Starting phenix.real_space_refine on Wed Sep 25 23:20:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_39237.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_39237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_39237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_39237.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yg6_39237/09_2024/8yg6_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.48, per 1000 atoms: 0.65 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: 3.11 Conformation dependent library (CDL) restraints added in 1.5 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: 1.20 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: 3.04 Time building geometry restraints manager: 3.56 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.630 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.900 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.355 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: 1.5189 time to fit residues: 156.3134 Evaluate side-chains 63 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.340 Fit side-chains REVERT: A 104 MET cc_start: 0.8933 (tpt) cc_final: 0.8630 (tpt) REVERT: B 364 ASP cc_start: 0.8761 (p0) cc_final: 0.8396 (p0) REVERT: B 484 MET cc_start: 0.5881 (mmt) cc_final: 0.5464 (ttt) outliers start: 12 outliers final: 2 residues processed: 71 average time/residue: 1.2557 time to fit residues: 97.2008 Evaluate side-chains 64 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 11664 Z= 0.162 Angle : 0.550 8.427 15777 Z= 0.283 Chirality : 0.043 0.234 1782 Planarity : 0.003 0.043 2019 Dihedral : 11.488 82.134 1875 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.87 % Allowed : 8.55 % Favored : 90.58 % 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: -0.43 (0.21), residues: 1389 helix: 2.53 (0.30), residues: 318 sheet: 0.42 (0.27), residues: 330 loop : -2.04 (0.18), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 121 HIS 0.009 0.001 HIS A 23 PHE 0.026 0.001 PHE C 485 TYR 0.013 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 74 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.459 Fit side-chains REVERT: A 370 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8347 (ttm) REVERT: B 364 ASP cc_start: 0.8750 (p0) cc_final: 0.8338 (p0) REVERT: B 484 MET cc_start: 0.5898 (mmt) cc_final: 0.5452 (ttt) REVERT: C 104 MET cc_start: 0.9277 (tpt) cc_final: 0.9073 (tpt) outliers start: 11 outliers final: 2 residues processed: 70 average time/residue: 1.3734 time to fit residues: 104.7260 Evaluate side-chains 65 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain B residue 24 CYS 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 124 optimal weight: 3.9990 chunk 94 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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** B 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11664 Z= 0.259 Angle : 0.585 8.934 15777 Z= 0.302 Chirality : 0.044 0.245 1782 Planarity : 0.003 0.047 2019 Dihedral : 10.048 70.201 1875 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.43 % Allowed : 9.42 % Favored : 89.15 % 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: 2.37 (0.30), residues: 318 sheet: 0.55 (0.27), residues: 321 loop : -2.12 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 121 HIS 0.012 0.001 HIS A 23 PHE 0.019 0.001 PHE B 485 TYR 0.017 0.001 TYR B 383 ARG 0.007 0.000 ARG A 108 *********************** 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 84 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.269 Fit side-chains REVERT: A 370 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8406 (ttm) REVERT: B 291 TYR cc_start: 0.5654 (OUTLIER) cc_final: 0.5188 (p90) REVERT: B 364 ASP cc_start: 0.8756 (p0) cc_final: 0.8377 (p0) REVERT: B 484 MET cc_start: 0.6053 (mmt) cc_final: 0.5609 (ttt) outliers start: 18 outliers final: 5 residues processed: 77 average time/residue: 1.1586 time to fit residues: 98.0526 Evaluate side-chains 72 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 291 TYR 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 75 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS C 324 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11664 Z= 0.326 Angle : 0.628 9.725 15777 Z= 0.323 Chirality : 0.045 0.251 1782 Planarity : 0.003 0.023 2019 Dihedral : 8.316 59.987 1875 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.66 % Allowed : 10.53 % Favored : 87.81 % 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: -0.74 (0.21), residues: 1389 helix: 2.46 (0.31), residues: 300 sheet: 0.41 (0.27), residues: 321 loop : -2.27 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 138 HIS 0.013 0.002 HIS A 23 PHE 0.014 0.001 PHE B 485 TYR 0.020 0.001 TYR A 383 ARG 0.006 0.000 ARG A 108 *********************** 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 85 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 