Starting phenix.real_space_refine on Tue Aug 4 19:32:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgi_44513/08_2026/9bgi_44513.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.012 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 4 5.21 5 S 18 5.16 5 C 3844 2.51 5 N 1140 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6511 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2672 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "F" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Time building chain proxies: 1.20, per 1000 atoms: 0.18 Number of scatterers: 6511 At special positions: 0 Unit cell: (84.66, 86.32, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 48 15.00 Mg 4 11.99 O 1457 8.00 N 1140 7.00 C 3844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 304.8 milliseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 47.6% alpha, 7.7% beta 22 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.694A pdb=" N GLU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 123 removed outlier: 3.521A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 178 removed outlier: 4.264A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.621A pdb=" N GLN A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.998A pdb=" N TRP A 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.618A pdb=" N GLN A 227 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.935A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 122 Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.962A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 250 through 266 removed outlier: 3.891A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.536A pdb=" N THR B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 7.133A pdb=" N VAL A 193 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 235 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N GLU A 276 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 148 removed outlier: 7.185A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 274 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 280 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER B 244 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1564 1.33 - 1.45: 1459 1.45 - 1.57: 3417 1.57 - 1.69: 92 1.69 - 1.80: 32 Bond restraints: 6564 Sorted by residual: bond pdb=" C3' DA C 11 " pdb=" C2' DA C 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.36e+00 bond pdb=" C3' DA E 11 " pdb=" C2' DA E 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.12e+00 bond pdb=" C3' DT F 16 " pdb=" C2' DT F 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.96e+00 bond pdb=" C3' DT D 16 " pdb=" C2' DT D 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.68e+00 bond pdb=" C3' DG F 15 " pdb=" C2' DG F 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.49e+00 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8790 1.47 - 2.94: 283 2.94 - 4.42: 27 4.42 - 5.89: 7 5.89 - 7.36: 1 Bond angle restraints: 9108 Sorted by residual: angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT E 4 " pdb=" C4 DT E 4 " pdb=" O4 DT E 4 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT F 18 " pdb=" C4 DT F 18 " pdb=" O4 DT F 18 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT D 18 " pdb=" C4 DT D 18 " pdb=" O4 DT D 18 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 9103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3076 17.70 - 35.41: 432 35.41 - 53.11: 244 53.11 - 70.82: 52 70.82 - 88.52: 6 Dihedral angle restraints: 3810 sinusoidal: 1852 harmonic: 1958 Sorted by residual: dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLN A 129 " pdb=" C GLN A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CB GLU B 292 " pdb=" CG GLU B 292 " pdb=" CD GLU B 292 " pdb=" OE1 GLU B 292 " ideal model delta sinusoidal sigma weight residual 0.00 -88.52 88.52 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 467 0.024 - 0.048: 288 0.048 - 0.073: 145 0.073 - 0.097: 50 0.097 - 0.121: 52 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C3' DT D 16 " pdb=" C4' DT D 16 " pdb=" O3' DT D 16 " pdb=" C2' DT D 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.61 -0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 999 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 186 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 187 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 187 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 187 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 129 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 130 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 130 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 130 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 129 " 0.023 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 130 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.019 5.00e-02 4.00e+02 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 117 2.50 - 3.10: 4258 3.10 - 3.70: 9785 3.70 - 4.30: 15291 4.30 - 4.90: 24863 Nonbonded interactions: 54314 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH C 105 " model vdw 1.899 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 515 " model vdw 1.918 2.170 nonbonded pdb=" OP2 DC F 12 " pdb="MG MG B 402 " model vdw 1.919 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH E 102 " model vdw 1.922 2.170 nonbonded pdb=" OP2 DC D 12 " pdb="MG MG A 402 " model vdw 1.926 2.170 ... (remaining 54309 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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: 2.560 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.630 