Starting phenix.real_space_refine on Sat Jan 18 00:27:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg6_39237/01_2025/8yg6_39237.cif" } resolution = 2.77 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 7101 2.51 5 N 1968 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11442 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3730 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 12, 'TRANS': 452} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, F, C, B Time building chain proxies: 7.74, per 1000 atoms: 0.68 Number of scatterers: 11442 At special positions: 0 Unit cell: (100.8, 99.84, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2286 8.00 N 1968 7.00 C 7101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 267 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 402 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " NAG-ASN " NAG A 501 " - " ASN A 197 " " NAG A 502 " - " ASN A 384 " " NAG A 503 " - " ASN A 426 " " NAG B 501 " - " ASN B 197 " " NAG B 502 " - " ASN B 384 " " NAG B 503 " - " ASN B 426 " " NAG C 501 " - " ASN C 197 " " NAG C 502 " - " ASN C 384 " " NAG C 503 " - " ASN C 426 " " NAG D 1 " - " ASN A 354 " " NAG E 1 " - " ASN B 354 " " NAG F 1 " - " ASN C 354 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 21 sheets defined 22.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.531A pdb=" N ARG A 130 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 Processing helix chain 'A' and resid 439 through 456 removed outlier: 5.273A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 475 " --> pdb=" O MET A 471 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.530A pdb=" N ARG B 130 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU B 302 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 Processing helix chain 'B' and resid 439 through 456 removed outlier: 5.272A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN B 448 " --> pdb=" O GLN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.530A pdb=" N ARG C 130 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 342 removed outlier: 3.582A pdb=" N LEU C 302 " --> pdb=" O THR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 439 through 456 removed outlier: 5.273A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 487 removed outlier: 4.459A pdb=" N GLU C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU C 475 " --> pdb=" O MET C 471 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE A 268 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 261 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 95 removed outlier: 4.341A pdb=" N LYS A 69 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS A 158 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 120 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS A 160 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE A 118 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 232 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE B 268 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 261 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 95 removed outlier: 4.342A pdb=" N LYS B 69 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 158 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 120 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS B 160 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 118 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AB3, first strand: chain 'B' and resid 228 through 232 Processing sheet with id=AB4, first strand: chain 'B' and resid 357 through 361 Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 389 Processing sheet with id=AB6, first strand: chain 'C' and resid 219 through 226 removed outlier: 3.863A pdb=" N ILE C 268 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN C 261 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'C' and resid 88 through 95 removed outlier: 4.340A pdb=" N LYS C 69 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS C 158 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 120 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C 160 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE C 118 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC1, first strand: chain 'C' and resid 228 through 232 Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 361 Processing sheet with id=AC3, first strand: chain 'C' and resid 386 through 389 393 hydrogen bonds defined for protein. 