.56: 12 Dihedral angle restraints: 3912 sinusoidal: 1588 harmonic: 2324 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 6.44 86.56 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 25.85 67.15 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -22.59 -63.41 1 1.00e+01 1.00e-02 5.30e+01 ... (remaining 3909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 579 0.028 - 0.056: 247 0.056 - 0.084: 80 0.084 - 0.111: 47 0.111 - 0.139: 6 Chirality restraints: 959 Sorted by residual: chirality pdb=" CA GLU A 589 " pdb=" N GLU A 589 " pdb=" C GLU A 589 " pdb=" CB GLU A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA THR C 372 " pdb=" N THR C 372 " pdb=" C THR C 372 " pdb=" CB THR C 372 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 956 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 583 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 235 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 463 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.018 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 79 2.63 - 3.20: 5772 3.20 - 3.76: 10356 3.76 - 4.33: 14430 4.33 - 4.90: 23518 Nonbonded interactions: 54155 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.062 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 183 " pdb=" OD2 ASP A 509 " model vdw 2.226 2.440 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.228 2.440 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.260 2.440 ... (remaining 54150 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 4133 2.51 5 N 1067 2.21 5 O 1230 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=0.50 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.640 Check model and map are aligned: 0.090 Process input model: 24.440 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 0.023 6649 Z= 0.153 Angle : 0.535 6.846 9042 Z= 0.309 Chirality : 0.039 0.139 959 Planarity : 0.003 0.038 1169 Dihedral : 14.101 86.321 2401 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -1.39 (0.27), residues: 788 helix: -0.30 (0.23), residues: 403 sheet: -1.61 (0.64), residues: 57 loop : -1.49 (0.31), residues: 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.760 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1836 time to fit residues: 34.9258 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0960 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 58 ASN A 210 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN A 338 ASN A 340 GLN C 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6649 Z= 0.233 Angle : 0.548 6.971 9042 Z= 0.277 Chirality : 0.042 0.146 959 Planarity : 0.004 0.038 1169 Dihedral : 3.981 17.449 885 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 788 helix: 0.59 (0.25), residues: 405 sheet: -0.97 (0.67), residues: 57 loop : -1.01 (0.32), residues: 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.789 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 117 average time/residue: 0.1619 time to fit residues: 26.4838 Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0794 time to fit residues: 2.0046 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6649 Z= 0.207 Angle : 0.517 5.918 9042 Z= 0.264 Chirality : 0.041 0.133 959 Planarity : 0.004 0.038 1169 Dihedral : 3.984 16.961 885 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 788 helix: 1.00 (0.25), residues: 406 sheet: -0.69 (0.68), residues: 57 loop : -0.74 (0.33), residues: 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.784 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 114 average time/residue: 0.1535 time to fit residues: 25.1571 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0650 time to fit residues: 1.4173 ------------------------------------------------------------------------------- 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: 0.7980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 6649 Z= 0.156 Angle : 0.505 7.197 9042 Z= 0.255 Chirality : 0.040 0.132 959 Planarity : 0.004 0.036 1169 Dihedral : 3.850 16.145 885 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.01 % 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: 0.52 (0.30), residues: 788 helix: 1.28 (0.26), residues: 405 sheet: -0.63 (0.69), residues: 57 loop : -0.59 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 0.918 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 114 average time/residue: 0.1699 time to fit residues: 27.7018 Evaluate side-chains 110 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0884 time to fit residues: 1.6383 ------------------------------------------------------------------------------- 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: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6649 Z= 0.196 Angle : 0.521 6.681 9042 Z= 0.266 Chirality : 0.041 0.128 959 Planarity : 0.004 0.038 1169 Dihedral : 3.981 19.260 885 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.86 % 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: 0.63 (0.30), residues: 788 helix: 1.32 (0.26), residues: 405 sheet: 0.13 (0.75), residues: 50 loop : -0.62 (0.33), residues: 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 0.748 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 108 average time/residue: 0.1518 time to fit residues: 23.4334 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0883 time to fit residues: 1.1874 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS C 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 6649 Z= 0.244 Angle : 0.558 6.859 9042 Z= 0.285 Chirality : 0.042 0.132 959 Planarity : 0.004 0.038 1169 Dihedral : 4.102 18.876 885 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.01 % 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: 0.56 (0.30), residues: 788 helix: 1.21 (0.26), residues: 406 sheet: 0.12 (0.74), residues: 50 loop : -0.58 (0.34), residues: 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.960 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.1555 time to fit residues: 24.4545 Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0782 time to fit residues: 1.7542 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6649 Z= 0.191 Angle : 0.546 9.282 9042 Z= 0.274 Chirality : 0.041 0.132 959 Planarity : 0.004 0.038 1169 Dihedral : 4.017 18.493 885 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 788 helix: 1.29 (0.26), residues: 405 sheet: 0.06 (0.73), residues: 50 loop : -0.53 (0.34), residues: 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 0.855 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 110 average time/residue: 0.1674 time to fit residues: 26.3479 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1564 time to fit residues: 1.4139 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 68 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 6649 Z= 0.190 Angle : 0.556 8.902 9042 Z= 0.278 Chirality : 0.041 0.132 959 Planarity : 0.004 0.035 1169 Dihedral : 4.007 18.098 885 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.01 % 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: 0.69 (0.30), residues: 788 helix: 1.32 (0.26), residues: 405 sheet: -0.01 (0.73), residues: 50 loop : -0.49 (0.33), residues: 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.728 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 104 average time/residue: 0.1478 time to fit residues: 22.0084 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0751 time to fit residues: 1.4115 ------------------------------------------------------------------------------- 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: 0.6980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS C 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 6649 Z= 0.240 Angle : 0.580 9.186 9042 Z= 0.291 Chirality : 0.042 0.146 959 Planarity : 0.004 0.038 1169 Dihedral : 4.114 18.545 885 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 788 helix: 1.21 (0.25), residues: 411 sheet: 0.02 (0.73), residues: 50 loop : -0.47 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.860 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.1533 time to fit residues: 23.3654 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0998 time to fit residues: 1.3718 ------------------------------------------------------------------------------- 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: 40.0000 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 6649 Z= 0.183 Angle : 0.554 8.753 9042 Z= 0.277 Chirality : 0.041 0.138 959 Planarity : 0.004 0.036 1169 Dihedral : 4.013 17.451 885 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.72 % 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: 788 helix: 1.33 (0.26), residues: 405 sheet: -0.06 (0.73), residues: 50 loop : -0.40 (0.34), residues: 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.769 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 111 average time/residue: 0.1496 time to fit residues: 23.9866 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0476 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.0020 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 41 optimal weight: 5.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116455 restraints weight = 13972.158| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.83 r_work: 0.3159 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 6649 Z= 0.144 Angle : 0.544 8.610 9042 Z= 0.273 Chirality : 0.041 0.135 959 Planarity : 0.004 0.033 1169 Dihedral : 3.914 17.287 885 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 788 helix: 1.54 (0.26), residues: 402 sheet: -0.09 (0.73), residues: 50 loop : -0.35 (0.34), residues: 336 =============================================================================== Job complete usr+sys time: 1652.15 seconds wall clock time: 31 minutes 1.81 seconds (1861.81 seconds total)