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 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 : 0.004 0.039 6564 Z= 0.327 Angle : 0.589 7.362 9108 Z= 0.430 Chirality : 0.044 0.121 1002 Planarity : 0.004 0.048 1032 Dihedral : 20.545 88.520 2546 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.77 % Allowed : 16.84 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.34), residues: 672 helix: 1.39 (0.32), residues: 284 sheet: -0.94 (0.69), residues: 54 loop : -0.32 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.010 0.001 TYR B 5 PHE 0.009 0.001 PHE B 3 TRP 0.015 0.002 TRP B 117 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.33 ( 6564) covalent geometry : angle 0.58876 / 0.43 ( 9108) hydrogen bonds : bond 0.14871 / 9.96 ( 281) hydrogen bonds : angle 5.56149 / 3.65 ( 759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.156 Fit side-chains REVERT: A 64 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 200 ASN cc_start: 0.8969 (m-40) cc_final: 0.8748 (m-40) REVERT: A 243 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7806 (ttt-90) REVERT: A 333 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7636 (tpt90) REVERT: B 200 ASN cc_start: 0.8832 (m-40) cc_final: 0.8562 (t0) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.0980 time to fit residues: 6.3866 Evaluate side-chains 49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104845 restraints weight = 7396.912| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.50 r_work: 0.3248 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6564 Z= 0.165 Angle : 0.548 6.308 9108 Z= 0.299 Chirality : 0.043 0.155 1002 Planarity : 0.004 0.041 1032 Dihedral : 21.525 84.280 1285 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.13 % Allowed : 17.02 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.34), residues: 672 helix: 1.55 (0.32), residues: 288 sheet: -1.00 (0.68), residues: 54 loop : -0.19 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 152 TYR 0.012 0.001 TYR A 5 PHE 0.011 0.001 PHE B 3 TRP 0.012 0.002 TRP B 117 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6564) covalent geometry : angle 0.54802 / 0.30 ( 9108) hydrogen bonds : bond 0.05280 / 3.61 ( 281) hydrogen bonds : angle 4.28590 / 2.89 ( 759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.130 Fit side-chains REVERT: A 64 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8265 (t80) REVERT: A 200 ASN cc_start: 0.8962 (m-40) cc_final: 0.8741 (m-40) REVERT: A 333 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7651 (tpt90) REVERT: B 169 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 200 ASN cc_start: 0.8831 (m-40) cc_final: 0.8574 (t0) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.0632 time to fit residues: 4.5350 Evaluate side-chains 50 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 13 optimal weight: 40.0000 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104683 restraints weight = 7342.585| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.49 r_work: 0.3245 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6564 Z= 0.158 Angle : 0.527 5.396 9108 Z= 0.286 Chirality : 0.042 0.150 1002 Planarity : 0.004 0.035 1032 Dihedral : 21.572 84.211 1275 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.84 % Allowed : 16.84 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.34), residues: 672 helix: 1.72 (0.32), residues: 288 sheet: -0.85 (0.69), residues: 52 loop : -0.18 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 152 TYR 0.012 0.001 TYR A 5 PHE 0.011 0.001 PHE B 3 TRP 0.012 0.002 TRP B 117 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6564) covalent geometry : angle 0.52672 / 0.29 ( 9108) hydrogen bonds : bond 0.04908 / 3.36 ( 281) hydrogen bonds : angle 3.97371 / 2.69 ( 759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.145 Fit side-chains REVERT: A 64 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8330 (t80) REVERT: A 333 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7639 (tpt90) REVERT: B 169 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7920 (mm-30) REVERT: B 200 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8574 (t0) outliers start: 16 outliers final: 9 residues processed: 55 average time/residue: 0.0777 time to fit residues: 5.6912 Evaluate side-chains 52 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103463 restraints weight = 7390.004| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.49 r_work: 0.3222 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6564 Z= 0.183 Angle : 0.545 5.443 9108 Z= 0.294 Chirality : 0.043 0.154 1002 Planarity : 0.004 0.033 1032 Dihedral : 21.657 83.466 1275 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.84 % Allowed : 16.49 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.34), residues: 672 helix: 1.67 (0.32), residues: 288 sheet: -0.93 (0.68), residues: 52 loop : -0.15 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.016 0.001 TYR A 5 PHE 0.011 0.001 PHE B 3 TRP 0.011 0.002 TRP B 156 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6564) covalent geometry : angle 0.54464 / 0.29 ( 9108) hydrogen bonds : bond 0.05110 / 3.50 ( 281) hydrogen bonds : angle 3.91357 / 2.66 ( 759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.205 Fit side-chains REVERT: A 64 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8365 (t80) REVERT: A 231 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8109 (mm-40) REVERT: A 333 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7659 (tpt90) REVERT: B 169 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 200 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (t0) REVERT: