Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:34:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yad_33709/04_2023/7yad_33709.pdb" } resolution = 2.66 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4267 2.51 5 N 1141 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "B" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "M" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1606 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "C" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 979 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1499 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.19, per 1000 atoms: 0.62 Number of scatterers: 6728 At special positions: 0 Unit cell: (111.89, 136.01, 88.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1291 8.00 N 1141 7.00 C 4267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.03 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 3 " NAG-ASN " NAG F 1 " - " ASN M 343 " " NAG G 1 " - " ASN E 343 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 16 sheets defined 11.7% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.903A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.068A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 Processing helix chain 'M' and resid 349 through 353 removed outlier: 3.967A pdb=" N TRP M 353 " --> pdb=" O VAL M 350 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 370 removed outlier: 3.879A pdb=" N TYR M 369 " --> pdb=" O TYR M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 390 removed outlier: 4.332A pdb=" N ASN M 388 " --> pdb=" O THR M 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU M 390 " --> pdb=" O LEU M 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 removed outlier: 3.997A pdb=" N ARG M 408 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 438 through 443 removed outlier: 3.553A pdb=" N SER M 443 " --> pdb=" O ASN M 439 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 505 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.928A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.617A pdb=" N PHE E 342 " --> pdb=" O PHE E 338 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 343' Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.769A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.921A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.761A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 116 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.761A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 5 removed outlier: 5.702A pdb=" N THR B 70 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLN B 27 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N SER B 68 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N VAL B 29 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N SER B 66 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.800A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN M 354 " --> pdb=" O SER M 399 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN M 394 " --> pdb=" O GLU M 516 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL M 433 " --> pdb=" O LYS M 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS M 378 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'M' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.756A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.845A pdb=" N ASP D 71 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.225A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 86 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.225A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN D 91 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.959A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 397 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 452 through 454 209 hydrogen bonds defined for protein. 525 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: 1.83 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2149 1.35 - 1.47: 1932 1.47 - 1.60: 2784 1.60 - 1.72: 0 1.72 - 1.84: 35 Bond restraints: 6900 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA ALA M 520 " pdb=" CB ALA M 520 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" C5 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.71: 137 105.71 - 112.77: 3511 112.77 - 119.83: 2213 119.83 - 126.89: 3428 126.89 - 133.95: 85 Bond angle restraints: 9374 Sorted by residual: angle pdb=" C LEU D 13 " pdb=" N SER D 14 " pdb=" CA SER D 14 " ideal model delta sigma weight residual 120.49 128.46 -7.97 1.42e+00 4.96e-01 3.15e+01 angle pdb=" CA LYS E 386 " pdb=" CB LYS E 386 " pdb=" CG LYS E 386 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.75e+00 angle pdb=" C HIS E 505 " pdb=" N GLN E 506 " pdb=" CA GLN E 506 " ideal model delta sigma weight residual 120.68 125.29 -4.61 1.52e+00 4.33e-01 9.19e+00 angle pdb=" CA PRO D 81 " pdb=" N PRO D 81 " pdb=" CD PRO D 81 " ideal model delta sigma weight residual 112.00 108.19 3.81 1.40e+00 5.10e-01 7.40e+00 angle pdb=" CA CYS M 379 " pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " ideal model delta sigma weight residual 114.40 120.41 -6.01 2.30e+00 1.89e-01 6.82e+00 ... (remaining 9369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 3619 17.19 - 34.39: 