1125 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: 2.94 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3794 1.34 - 1.47: 2697 1.47 - 1.59: 5041 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 11664 Sorted by residual: bond pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.37e+01 bond pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.35e+01 bond pdb=" N VAL C 88 " pdb=" CA VAL C 88 " ideal model delta sigma weight residual 1.464 1.494 -0.031 1.13e-02 7.83e+03 7.33e+00 bond pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta sigma weight residual 1.464 1.494 -0.030 1.13e-02 7.83e+03 7.24e+00 ... (remaining 11659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 15147 1.48 - 2.95: 514 2.95 - 4.43: 77 4.43 - 5.90: 21 5.90 - 7.38: 18 Bond angle restraints: 15777 Sorted by residual: angle pdb=" C LYS A 290 " pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " ideal model delta sigma weight residual 116.54 109.87 6.67 1.15e+00 7.56e-01 3.37e+01 angle pdb=" C LYS C 290 " pdb=" CA LYS C 290 " pdb=" CB LYS C 290 " ideal model delta sigma weight residual 116.54 109.88 6.66 1.15e+00 7.56e-01 3.36e+01 angle pdb=" C LYS B 290 " pdb=" CA LYS B 290 " pdb=" CB LYS B 290 " ideal model delta sigma weight residual 116.54 109.91 6.63 1.15e+00 7.56e-01 3.32e+01 angle pdb=" N PRO B 84 " pdb=" CA PRO B 84 " pdb=" C PRO B 84 " ideal model delta sigma weight residual 114.27 108.24 6.03 1.35e+00 5.49e-01 1.99e+01 angle pdb=" N PRO C 84 " pdb=" CA PRO C 84 " pdb=" C PRO C 84 " ideal model delta sigma weight residual 114.27 108.25 6.02 1.35e+00 5.49e-01 1.99e+01 ... (remaining 15772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 6804 21.12 - 42.24: 338 42.24 - 63.37: 64 63.37 - 84.49: 45 84.49 - 105.61: 36 Dihedral angle restraints: 7287 sinusoidal: 3207 harmonic: 4080 Sorted by residual: dihedral pdb=" CD ARG C 87 " pdb=" NE ARG C 87 " pdb=" CZ ARG C 87 " pdb=" NH1 ARG C 87 " ideal model delta sinusoidal sigma weight residual 0.00 70.85 -70.85 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CD ARG A 87 " pdb=" NE ARG A 87 " pdb=" CZ ARG A 87 " pdb=" NH1 ARG A 87 " ideal model delta sinusoidal sigma weight residual 0.00 70.77 -70.77 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CD ARG B 87 " pdb=" NE ARG B 87 " pdb=" CZ ARG B 87 " pdb=" NH1 ARG B 87 " ideal model delta sinusoidal sigma weight residual 0.00 70.74 -70.74 1 1.00e+01 1.00e-02 6.43e+01 ... (remaining 7284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1451 0.053 - 0.107: 249 0.107 - 0.160: 69 0.160 - 0.213: 7 0.213 - 0.267: 6 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CA ASN C 85 " pdb=" N ASN C 85 " pdb=" C ASN C 85 " pdb=" CB ASN C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN A 85 " pdb=" N ASN A 85 " pdb=" C ASN A 85 " pdb=" CB ASN A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN B 85 " pdb=" N ASN B 85 " pdb=" C ASN B 85 " pdb=" CB ASN B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1779 not shown) Planarity restraints: 2031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 87 " -1.039 9.50e-02 1.11e+02 4.66e-01 1.31e+02 pdb=" NE ARG C 87 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 87 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 87 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 87 " 1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG A 87 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 87 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 87 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 87 " -1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG B 87 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 87 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 87 " -0.022 2.00e-02 2.50e+03 ... (remaining 2028 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 122 2.60 - 3.18: 9360 3.18 - 3.75: 16213 3.75 - 4.33: 21394 4.33 - 4.90: 37096 Nonbonded interactions: 84185 Sorted by model distance: nonbonded pdb=" SG CYS B 111 " pdb=" SG CYS B 164 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 111 " pdb=" SG CYS C 164 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS B 177 " pdb=" SG CYS B 184 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 228 " pdb=" SG CYS B 246 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 228 " pdb=" SG CYS C 246 " model vdw 2.030 3.760 ... (remaining 84180 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: 0.06 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.400 Find NCS groups from input model: 0.350 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.034 11664 Z= 0.227 Angle : 0.663 7.380 15777 Z= 0.388 Chirality : 0.046 0.267 1782 Planarity : 0.023 0.466 2019 Dihedral : 16.651 105.611 4629 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.24 % Allowed : 0.95 % Favored : 98.81 % 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: -0.49 (0.22), residues: 1389 helix: 2.75 (0.31), residues: 315 sheet: -0.19 (0.28), residues: 315 loop : -1.84 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 121 HIS 0.005 0.001 HIS B 285 PHE 0.010 0.001 PHE B 485 TYR 0.012 0.001 TYR B 383 ARG 0.004 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8906 (tpt) cc_final: 0.8575 (tpt) REVERT: A 484 MET cc_start: 0.4615 (mmt) cc_final: 0.4397 (ttt) REVERT: B 104 MET cc_start: 0.8781 (tpt) cc_final: 0.8377 (tpt) REVERT: B 364 ASP cc_start: 0.8497 (p0) cc_final: 0.8135 (p0) REVERT: B 484 MET cc_start: 0.5848 (mmt) cc_final: 0.5497 (ttt) REVERT: C 104 MET cc_start: 0.9230 (tpt) cc_final: 0.8971 (tpt) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 1.6663 time to fit residues: 171.3867 Evaluate side-chains 63 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN C 85 ASN C 245 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.057368 restraints weight = 46101.310| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.81 r_work: 0.2869 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11664 Z= 0.400 Angle : 0.698 7.641 15777 Z= 0.359 Chirality : 0.048 0.243 1782 Planarity : 0.004 0.066 2019 Dihedral : 13.431 89.031 1875 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.95 % Allowed : 6.41 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1389 helix: 2.29 (0.30), residues: 318 sheet: -0.06 (0.26), residues: 348 loop : -2.13 (0.19), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 121 HIS 0.009 0.002 HIS C 23 PHE 0.028 0.002 PHE C 485 TYR 0.020 0.002 TYR B 383 ARG 0.007 0.001 ARG C 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 1.075 Fit side-chains REVERT: A 104 MET cc_start: 0.9398 (tpt) cc_final: 0.9076 (tpt) REVERT: A 484 MET cc_start: 0.5113 (mmt) cc_final: 0.4869 (tpt) REVERT: B 364 ASP cc_start: 0.9108 (p0) cc_final: 0.8760 (p0) REVERT: B 484 MET cc_start: 0.6139 (mmt) cc_final: 0.5532 (ttt) outliers start: 12 outliers final: 2 residues processed: 71 average time/residue: 1.4613 time to fit residues: 112.5518 Evaluate side-chains 64 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.072462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.061766 restraints weight = 45512.625| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.88 r_work: 0.2929 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11664 Z= 0.167 Angle : 0.551 8.399 15777 Z= 0.283 Chirality : 0.043 0.234 1782 Planarity : 0.003 0.044 2019 Dihedral : 11.490 82.135 1875 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.87 % Allowed : 8.39 % 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: -0.45 (0.21), residues: 1389 helix: 2.52 (0.30), residues: 318 sheet: 0.41 (0.27), residues: 330 loop : -2.05 (0.18), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 121 HIS 0.010 0.001 HIS A 23 PHE 0.026 0.001 PHE C 485 TYR 0.014 0.001 TYR A 383 ARG 0.008 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 1.346 Fit side-chains REVERT: A 104 MET cc_start: 0.9426 (tpt) cc_final: 0.9218 (tpt) REVERT: B 364 ASP cc_start: 0.9100 (p0) cc_final: 0.8708 (p0) REVERT: B 484 MET cc_start: 0.6080 (mmt) cc_final: 0.5495 (ttt) outliers start: 11 outliers final: 3 residues processed: 69 average time/residue: 1.4529 time to fit residues: 109.1242 Evaluate side-chains 65 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 85 optimal weight: 0.0060 chunk 131 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061784 restraints weight = 45206.898| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.87 r_work: 0.2942 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11664 Z= 0.157 Angle : 0.535 8.343 15777 Z= 0.271 Chirality : 0.043 0.247 1782 Planarity : 0.002 0.033 2019 Dihedral : 9.992 71.074 1875 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.19 % Allowed : 9.58 % Favored : 89.23 % 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: -0.27 (0.22), residues: 1389 helix: 2.57 (0.31), residues: 321 sheet: 0.63 (0.27), residues: 327 loop : -1.96 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.012 0.001 HIS A 23 PHE 0.021 0.001 PHE B 485 TYR 0.012 0.001 TYR A 383 ARG 0.005 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.342 Fit side-chains REVERT: A 104 MET cc_start: 0.9403 (tpt) cc_final: 0.9146 (tpt) REVERT: B 291 TYR cc_start: 0.5415 (OUTLIER) cc_final: 0.4687 (p90) REVERT: B 364 ASP cc_start: 0.9078 (p0) cc_final: 0.8677 (p0) REVERT: B 484 MET cc_start: 0.6048 (mmt) cc_final: 0.5402 (ttt) outliers start: 15 outliers final: 5 residues processed: 78 average time/residue: 1.2812 time to fit residues: 109.1923 Evaluate side-chains 70 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 72 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.070673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.060137 restraints weight = 45215.338| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.84 r_work: 0.2887 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11664 Z= 0.251 Angle : 0.587 9.826 15777 Z= 0.298 Chirality : 0.044 0.251 1782 Planarity : 0.002 0.023 2019 Dihedral : 8.369 57.230 1875 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.27 % Allowed : 10.13 % Favored : 88.60 % 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: -0.42 (0.21), residues: 1389 helix: 2.42 (0.31), residues: 318 sheet: 0.65 (0.27), residues: 321 loop : -2.06 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 138 HIS 0.012 0.001 HIS A 23 PHE 0.015 0.001 PHE B 485 TYR 0.017 0.001 TYR B 383 ARG 0.006 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.302 Fit side-chains REVERT: A 104 MET cc_start: 0.9431 (tpt) cc_final: 0.9199 (tpt) REVERT: B 291 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5428 (p90) REVERT: B 364 ASP cc_start: 0.9120 (p0) cc_final: 0.8762 (p0) REVERT: B 484 MET cc_start: 0.6054 (mmt) cc_final: 0.5362 (ttt) REVERT: C 370 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (ptp) outliers start: 16 outliers final: 6 residues processed: 78 average time/residue: 1.2699 time to fit residues: 108.1412 Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 0.0010 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.067817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.057346 restraints weight = 46507.222| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.86 r_work: 0.2823 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11664 Z= 0.258 Angle : 0.589 11.039 15777 Z= 0.299 Chirality : 0.043 0.223 1782 Planarity : 0.003 0.035 2019 Dihedral : 6.953 58.065 1875 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.35 % Allowed : 10.69 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.21), residues: 1389 helix: 2.35 (0.30), residues: 318 sheet: 0.54 (0.27), residues: 321 loop : -2.11 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 121 HIS 0.010 0.001 HIS A 23 PHE 0.012 0.001 PHE B 485 TYR 0.017 0.001 TYR A 383 ARG 0.006 0.000 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 1.304 Fit side-chains REVERT: A 104 MET cc_start: 0.9366 (tpt) cc_final: 0.9162 (tpt) REVERT: B 121 TRP cc_start: 0.8224 (m100) cc_final: 0.7928 (m100) REVERT: B 291 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5696 (p90) REVERT: B 364 ASP cc_start: 0.9000 (p0) cc_final: 0.8641 (p0) REVERT: B 484 MET cc_start: 0.6254 (mmt) cc_final: 0.5659 (ttt) REVERT: C 192 GLU cc_start: 0.9031 (mp0) cc_final: 0.8732 (mp0) REVERT: C 370 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8356 (ptp) outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 1.2070 time to fit residues: 104.5683 Evaluate side-chains 74 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057051 restraints weight = 48423.936| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.82 r_work: 0.2818 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11664 Z= 0.341 Angle : 0.636 11.962 15777 Z= 0.327 Chirality : 0.045 0.169 1782 Planarity : 0.003 0.025 2019 Dihedral : 6.263 59.385 1875 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.43 % Allowed : 11.16 % Favored : 87.41 % 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: -0.72 (0.21), residues: 1389 helix: 2.44 (0.31), residues: 300 sheet: 0.48 (0.27), residues: 318 loop : -2.27 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 121 HIS 0.015 0.002 HIS B 23 PHE 0.012 0.001 PHE C 485 TYR 0.020 0.001 TYR A 383 ARG 0.007 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.362 Fit side-chains REVERT: A 104 MET cc_start: 0.9394 (tpt) cc_final: 0.9190 (tpt) REVERT: A 291 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6206 (p90) REVERT: B 266 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8891 (mmm-85) REVERT: B 291 TYR cc_start: 0.6424 (OUTLIER) cc_final: 0.5892 (p90) REVERT: B 364 ASP cc_start: 0.9133 (p0) cc_final: 0.8785 (p0) REVERT: B 484 MET cc_start: 0.6202 (mmt) cc_final: 0.5701 (ttt) REVERT: C 192 GLU cc_start: 0.8934 (mp0) cc_final: 0.8637 (mp0) REVERT: C 291 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6018 (p90) REVERT: C 370 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8425 (ptp) REVERT: C 484 MET cc_start: 0.6966 (mmp) cc_final: 0.6180 (ttp) outliers start: 18 outliers final: 7 residues processed: 80 average time/residue: 1.3207 time to fit residues: 115.3059 Evaluate side-chains 76 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.068514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.058113 restraints weight = 45947.126| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.86 r_work: 0.2865 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11664 Z= 0.178 Angle : 0.558 8.446 15777 Z= 0.284 Chirality : 0.042 0.167 1782 Planarity : 0.002 0.027 2019 Dihedral : 5.703 55.727 1875 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.27 % Allowed : 11.64 % Favored : 87.09 % 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: -0.55 (0.21), residues: 1389 helix: 2.67 (0.31), residues: 300 sheet: 0.46 (0.26), residues: 321 loop : -2.13 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 