64 time to evaluate : 1.465 Fit side-chains REVERT: B 291 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5611 (p90) REVERT: B 364 ASP cc_start: 0.8790 (p0) cc_final: 0.8421 (p0) REVERT: B 484 MET cc_start: 0.5997 (mmt) cc_final: 0.5601 (ttt) REVERT: C 192 GLU cc_start: 0.8673 (mp0) cc_final: 0.8365 (mp0) REVERT: C 330 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8177 (mp) outliers start: 21 outliers final: 9 residues processed: 78 average time/residue: 1.2287 time to fit residues: 105.2064 Evaluate side-chains 75 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 113 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 330 LEU 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 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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** C 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11664 Z= 0.163 Angle : 0.561 11.435 15777 Z= 0.280 Chirality : 0.043 0.212 1782 Planarity : 0.002 0.023 2019 Dihedral : 7.025 55.448 1875 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.50 % Allowed : 10.93 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1389 helix: 2.48 (0.31), residues: 318 sheet: 0.57 (0.27), residues: 321 loop : -2.08 (0.18), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 121 HIS 0.015 0.001 HIS B 23 PHE 0.013 0.001 PHE B 485 TYR 0.014 0.001 TYR A 383 ARG 0.004 0.000 ARG B 87 *********************** 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 87 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 1.400 Fit side-chains REVERT: A 121 TRP cc_start: 0.8257 (m100) cc_final: 0.8022 (m100) REVERT: A 291 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5775 (p90) REVERT: B 121 TRP cc_start: 0.8151 (m100) cc_final: 0.7841 (m100) REVERT: B 291 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5560 (p90) REVERT: B 364 ASP cc_start: 0.8717 (p0) cc_final: 0.8319 (p0) REVERT: B 484 MET cc_start: 0.5997 (mmt) cc_final: 0.5582 (ttt) REVERT: C 370 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7996 (ptp) outliers start: 19 outliers final: 9 residues processed: 83 average time/residue: 1.1441 time to fit residues: 104.3967 Evaluate side-chains 78 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 24 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 23 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 370 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11664 Z= 0.192 Angle : 0.565 11.508 15777 Z= 0.283 Chirality : 0.042 0.182 1782 Planarity : 0.002 0.030 2019 Dihedral : 6.276 55.049 1875 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.66 % Allowed : 11.32 % Favored : 87.02 % 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: -0.40 (0.21), residues: 1389 helix: 2.45 (0.31), residues: 321 sheet: 0.60 (0.27), residues: 321 loop : -2.04 (0.18), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 121 HIS 0.007 0.001 HIS B 23 PHE 0.011 0.001 PHE B 485 TYR 0.014 0.001 TYR A 383 ARG 0.006 0.000 ARG C 288 *********************** 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 88 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.370 Fit side-chains REVERT: A 121 TRP cc_start: 0.8273 (m100) cc_final: 0.8009 (m100) REVERT: A 291 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.5915 (p90) REVERT: B 121 TRP cc_start: 0.8143 (m100) cc_final: 0.7824 (m100) REVERT: B 266 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8956 (mmm-85) REVERT: B 291 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5545 (p90) REVERT: B 364 ASP cc_start: 0.8717 (p0) cc_final: 0.8332 (p0) REVERT: B 484 MET cc_start: 0.6010 (mmt) cc_final: 0.5682 (ttt) REVERT: C 291 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5789 (p90) REVERT: C 370 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8022 (ptp) outliers start: 21 outliers final: 8 residues processed: 83 average time/residue: 1.1459 time to fit residues: 104.7951 Evaluate side-chains 80 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2876 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= 0.328 Angle : 0.622 12.236 15777 Z= 0.320 Chirality : 0.044 0.175 1782 Planarity : 0.003 0.027 2019 Dihedral : 5.977 59.724 1875 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.58 % Allowed : 11.80 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1389 helix: 2.52 (0.31), residues: 300 sheet: 0.58 (0.27), residues: 318 loop : -2.26 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 121 HIS 0.013 0.001 HIS B 23 PHE 0.008 0.001 PHE A 485 TYR 0.020 0.001 TYR A 383 ARG 0.006 0.000 ARG C 288 *********************** 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 87 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 1.303 Fit side-chains REVERT: A 121 TRP cc_start: 0.8286 (m100) cc_final: 0.7974 (m100) REVERT: A 291 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6422 (p90) REVERT: B 121 TRP cc_start: 0.8123 (m100) cc_final: 0.7767 (m100) REVERT: B 266 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8972 (mmm-85) REVERT: B 291 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5873 (p90) REVERT: B 364 ASP cc_start: 0.8788 (p0) cc_final: 0.8436 (p0) REVERT: B 484 MET cc_start: 0.5993 (mmt) cc_final: 0.5610 (ttt) REVERT: C 192 GLU cc_start: 0.8370 (mp0) cc_final: 0.8111 (pm20) REVERT: C 291 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6027 (p90) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 1.1229 time to fit residues: 101.3464 Evaluate side-chains 79 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 476 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8587 moved from start: 0.2821 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= 0.190 Angle : 0.562 12.074 15777 Z= 0.285 Chirality : 0.042 0.160 1782 Planarity : 0.002 0.024 2019 Dihedral : 5.533 56.127 1875 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.27 % Allowed : 11.96 % 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: -0.56 (0.21), residues: 1389 helix: 2.67 (0.31), residues: 300 sheet: 0.53 (0.27), residues: 321 loop : -2.19 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 121 HIS 0.010 0.001 HIS B 23 PHE 0.008 0.001 PHE B 485 TYR 0.014 0.001 TYR A 383 ARG 0.008 0.000 ARG C 163 *********************** 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 82 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 1.396 Fit side-chains REVERT: A 121 TRP cc_start: 0.8275 (m100) cc_final: 0.8035 (m100) REVERT: A 291 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6237 (p90) REVERT: B 121 TRP cc_start: 0.8095 (m100) cc_final: 0.7837 (m100) REVERT: B 266 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8977 (mmm-85) REVERT: B 291 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5828 (p90) REVERT: B 364 ASP cc_start: 0.8731 (p0) cc_final: 0.8347 (p0) REVERT: B 484 MET cc_start: 0.6031 (mmt) cc_final: 0.5761 (ttt) REVERT: C 192 GLU cc_start: 0.8292 (mp0) cc_final: 0.7990 (pm20) REVERT: C 291 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5909 (p90) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 1.1530 time to fit residues: 102.4087 Evaluate side-chains 78 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 88 VAL 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 79 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11664 Z= 0.198 Angle : 0.561 8.920 15777 Z= 0.285 Chirality : 0.042 0.159 1782 Planarity : 0.002 0.025 2019 Dihedral : 5.408 56.068 1875 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.19 % Allowed : 12.35 % Favored : 86.46 % 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: -0.52 (0.21), residues: 1389 helix: 2.64 (0.31), residues: 303 sheet: 0.56 (0.27), residues: 321 loop : -2.16 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 121 HIS 0.011 0.001 HIS B 23 PHE 0.008 0.001 PHE B 485 TYR 0.015 0.001 TYR A 383 ARG 0.007 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 83 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.272 Fit side-chains REVERT: A 121 TRP cc_start: 0.8278 (m100) cc_final: 0.8034 (m100) REVERT: A 291 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6347 (p90) REVERT: B 121 TRP cc_start: 0.8119 (m100) cc_final: 0.7874 (m100) REVERT: B 291 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5760 (p90) REVERT: B 364 ASP cc_start: 0.8727 (p0) cc_final: 0.8354 (p0) REVERT: B 484 MET cc_start: 0.5919 (mmt) cc_final: 0.5587 (ttt) REVERT: C 192 GLU cc_start: 0.8308 (mp0) cc_final: 0.8021 (pm20) REVERT: C 291 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5926 (p90) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 1.1423 time to fit residues: 101.6091 Evaluate side-chains 78 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain B residue 292 THR 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 33 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.066451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056328 restraints weight = 46161.339| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.81 r_work: 0.2816 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3083 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= 0.350 Angle : 0.643 11.989 15777 Z= 0.333 Chirality : 0.045 0.161 1782 Planarity : 0.003 0.045 2019 Dihedral : 5.808 59.498 1875 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 1.11 % Allowed : 12.67 % Favored : 86.22 % 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: -0.80 (0.21), residues: 1389 helix: 2.46 (0.31), residues: 300 sheet: 0.46 (0.27), residues: 318 loop : -2.38 (0.18), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.013 0.001 HIS B 23 PHE 0.009 0.001 PHE B 485 TYR 0.021 0.002 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: 3000.34 seconds wall clock time: 54 minutes 5.59 seconds (3245.59 seconds total)