321 34.39 - 51.58: 52 51.58 - 68.77: 8 68.77 - 85.96: 3 Dihedral angle restraints: 4003 sinusoidal: 1565 harmonic: 2438 Sorted by residual: dihedral pdb=" CB CYS M 379 " pdb=" SG CYS M 379 " pdb=" SG CYS M 432 " pdb=" CB CYS M 432 " ideal model delta sinusoidal sigma weight residual 93.00 31.66 61.34 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CA ALA M 520 " pdb=" C ALA M 520 " pdb=" N PRO M 521 " pdb=" CA PRO M 521 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual -86.00 -129.46 43.46 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 4000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 630 0.032 - 0.064: 249 0.064 - 0.097: 80 0.097 - 0.129: 54 0.129 - 0.161: 6 Chirality restraints: 1019 Sorted by residual: chirality pdb=" CA PRO D 81 " pdb=" N PRO D 81 " pdb=" C PRO D 81 " pdb=" CB PRO D 81 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE B 76 " pdb=" N ILE B 76 " pdb=" C ILE B 76 " pdb=" CB ILE B 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1016 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 80 " 0.046 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO D 81 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 81 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 81 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 385 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR E 385 " 0.033 2.00e-02 2.50e+03 pdb=" O THR E 385 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 386 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA M 520 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO M 521 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO M 521 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO M 521 " 0.021 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 230 2.71 - 3.26: 6147 3.26 - 3.81: 9889 3.81 - 4.35: 12177 4.35 - 4.90: 21925 Nonbonded interactions: 50368 Sorted by model distance: nonbonded pdb=" OD1 ASP E 442 " pdb=" OH TYR E 451 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR M 369 " pdb=" O PRO M 384 " model vdw 2.175 2.440 nonbonded pdb=" NH2 ARG E 457 " pdb=" OD1 ASN E 460 " model vdw 2.219 2.520 nonbonded pdb=" O ASN M 439 " pdb=" OG SER M 443 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 12 " pdb=" OE2 GLU B 105 " model vdw 2.254 2.440 ... (remaining 50363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 1 through 124) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 105) } ncs_group { reference = chain 'E' selection = (chain 'M' and resid 332 through 516) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.710 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: 27.330 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6900 Z= 0.231 Angle : 0.555 7.971 9374 Z= 0.293 Chirality : 0.044 0.161 1019 Planarity : 0.004 0.068 1203 Dihedral : 12.577 85.964 2431 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.22 (0.28), residues: 836 helix: -3.96 (0.55), residues: 33 sheet: 0.49 (0.32), residues: 281 loop : -1.40 (0.25), residues: 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.8834 time to fit residues: 139.2985 Evaluate side-chains 137 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 59 ASN M 439 ASN ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6900 Z= 0.226 Angle : 0.544 7.959 9374 Z= 0.287 Chirality : 0.044 0.181 1019 Planarity : 0.004 0.040 1203 Dihedral : 4.398 29.783 945 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.45 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.06 (0.28), residues: 836 helix: -4.09 (0.43), residues: 41 sheet: 0.78 (0.32), residues: 285 loop : -1.35 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 132 average time/residue: 0.7807 time to fit residues: 111.3288 Evaluate side-chains 131 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.8712 time to fit residues: 2.9540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN M 439 ASN ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 6900 Z= 0.260 Angle : 0.537 7.774 9374 Z= 0.282 Chirality : 0.044 0.178 1019 Planarity : 0.004 0.041 1203 Dihedral : 4.431 30.967 945 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.86 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.14 (0.28), residues: 836 helix: -4.74 (0.30), residues: 40 sheet: 0.81 (0.31), residues: 283 loop : -1.42 (0.25), residues: 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 137 average time/residue: 0.7342 time to fit residues: 109.2724 Evaluate side-chains 136 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.1570 time to fit residues: 1.9266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 43 GLN M 439 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6900 Z= 0.226 Angle : 0.520 8.172 9374 Z= 0.272 Chirality : 0.044 0.215 1019 Planarity : 0.004 0.043 1203 Dihedral : 4.355 31.182 945 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.09 (0.28), residues: 836 helix: -4.73 (0.31), residues: 38 sheet: 0.87 (0.31), residues: 283 loop : -1.42 (0.26), residues: 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 136 average time/residue: 0.7594 time to fit residues: 111.8695 Evaluate side-chains 139 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1046 time to fit residues: 1.5461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 