Starting phenix.real_space_refine on Thu Sep 26 09:49:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/09_2024/7x93_33065_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/09_2024/7x93_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_33065/09_2024/7x93_33065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/09_2024/7x93_33065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/09_2024/7x93_33065_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x93_33065/09_2024/7x93_33065_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.73, per 1000 atoms: 0.53 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 - 3.00 Amino acid : True - 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: 3.27 Conformation dependent library (CDL) restraints added in 1.0 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: 0.98 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: 4.13 Time building geometry restraints manager: 3.93 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: 0.00 - 7.05: 23101 7.05 - 14.11: 4 14.11 - 21.16: 0 21.16 - 28.22: 3 28.22 - 35.27: 3 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 - 24.16: 5971 24.16 - 48.33: 327 48.33 - 72.49: 68 72.49 - 96.65: 10 96.65 - 120.82: 5 Dihedral angle restraints: 6381 sinusoidal: 3413 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 6378 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 2.450 nonbonded pdb=" O ASP F 28 " pdb=" H GLY F 31 " model vdw 1.591 2.450 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 2.450 nonbonded pdb=" OD1 ASN G 439 " pdb=" HG SER G 443 " model vdw 1.657 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.700 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.210 Find NCS groups from input model: 0.300 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- 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 : 14.998 120.819 2516 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 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 436 HIS 0.004 0.001 HIS A 519 PHE 0.008 0.001 PHE F 101 TYR 0.009 0.001 TYR D 369 ARG 0.005 0.000 ARG F 8 *********************** 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 : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8374 (m-30) cc_final: 0.8127 (m-30) REVERT: A 493 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7854 (tm-30) REVERT: D 417 LYS cc_start: 0.9337 (tppt) cc_final: 0.9016 (tppt) REVERT: D 467 ASP cc_start: 0.7996 (t0) cc_final: 0.7745 (t70) REVERT: D 486 PHE cc_start: 0.8782 (p90) cc_final: 0.8572 (p90) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4906 time to fit residues: 62.4405 Evaluate side-chains 85 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN G 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0907 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= 0.220 Angle : 0.542 11.378 9195 Z= 0.272 Chirality : 0.064 1.424 998 Planarity : 0.003 0.036 1189 Dihedral : 10.275 116.310 1085 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Rotamer: Outliers : 0.43 % Allowed : 4.99 % Favored : 94.59 % 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: -1.05 (0.30), residues: 818 helix: -2.03 (0.54), residues: 86 sheet: 0.51 (0.39), residues: 190 loop : -0.94 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 353 HIS 0.002 0.001 HIS G 519 PHE 0.015 0.001 PHE G 486 TYR 0.014 0.001 TYR G 380 ARG 0.003 0.000 ARG F 8 *********************** 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 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.928 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: A 420 ASP cc_start: 0.8389 (m-30) cc_final: 0.8180 (m-30) REVERT: D 467 ASP cc_start: 0.8087 (t0) cc_final: 0.7808 (t0) REVERT: D 486 PHE cc_start: 0.8777 (p90) cc_final: 0.8561 (p90) outliers start: 3 outliers final: 3 residues processed: 94 average time/residue: 0.4914 time to fit residues: 58.3097 Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain F residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8278 moved from start: 0.1040 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= 0.187 Angle : 0.523 11.372 9195 Z= 0.263 Chirality : 0.064 1.423 998 Planarity : 0.003 0.034 1189 Dihedral : 9.152 116.524 1085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 0.57 % Allowed : 6.84 % Favored : 92.59 % 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: -1.17 (0.30), residues: 818 helix: -2.27 (0.51), residues: 92 sheet: 0.30 (0.38), residues: 198 loop : -0.94 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE G 486 TYR 0.006 0.001 TYR G 380 ARG 0.003 0.000 ARG F 8 *********************** 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 96 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.962 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: A 420 ASP cc_start: 0.8380 (m-30) cc_final: 0.8166 (m-30) REVERT: A 484 GLU cc_start: 0.7677 (tp30) cc_final: 0.7378 (tp30) REVERT: D 406 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: D 417 LYS cc_start: 0.9331 (tppt) cc_final: 0.8862 (tppt) REVERT: D 467 ASP cc_start: 0.8114 (t0) cc_final: 0.7770 (t0) REVERT: D 486 PHE cc_start: 0.8828 (p90) cc_final: 0.8572 (p90) outliers start: 4 outliers final: 3 residues processed: 94 average time/residue: 0.4917 time to fit residues: 58.2349 Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain G residue 444 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 0.0020 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6757 Z= 0.161 Angle : 0.518 11.384 9195 Z= 0.259 Chirality : 0.064 1.425 998 Planarity : 0.003 0.031 1189 Dihedral : 8.637 115.320 1085 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 0.57 % Allowed : 7.69 % Favored : 91.74 % 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: -1.07 (0.30), residues: 818 helix: -2.29 (0.56), residues: 80 sheet: 0.37 (0.38), residues: 195 loop : -0.89 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 436 HIS 0.001 0.000 HIS E 35 PHE 0.008 0.001 PHE G 486 TYR 0.006 0.001 TYR E 53 ARG 0.003 0.000 ARG F 8 *********************** 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 95 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 1.015 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: A 420 ASP cc_start: 0.8353 (m-30) cc_final: 0.8122 (m-30) REVERT: A 484 GLU cc_start: 0.7721 (tp30) cc_final: 0.7405 (tp30) REVERT: D 406 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: D 417 LYS cc_start: 0.9319 (tppt) cc_final: 0.8798 (tppt) REVERT: D 467 ASP cc_start: 0.8128 (t0) cc_final: 0.7793 (t0) REVERT: D 486 PHE cc_start: 0.8822 (p90) cc_final: 0.8535 (p90) outliers start: 4 outliers final: 1 residues processed: 93 average time/residue: 0.4900 time to fit residues: 58.2277 Evaluate side-chains 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain F residue 77 ILE 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: 5.9990 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8310 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6757 Z= 0.294 Angle : 0.546 11.381 9195 Z= 0.275 Chirality : 0.064 1.427 998 Planarity : 0.003 0.036 1189 Dihedral : 8.478 113.733 1085 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.58 % Favored : 92.30 % Rotamer: Outliers : 0.71 % Allowed : 8.55 % Favored : 90.74 % 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: -1.29 (0.29), residues: 818 helix: -2.25 (0.50), residues: 92 sheet: 0.30 (0.38), residues: 193 loop : -1.07 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.002 0.001 HIS G 519 PHE 0.009 0.001 PHE F 101 TYR 0.008 0.001 TYR A 380 ARG 0.003 0.000 ARG F 8 *********************** 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 88 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.924 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: A 420 ASP cc_start: 0.8358 (m-30) cc_final: 0.8125 (m-30) REVERT: A 484 GLU cc_start: 0.7722 (tp30) cc_final: 0.7442 (tp30) REVERT: D 406 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: D 417 LYS cc_start: 0.9330 (tppt) cc_final: 0.8869 (tppt) REVERT: D 467 ASP cc_start: 0.8157 (t0) cc_final: 0.7772 (t0) REVERT: D 486 PHE cc_start: 0.8871 (p90) cc_final: 0.8490 (p90) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.5005 time to fit residues: 53.1266 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain F residue 77 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8283 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6757 Z= 0.161 Angle : 0.526 11.408 9195 Z= 0.264 Chirality : 0.064 1.430 998 Planarity : 0.003 0.033 1189 Dihedral : 8.200 112.074 1085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.74 % Rotamer: Outliers : 0.28 % Allowed : 9.40 % Favored : 90.31 % 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: -1.13 (0.29), residues: 818 helix: -2.11 (0.54), residues: 86 sheet: 0.30 (0.38), residues: 198 loop : -0.94 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS E 35 PHE 0.006 0.001 PHE G 486 TYR 0.006 0.001 TYR F 88 ARG 0.003 0.000 ARG F 8 *********************** 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 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.047 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: A 420 ASP cc_start: 0.8259 (m-30) cc_final: 0.8036 (m-30) REVERT: A 484 GLU cc_start: 0.7718 (tp30) cc_final: 0.7437 (tp30) REVERT: D 406 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: D 417 LYS cc_start: 0.9318 (tppt) cc_final: 0.8840 (tppt) REVERT: D 467 ASP cc_start: 0.8126 (t0) cc_final: 0.7813 (t70) REVERT: D 486 PHE cc_start: 0.8866 (p90) cc_final: 0.8465 (p90) outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.5322 time to fit residues: 56.4895 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 406 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6757 Z= 0.141 Angle : 0.516 11.421 9195 Z= 0.258 Chirality : 0.064 1.433 998 Planarity : 0.003 0.031 1189 Dihedral : 7.920 109.402 1085 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 0.43 % Allowed : 9.83 % Favored : 89.74 % 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: -1.01 (0.29), residues: 818 helix: -2.10 (0.56), residues: 80 sheet: 0.38 (0.38), residues: 198 loop : -0.86 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.002 0.001 HIS E 35 PHE 0.006 0.001 PHE G 486 TYR 0.007 0.001 TYR A 369 ARG 0.004 0.000 ARG F 8 *********************** 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 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.076 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: A 420 ASP cc_start: 0.8244 (m-30) cc_final: 0.8002 (m-30) REVERT: A 484 GLU cc_start: 0.7719 (tp30) cc_final: 