B 229 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8307 (mmt-90) outliers start: 16 outliers final: 11 residues processed: 55 average time/residue: 0.0787 time to fit residues: 5.7841 Evaluate side-chains 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.139222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105816 restraints weight = 7475.981| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.50 r_work: 0.3256 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6564 Z= 0.131 Angle : 0.507 6.150 9108 Z= 0.275 Chirality : 0.041 0.155 1002 Planarity : 0.004 0.033 1032 Dihedral : 21.607 83.987 1275 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.48 % Allowed : 17.02 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.34), residues: 672 helix: 1.88 (0.32), residues: 288 sheet: -0.97 (0.68), residues: 52 loop : -0.03 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 152 TYR 0.011 0.001 TYR A 5 PHE 0.007 0.001 PHE B 3 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6564) covalent geometry : angle 0.50666 / 0.27 ( 9108) hydrogen bonds : bond 0.04429 / 3.03 ( 281) hydrogen bonds : angle 3.73989 / 2.54 ( 759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.226 Fit side-chains REVERT: A 64 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8443 (t80) REVERT: A 333 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7675 (tpt90) REVERT: B 169 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 176 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7949 (tpt90) REVERT: B 200 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8557 (t0) REVERT: B 229 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8274 (mmt-90) outliers start: 14 outliers final: 9 residues processed: 52 average time/residue: 0.0924 time to fit residues: 6.2764 Evaluate side-chains 51 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107330 restraints weight = 7300.005| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.53 r_work: 0.3296 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6564 Z= 0.116 Angle : 0.497 5.364 9108 Z= 0.269 Chirality : 0.041 0.155 1002 Planarity : 0.003 0.031 1032 Dihedral : 21.604 84.016 1275 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.66 % Allowed : 16.67 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.35), residues: 672 helix: 1.98 (0.32), residues: 288 sheet: -0.76 (0.73), residues: 48 loop : 0.11 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.008 0.001 TYR B 5 PHE 0.005 0.001 PHE B 3 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 6564) covalent geometry : angle 0.49695 / 0.27 ( 9108) hydrogen bonds : bond 0.04181 / 2.87 ( 281) hydrogen bonds : angle 3.66333 / 2.49 ( 759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.213 Fit side-chains REVERT: A 64 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 333 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7693 (tpt90) REVERT: B 169 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7901 (mm-30) REVERT: B 176 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7889 (tpt90) REVERT: B 200 ASN cc_start: 0.8846 (m-40) cc_final: 0.8565 (t0) REVERT: B 229 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8245 (mmt-90) outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 0.0810 time to fit residues: 5.9727 Evaluate side-chains 55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 36 optimal weight: 0.0980 chunk 65 optimal weight: 20.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102511 restraints weight = 7385.475| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.49 r_work: 0.3208 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6564 Z= 0.215 Angle : 0.567 5.506 9108 Z= 0.303 Chirality : 0.044 0.158 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.696 82.369 1275 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.19 % Allowed : 16.31 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.34), residues: 672 helix: 1.70 (0.32), residues: 288 sheet: -1.10 (0.66), residues: 52 loop : -0.07 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.027 0.002 TYR B 5 PHE 0.011 0.001 PHE B 3 TRP 0.013 0.002 TRP B 117 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 6564) covalent geometry : angle 0.56678 / 0.30 ( 9108) hydrogen bonds : bond 0.05287 / 3.63 ( 281) hydrogen bonds : angle 3.82240 / 2.61 ( 759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.240 Fit side-chains REVERT: A 64 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8480 (t80) REVERT: A 231 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 333 ARG cc_start: 0.8113 (mmm-85) cc_final: 0.7737 (tpt90) REVERT: B 169 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7958 (mm-30) REVERT: B 176 ARG cc_start: 0.8422 (mmm160) cc_final: 0.7961 (tpt90) REVERT: B 200 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8527 (t0) REVERT: B 229 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8322 (mmt-90) outliers start: 18 outliers final: 14 residues processed: 55 average time/residue: 0.0869 time to fit residues: 6.2694 Evaluate side-chains 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 overall best weight: 3.