59 optimal weight: 0.0000 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 43 GLN M 439 ASN ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6900 Z= 0.181 Angle : 0.515 8.639 9374 Z= 0.267 Chirality : 0.044 0.193 1019 Planarity : 0.004 0.044 1203 Dihedral : 4.250 30.085 945 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.14 % Favored : 94.74 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.04 (0.28), residues: 836 helix: -4.52 (0.38), residues: 44 sheet: 0.93 (0.31), residues: 282 loop : -1.35 (0.26), residues: 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 0.6730 time to fit residues: 109.3058 Evaluate side-chains 143 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1296 time to fit residues: 1.4815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN M 439 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 6900 Z= 0.329 Angle : 0.574 9.126 9374 Z= 0.297 Chirality : 0.045 0.173 1019 Planarity : 0.004 0.046 1203 Dihedral : 4.566 34.388 945 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.12 (0.28), residues: 836 helix: -4.73 (0.31), residues: 38 sheet: 0.90 (0.31), residues: 281 loop : -1.46 (0.26), residues: 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 0.7322 time to fit residues: 121.8567 Evaluate side-chains 153 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 3 residues processed: 10 average time/residue: 0.1103 time to fit residues: 2.8200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 6900 Z= 0.273 Angle : 0.584 10.203 9374 Z= 0.298 Chirality : 0.045 0.178 1019 Planarity : 0.004 0.051 1203 Dihedral : 4.514 33.620 945 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.10 % Favored : 93.78 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.11 (0.28), residues: 836 helix: -4.75 (0.30), residues: 38 sheet: 0.94 (0.31), residues: 282 loop : -1.48 (0.25), residues: 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 139 average time/residue: 0.6870 time to fit residues: 104.1627 Evaluate side-chains 139 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.0921 time to fit residues: 1.6615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 6900 Z= 0.339 Angle : 0.609 11.593 9374 Z= 0.310 Chirality : 0.046 0.178 1019 Planarity : 0.004 0.053 1203 Dihedral : 4.677 35.179 945 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.58 % Favored : 93.30 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.21 (0.28), residues: 836 helix: -4.78 (0.29), residues: 38 sheet: 0.85 (0.31), residues: 283 loop : -1.54 (0.25), residues: 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 139 average time/residue: 0.7165 time to fit residues: 108.4666 Evaluate side-chains 148 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 9 average time/residue: 0.2733 time to fit residues: 4.0169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN M 439 ASN ** M 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 6900 Z= 0.280 Angle : 0.589 13.028 9374 Z= 0.298 Chirality : 0.045 0.168 1019 Planarity : 0.004 0.054 1203 Dihedral : 4.588 33.728 945 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.02 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.20 (0.28), residues: 836 helix: -4.79 (0.28), residues: 38 sheet: 0.85 (0.31), residues: 284 loop : -1.54 (0.25), residues: 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 142 average time/residue: 0.7153 time to fit residues: 110.6277 Evaluate side-chains 144 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1205 time to fit residues: 1.3764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 65 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 388 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 6900 Z= 0.283 Angle : 0.600 12.911 9374 Z= 0.304 Chirality : 0.045 0.173 1019 Planarity : 0.004 0.055 1203 Dihedral : 4.590 34.050 945 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.34 % Favored : 93.54 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.24 (0.28), residues: 836 helix: -4.79 (0.29), residues: 38 sheet: 0.85 (0.31), residues: 283 loop : -1.58 (0.25), residues: 515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 152 average time/residue: 0.6841 time to fit residues: 113.6484 Evaluate side-chains 152 residues out of total 717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1492 time to fit residues: 1.8055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 388 ASN ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 439 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.151912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129289 restraints weight = 10246.623| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.50 r_work: 0.3701 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6900 Z= 0.196 Angle : 0.562 12.732 9374 Z= 0.285 Chirality : 0.044 0.159 1019 Planarity : 0.004 0.057 1203 Dihedral : 4.358 32.014 945 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.14 (0.28), residues: 836 helix: -4.78 (0.29), residues: 38 sheet: 0.89 (0.31), residues: 288 loop : -1.51 (0.26), residues: 510 =============================================================================== Job complete usr+sys time: 3079.89 seconds wall clock time: 55 minutes 17.00 seconds (3317.00 seconds total)