Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 5 19:49:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/05_2023/7x93_33065_trim.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 C 4191 2.51 5 N 1093 2.21 5 O 1265 1.98 5 H 6162 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "D TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "G TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 406": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3057 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "D" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3113 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1797 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1581 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3091 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: 5.90, per 1000 atoms: 0.46 Number of scatterers: 12742 At special positions: 0 Unit cell: (92.848, 103.625, 102.796, 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) S 31 16.00 O 1265 8.00 N 1093 7.00 C 4191 6.00 H 6162 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN D 343 " " NAG G1301 " - " ASN G 343 " Time building additional restraints: 10.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 15.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.013A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.526A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.150A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.665A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.698A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 364 through 370 removed outlier: 4.318A pdb=" N LEU D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.829A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.597A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'G' and resid 337 through 343 removed outlier: 3.557A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 353 Processing helix chain 'G' and resid 364 through 371 removed outlier: 4.340A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 389 removed outlier: 4.135A pdb=" N ASN G 388 " --> pdb=" O THR G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.140A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AA6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.531A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE E 34 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.626A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 105 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP F 87 " --> pdb=" O HIS F 40 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.626A pdb=" N VAL F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 105 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AB5, first strand: chain 'G' and resid 391 through 392 removed outlier: 3.524A pdb=" N PHE G 392 " --> pdb=" O VAL G 524 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL G 524 " --> pdb=" O PHE G 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.612A pdb=" N TYR G 489 " --> pdb=" O TYR G 473 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 411 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: 4.38 Time building geometry restraints manager: 10.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6161 1.03 - 1.23: 112 1.23 - 1.43: 2915 1.43 - 1.62: 3698 1.62 - 1.82: 33 Bond restraints: 12919 Sorted by residual: bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.410 1.455 -0.045 2.00e-02 2.50e+03 5.15e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" C5 MAN C 4 " pdb=" O5 MAN C 4 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 NAG G1301 " pdb=" O5 NAG G1301 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 12914 not shown) Histogram of bond angle deviations from ideal: 73.73 - 85.77: 6 85.77 - 97.82: 0 97.82 - 109.86: 9233 109.86 - 121.90: 11519 121.90 - 133.95: 2353 Bond angle restraints: 23111 Sorted by residual: angle pdb=" C ALA A 344 " pdb=" CA ALA A 344 " pdb=" HA ALA A 344 " ideal model delta sigma weight residual 109.00 73.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ALA A 344 " pdb=" CA ALA A 344 " pdb=" HA ALA A 344 " ideal model delta sigma weight residual 109.00 75.95 33.05 3.00e+00 1.11e-01 1.21e+02 angle pdb=" N ALA A 344 " pdb=" CA ALA A 344 " pdb=" HA ALA A 344 " ideal model delta sigma weight residual 110.00 77.34 32.66 3.00e+00 1.11e-01 1.19e+02 angle pdb=" CG2 THR A 478 " pdb=" CB THR A 478 " pdb=" HB THR A 478 " ideal model delta sigma weight residual 108.00 80.59 27.41 3.00e+00 1.11e-01 8.35e+01 angle pdb=" OG1 THR A 478 " pdb=" CB THR A 478 " pdb=" HB THR A 478 " ideal model delta sigma weight residual 109.00 83.22 25.78 3.00e+00 1.11e-01 7.38e+01 ... (remaining 23106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 4780 16.06 - 32.11: 388 32.11 - 48.17: 88 48.17 - 64.23: 13 64.23 - 80.29: 2 Dihedral angle restraints: 5271 sinusoidal: 2303 harmonic: 2968 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -130.42 44.42 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 488 " pdb=" CB CYS D 488 " ideal model delta sinusoidal sigma weight residual -86.00 -126.32 40.32 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -124.14 38.14 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 5268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 995 0.289 - 0.579: 2 0.579 - 0.868: 0 0.868 - 1.157: 0 1.157 - 1.447: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" CB THR A 478 " pdb=" CA THR A 478 " pdb=" OG1 THR A 478 " pdb=" CG2 THR A 478 " both_signs ideal model delta sigma weight residual False 2.55 1.10 1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" CA ALA A 344 " pdb=" N ALA A 344 " pdb=" C ALA A 344 " pdb=" CB ALA A 344 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 995 not shown) Planarity restraints: 1970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 346 " -0.083 9.50e-02 1.11e+02 2.78e-02 9.20e-01 pdb=" NE ARG D 346 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 346 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 346 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 346 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 346 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 346 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG F 56 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.26e-01 pdb=" N PRO F 57 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 506 " -0.012 5.00e-02 4.00e+02 1.85e-02 5.50e-01 pdb=" N PRO G 507 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO G 507 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO G 507 " -0.010 5.00e-02 4.00e+02 ... (remaining 1967 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 477 2.16 - 2.77: 23876 2.77 - 3.38: 33387 3.38 - 3.99: 43760 3.99 - 4.60: 67306 Nonbonded interactions: 168806 Sorted by model distance: nonbonded pdb=" H GLN A 498 " pdb=" OD1 ASN A 501 " model vdw 1.554 1.850 nonbonded pdb=" O ASP F 28 " pdb=" H GLY F 31 " model vdw 1.591 1.850 nonbonded pdb=" HA ALA A 344 " pdb=" HB3 ALA A 344 " model vdw 1.634 1.952 nonbonded pdb="HH22 ARG E 67 " pdb=" OD2 ASP E 90 " model vdw 1.652 1.850 nonbonded pdb=" OD1 ASN G 439 " pdb=" HG SER G 443 " model vdw 1.657 1.850 ... (remaining 168801 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 'D' and ((resid 331 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name H \ D21 or name HD22)) or resid 332 through 528)) selection = (chain 'G' and ((resid 331 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name HA or name HB2 or name HB3 or name H \ D21 or name HD22)) or resid 332 through 528)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.190 Extract box with map and model: 3.350 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 40.860 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 0.054 6757 Z= 0.201 Angle : 0.539 11.479 9195 Z= 0.261 Chirality : 0.065 1.447 998 Planarity : 0.003 0.036 1189 Dihedral : 13.005 80.287 2354 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.25 % 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: -0.89 (0.30), residues: 818 helix: -1.63 (0.60), residues: 81 sheet: 0.43 (0.38), residues: 198 loop : -0.83 (0.27), residues: 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4941 time to fit residues: 62.9708 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6757 Z= 0.172 Angle : 0.523 11.379 9195 Z= 0.264 Chirality : 0.063 1.424 998 Planarity : 0.003 0.028 1189 Dihedral : 3.408 14.038 923 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % 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: -1.00 (0.30), residues: 818 helix: -1.76 (0.61), residues: 75 sheet: 0.43 (0.39), residues: 198 loop : -0.95 (0.27), residues: 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 93 average time/residue: 0.5160 time to fit residues: 61.1589 Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1687 time to fit residues: 2.4743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 6757 Z= 0.239 Angle : 0.517 11.382 9195 Z= 0.261 Chirality : 0.063 1.426 998 Planarity : 0.003 0.023 1189 Dihedral : 3.538 14.371 923 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.48 % Favored : 93.40 % Rotamer Outliers : 0.28 % 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: -1.19 (0.30), residues: 818 helix: -1.71 (0.59), residues: 81 sheet: 0.30 (0.38), residues: 198 loop : -1.10 (0.27), residues: 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 87 average time/residue: 0.5045 time to fit residues: 55.0272 Evaluate side-chains 85 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3774 time to fit residues: 2.2407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 6757 Z= 0.232 Angle : 0.519 11.376 9195 Z= 0.262 Chirality : 0.063 1.425 998 Planarity : 0.003 0.025 1189 Dihedral : 3.574 14.896 923 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.03 % 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: -1.24 (0.29), residues: 818 helix: -1.83 (0.56), residues: 87 sheet: 0.27 (0.38), residues: 198 loop : -1.11 (0.27), residues: 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.5038 time to fit residues: 55.6369 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1917 time to fit residues: 1.