121 HIS 0.010 0.001 HIS B 23 PHE 0.010 0.001 PHE B 485 TYR 0.014 0.001 TYR A 383 ARG 0.006 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 1.319 Fit side-chains REVERT: A 291 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6094 (p90) REVERT: B 266 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8889 (mmm-85) REVERT: B 291 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5764 (p90) REVERT: B 364 ASP cc_start: 0.9100 (p0) cc_final: 0.8737 (p0) REVERT: B 484 MET cc_start: 0.6202 (mmt) cc_final: 0.5650 (ttt) REVERT: C 192 GLU cc_start: 0.8921 (mp0) cc_final: 0.8616 (mp0) REVERT: C 291 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5950 (p90) REVERT: C 370 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8376 (ptp) REVERT: C 484 MET cc_start: 0.7045 (mmp) cc_final: 0.6810 (tpp) outliers start: 16 outliers final: 9 residues processed: 79 average time/residue: 1.2242 time to fit residues: 106.1917 Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 266 ARG Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 23 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 370 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 24 optimal weight: 0.0770 chunk 94 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.0030 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059211 restraints weight = 45672.915| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.86 r_work: 0.2888 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11664 Z= 0.138 Angle : 0.540 9.264 15777 Z= 0.272 Chirality : 0.042 0.171 1782 Planarity : 0.002 0.029 2019 Dihedral : 5.074 52.615 1875 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.03 % Allowed : 11.88 % Favored : 87.09 % 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: -0.24 (0.22), residues: 1389 helix: 2.61 (0.31), residues: 321 sheet: 0.68 (0.27), residues: 321 loop : -1.93 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 121 HIS 0.004 0.001 HIS A 23 PHE 0.011 0.001 PHE B 153 TYR 0.011 0.001 TYR A 383 ARG 0.005 0.000 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: B 291 TYR cc_start: 0.6325 (OUTLIER) cc_final: 0.5732 (p90) REVERT: B 364 ASP cc_start: 0.8969 (p0) cc_final: 0.8601 (p0) REVERT: B 484 MET cc_start: 0.6130 (mmt) cc_final: 0.5686 (ttt) REVERT: C 291 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6070 (p90) outliers start: 13 outliers final: 5 residues processed: 77 average time/residue: 1.2655 time to fit residues: 106.7158 Evaluate side-chains 71 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058180 restraints weight = 46035.917| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.83 r_work: 0.2890 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11664 Z= 0.210 Angle : 0.560 11.904 15777 Z= 0.284 Chirality : 0.042 0.148 1782 Planarity : 0.002 0.027 2019 Dihedral : 5.241 56.694 1875 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.03 % Allowed : 12.19 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1389 helix: 2.52 (0.31), residues: 321 sheet: 0.67 (0.27), residues: 321 loop : -2.01 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 121 HIS 0.005 0.001 HIS A 23 PHE 0.008 0.001 PHE B 485 TYR 0.015 0.001 TYR A 383 ARG 0.011 0.000 ARG C 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.402 Fit side-chains REVERT: B 291 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5711 (p90) REVERT: B 364 ASP cc_start: 0.9085 (p0) cc_final: 0.8734 (p0) REVERT: B 484 MET cc_start: 0.6195 (mmt) cc_final: 0.5682 (ttt) REVERT: C 171 MET cc_start: 0.8660 (tpp) cc_final: 0.8366 (tpt) REVERT: C 291 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.5992 (p90) outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 1.2745 time to fit residues: 106.1047 Evaluate side-chains 73 residues out of total 1263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 291 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.068763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.058384 restraints weight = 45710.665| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.82 r_work: 0.2891 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11664 Z= 0.186 Angle : 0.559 11.884 15777 Z= 0.282 Chirality : 0.042 0.163 1782 Planarity : 0.002 0.037 2019 Dihedral : 5.197 56.204 1875 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.87 % Allowed : 12.59 % Favored : 86.54 % 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: -0.31 (0.21), residues: 1389 helix: 2.51 (0.31), residues: 321 sheet: 0.64 (0.26), residues: 327 loop : -1.99 (0.19), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 121 HIS 0.009 0.001 HIS B 23 PHE 0.010 0.001 PHE C 483 TYR 0.014 0.001 TYR A 383 ARG 0.009 0.000 ARG C 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.19 seconds wall clock time: 120 minutes 44.86 seconds (7244.86 seconds total)