0.7426 (tp30) REVERT: D 406 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: D 417 LYS cc_start: 0.9308 (tppt) cc_final: 0.8865 (tppt) REVERT: D 467 ASP cc_start: 0.8115 (t0) cc_final: 0.7808 (t70) outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 0.5007 time to fit residues: 55.0289 Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 406 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8298 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6757 Z= 0.245 Angle : 0.535 11.403 9195 Z= 0.268 Chirality : 0.063 1.428 998 Planarity : 0.003 0.029 1189 Dihedral : 7.910 107.791 1085 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.09 % Favored : 92.79 % Rotamer: Outliers : 0.57 % Allowed : 10.40 % Favored : 89.03 % 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: -1.15 (0.29), residues: 818 helix: -2.05 (0.52), residues: 86 sheet: 0.26 (0.38), residues: 198 loop : -0.95 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS G 519 PHE 0.010 0.001 PHE F 101 TYR 0.017 0.001 TYR E 80 ARG 0.004 0.000 ARG F 8 *********************** 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 85 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.975 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: A 420 ASP cc_start: 0.8266 (m-30) cc_final: 0.8026 (m-30) REVERT: A 484 GLU cc_start: 0.7717 (tp30) cc_final: 0.7426 (tp30) REVERT: D 406 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: D 417 LYS cc_start: 0.9336 (tppt) cc_final: 0.8894 (tppt) REVERT: D 467 ASP cc_start: 0.8146 (t0) cc_final: 0.7815 (t70) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 0.5014 time to fit residues: 51.2123 Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 406 GLU 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: 4.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6757 Z= 0.190 Angle : 0.532 11.433 9195 Z= 0.266 Chirality : 0.064 1.435 998 Planarity : 0.003 0.028 1189 Dihedral : 7.765 106.504 1085 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 0.57 % Allowed : 10.54 % Favored : 88.89 % 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: -1.09 (0.29), residues: 818 helix: -2.01 (0.52), residues: 86 sheet: 0.30 (0.37), residues: 198 loop : -0.92 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS E 35 PHE 0.008 0.001 PHE F 101 TYR 0.014 0.001 TYR E 80 ARG 0.004 0.000 ARG F 8 *********************** 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 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 1.035 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: A 420 ASP cc_start: 0.8238 (m-30) cc_final: 0.7993 (m-30) REVERT: A 484 GLU cc_start: 0.7709 (tp30) cc_final: 0.7421 (tp30) REVERT: D 406 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8411 (tt0) REVERT: D 417 LYS cc_start: 0.9330 (tppt) cc_final: 0.8895 (tppt) REVERT: D 467 ASP cc_start: 0.8123 (t0) cc_final: 0.7798 (t70) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 0.5367 time to fit residues: 54.2006 Evaluate side-chains 81 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 406 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1650 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 : 0.531 11.431 9195 Z= 0.265 Chirality : 0.064 1.434 998 Planarity : 0.003 0.028 1189 Dihedral : 7.585 104.459 1085 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.25 % Rotamer: Outliers : 0.57 % Allowed : 10.97 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.29), residues: 818 helix: -1.94 (0.55), residues: 80 sheet: 0.30 (0.37), residues: 198 loop : -0.87 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS E 35 PHE 0.007 0.001 PHE F 101 TYR 0.011 0.001 TYR E 80 ARG 0.004 0.000 ARG F 8 ********************** REFINEMENT MACRO_CYCLE 10 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: 4 poor density : 79 time to evaluate : 1.151 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: A 420 ASP cc_start: 0.8190 (m-30) cc_final: 0.7959 (m-30) REVERT: A 484 GLU cc_start: 0.7707 (tp30) cc_final: 0.7420 (tp30) REVERT: D 406 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: D 417 LYS cc_start: 0.9332 (tppt) cc_final: 0.8896 (tppt) REVERT: D 467 ASP cc_start: 0.8128 (t0) cc_final: 0.7805 (t70) REVERT: E 19 ARG cc_start: 0.8783 (tpp80) cc_final: 0.8533 (tpp80) outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 0.5323 time to fit residues: 53.0680 Evaluate side-chains 81 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain G residue 398 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.061721 restraints weight = 50584.706| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.70 r_work: 0.2918 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6757 Z= 0.147 Angle : 0.528 11.443 9195 Z= 0.264 Chirality : 0.064 1.437 998 Planarity : 0.003 0.034 1189 Dihedral : 7.359 102.345 1085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 0.57 % Allowed : 10.97 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 818 helix: -1.88 (0.55), residues: 80 sheet: 0.38 (0.38), residues: 198 loop : -0.82 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 436 HIS 0.002 0.001 HIS E 35 PHE 0.006 0.001 PHE G 486 TYR 0.010 0.001 TYR E 80 ARG 0.005 0.000 ARG F 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.59 seconds wall clock time: 56 minutes 49.05 seconds (3409.05 seconds total)