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103701 restraints weight = 7403.968| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.48 r_work: 0.3227 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6564 Z= 0.170 Angle : 0.537 5.889 9108 Z= 0.288 Chirality : 0.042 0.160 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.655 82.607 1275 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.19 % Allowed : 16.31 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.34), residues: 672 helix: 1.76 (0.32), residues: 288 sheet: -1.04 (0.67), residues: 52 loop : -0.01 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.022 0.001 TYR B 5 PHE 0.008 0.001 PHE B 3 TRP 0.011 0.002 TRP B 156 HIS 0.001 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6564) covalent geometry : angle 0.53716 / 0.29 ( 9108) hydrogen bonds : bond 0.04872 / 3.34 ( 281) hydrogen bonds : angle 3.77312 / 2.58 ( 759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.175 Fit side-chains REVERT: A 64 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8379 (t80) REVERT: A 231 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8134 (mm-40) REVERT: A 333 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7770 (tpt90) REVERT: B 169 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 176 ARG cc_start: 0.8412 (mmm160) cc_final: 0.7954 (tpt90) REVERT: B 200 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8527 (t0) REVERT: B 229 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8341 (mmt-90) outliers start: 18 outliers final: 13 residues processed: 55 average time/residue: 0.0990 time to fit residues: 7.0654 Evaluate side-chains 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104727 restraints weight = 7474.887| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.50 r_work: 0.3246 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6564 Z= 0.143 Angle : 0.518 5.834 9108 Z= 0.278 Chirality : 0.042 0.160 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.624 82.803 1275 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.01 % Allowed : 15.96 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.34), residues: 672 helix: 1.84 (0.32), residues: 288 sheet: -1.02 (0.68), residues: 52 loop : 0.05 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.018 0.001 TYR B 5 PHE 0.007 0.001 PHE B 3 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6564) covalent geometry : angle 0.51788 / 0.28 ( 9108) hydrogen bonds : bond 0.04514 / 3.10 ( 281) hydrogen bonds : angle 3.70189 / 2.52 ( 759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.139 Fit side-chains REVERT: A 64 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8457 (t80) REVERT: A 231 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8167 (mm-40) REVERT: A 333 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7744 (tpt90) REVERT: B 169 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7924 (mm-30) REVERT: B 176 ARG cc_start: 0.8405 (mmm160) cc_final: 0.7931 (tpt90) REVERT: B 200 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8555 (t0) REVERT: B 229 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8263 (mmt-90) outliers start: 17 outliers final: 13 residues processed: 53 average time/residue: 0.0768 time to fit residues: 5.3493 Evaluate side-chains 55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 30.0000 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106309 restraints weight = 7270.942| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.47 r_work: 0.3282 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6564 Z= 0.135 Angle : 0.512 5.666 9108 Z= 0.275 Chirality : 0.041 0.161 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.610 82.629 1275 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.84 % Allowed : 16.31 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.34), residues: 672 helix: 1.91 (0.32), residues: 288 sheet: -0.78 (0.72), residues: 48 loop : 0.14 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.018 0.001 TYR B 5 PHE 0.006 0.001 PHE B 3 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6564) covalent geometry : angle 0.51230 / 0.28 ( 9108) hydrogen bonds : bond 0.04410 / 3.03 ( 281) hydrogen bonds : angle 3.68007 / 2.51 ( 759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.177 Fit side-chains REVERT: A 64 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8446 (t80) REVERT: A 231 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8185 (mm-40) REVERT: A 260 MET cc_start: 0.8960 (ttm) cc_final: 0.8745 (ttt) REVERT: A 333 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7757 (tpt90) REVERT: B 169 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 176 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7933 (tpt90) REVERT: B 200 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8532 (t0) REVERT: B 229 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8256 (mmt-90) outliers start: 16 outliers final: 12 residues processed: 53 average time/residue: 0.0729 time to fit residues: 5.1260 Evaluate side-chains 58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103091 restraints weight = 7373.571| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.49 r_work: 0.3219 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6564 Z= 0.184 Angle : 0.545 5.559 9108 Z= 0.291 Chirality : 0.043 0.164 1002 Planarity : 0.004 0.031 1032 Dihedral : 21.625 81.650 1272 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.66 % Allowed : 16.31 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.34), residues: 672 helix: 1.78 (0.32), residues: 288 sheet: -1.10 (0.67), residues: 52 loop : 0.04 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.024 0.002 TYR B 5 PHE 0.009 0.001 PHE B 3 TRP 0.012 0.002 TRP B 156 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 6564) covalent geometry : angle 0.54542 / 0.29 ( 9108) hydrogen bonds : bond 0.04958 / 3.41 ( 281) hydrogen bonds : angle 3.74964 / 2.57 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.74 seconds wall clock time: 22 minutes 12.40 seconds (1332.40 seconds total)