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 6757 Z= 0.267 Angle : 0.533 11.387 9195 Z= 0.270 Chirality : 0.063 1.427 998 Planarity : 0.003 0.026 1189 Dihedral : 3.666 14.973 923 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.54 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.29), residues: 818 helix: -1.82 (0.57), residues: 87 sheet: 0.23 (0.38), residues: 198 loop : -1.16 (0.27), residues: 533 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.4877 time to fit residues: 51.5618 Evaluate side-chains 81 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1857 time to fit residues: 1.9652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6757 Z= 0.217 Angle : 0.529 11.406 9195 Z= 0.268 Chirality : 0.063 1.431 998 Planarity : 0.003 0.027 1189 Dihedral : 3.622 14.961 923 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.85 % Favored : 93.03 % Rotamer Outliers : 0.28 % 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: -1.30 (0.29), residues: 818 helix: -1.85 (0.56), residues: 85 sheet: 0.22 (0.37), residues: 200 loop : -1.16 (0.27), residues: 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.5050 time to fit residues: 51.8908 Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6757 Z= 0.174 Angle : 0.525 11.420 9195 Z= 0.265 Chirality : 0.063 1.433 998 Planarity : 0.003 0.025 1189 Dihedral : 3.577 14.707 923 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.60 % Favored : 93.28 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.29), residues: 818 helix: -1.77 (0.56), residues: 85 sheet: 0.26 (0.38), residues: 200 loop : -1.11 (0.27), residues: 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 84 average time/residue: 0.5099 time to fit residues: 55.0664 Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1813 time to fit residues: 1.9250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6757 Z= 0.175 Angle : 0.521 11.425 9195 Z= 0.262 Chirality : 0.063 1.433 998 Planarity : 0.003 0.024 1189 Dihedral : 3.550 14.570 923 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.52 % Rotamer Outliers : 0.28 % 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: -1.11 (0.29), residues: 818 helix: -1.48 (0.61), residues: 73 sheet: 0.26 (0.37), residues: 200 loop : -1.05 (0.27), residues: 545 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.5045 time to fit residues: 52.1016 Evaluate side-chains 78 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1324 time to fit residues: 1.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.028 6757 Z= 0.305 Angle : 0.553 11.398 9195 Z= 0.279 Chirality : 0.063 1.431 998 Planarity : 0.003 0.028 1189 Dihedral : 3.743 14.749 923 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.56 % Favored : 91.32 % Rotamer Outliers : 0.28 % 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: -1.31 (0.29), residues: 818 helix: -1.56 (0.58), residues: 79 sheet: 0.15 (0.37), residues: 200 loop : -1.21 (0.27), residues: 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.5179 time to fit residues: 50.1814 Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2049 time to fit residues: 1.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5996 > 50: distance: 142 - 194: 37.074 distance: 149 - 206: 35.953 distance: 168 - 227: 36.237 distance: 186 - 194: 34.249 distance: 194 - 195: 56.429 distance: 194 - 202: 40.614 distance: 195 - 198: 56.292 distance: 196 - 206: 39.644 distance: 198 - 204: 40.578 distance: 198 - 205: 39.968 distance: 206 - 207: 39.378 distance: 206 - 218: 40.776 distance: 207 - 208: 56.978 distance: 207 - 210: 40.139 distance: 207 - 219: 39.362 distance: 208 - 227: 40.350 distance: 210 - 211: 39.625 distance: 210 - 220: 39.283 distance: 210 - 221: 40.426 distance: 211 - 212: 25.777 distance: 212 - 214: 14.520 distance: 212 - 222: 14.121 distance: 213 - 215: 39.147 distance: 213 - 223: 40.852 distance: 214 - 216: 40.338 distance: 214 - 224: 39.821 distance: 215 - 216: 40.059 distance: 216 - 217: 41.004 distance: 217 - 226: 40.318 distance: 227 - 235: 9.081 distance: 228 - 229: 34.585 distance: 229 - 230: 4.945 distance: 229 - 241: 6.326 distance: 231 - 237: 40.293 distance: 232 - 234: 54.137 distance: 234 - 239: 4.651 distance: 234 - 240: 34.598 distance: 241 - 242: 55.828 distance: 241 - 253: 40.362 distance: 242 - 243: 40.621 distance: 243 - 244: 57.118 distance: 245 - 255: 39.507 distance: 262 - 263: 10.495 distance: 262 - 271: 40.052 distance: 263 - 264: 57.523 distance: 263 - 266: 8.472 distance: 263 - 272: 41.692 distance: 264 - 265: 48.024 distance: 264 - 284: 42.307 distance: 266 - 267: 40.896 distance: 268 - 269: 39.391 distance: 269 - 270: 40.078 distance: 270 - 282: 46.101 distance: 270 - 283: 40.511 distance: 288 - 294: 14.264 distance: 291 - 300: 56.858 distance: 291 - 302: 39.845 distance: 303 - 309: 40.087 distance: 304 - 307: 57.551 distance: 304 - 310: 39.689 distance: 305 - 317: 40.345 distance: 307 - 308: 39.861 distance: 309 - 316: 40.132 distance: 317 - 318: 56.061 distance: 319 - 320: 39.595 distance: 321 - 322: 40.994 distance: 321 - 327: 56.226 distance: 321 - 328: 40.289 distance: 329 - 337: 40.191 distance: 330 - 331: 39.664 distance: 331 - 341: 56.567 distance: 333 - 339: 39.350 distance: 333 - 340: 40.027 distance: 334 - 336: 40.904 distance: 341 - 342: 53.820 distance: 341 - 352: 55.995 distance: 342 - 343: 35.473 distance: 342 - 345: 6.137 distance: 342 - 353: 5.602 distance: 343 - 344: 6.021 distance: 343 - 361: 31.484 distance: 345 - 346: 56.940 distance: 345 - 354: 40.627 distance: 345 - 355: 39.123 distance: 346 - 347: 53.191 distance: 346 - 348: 40.105 distance: 347 - 349: 34.692 distance: 347 - 356: 40.855 distance: 348 - 357: 40.169 distance: 349 - 358: 25.393 distance: 350 - 359: 6.717 distance: 351 - 360: 39.697