Starting phenix.real_space_refine on Thu Jul 2 03:40:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgi_44513/07_2026/9bgi_44513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgi_44513/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bgi_44513/07_2026/9bgi_44513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgi_44513/07_2026/9bgi_44513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgi_44513/07_2026/9bgi_44513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgi_44513/07_2026/9bgi_44513.map" } 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-dev-6108/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: 1.81, per 1000 atoms: 0.28 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: 0.58 Conformation dependent library (CDL) restraints added in 371.6 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: 0.75 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: 1.09 Time building geometry restraints manager: 0.76 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: 8793 1.47 - 2.94: 280 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: 3.100 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- 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 : 0.586 7.362 9108 Z= 0.427 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 0.58594 / 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 : 0.160 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: 0.1163 time to fit residues: 7.4636 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 : 0.223 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.138284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104467 restraints weight = 7397.873| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.54 r_work: 0.3240 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.0501 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= 0.167 Angle : 0.544 6.376 9108 Z= 0.297 Chirality : 0.043 0.148 1002 Planarity : 0.004 0.043 1032 Dihedral : 21.543 84.453 1285 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.13 % Allowed : 16.84 % 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: 0.69 (0.34), residues: 672 helix: 1.55 (0.32), residues: 288 sheet: -0.99 (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 0.010 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 0.00375 / 0.17 ( 6564) covalent geometry : angle 0.54355 / 0.30 ( 9108) hydrogen bonds : bond 0.05350 / 3.66 ( 281) hydrogen bonds : angle 4.31159 / 2.91 ( 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 : 0.237 Fit side-chains REVERT: A 64 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 200 ASN cc_start: 0.8960 (m-40) cc_final: 0.8741 (m-40) REVERT: A 333 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7658 (tpt90) REVERT: B 169 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7881 (mm-30) REVERT: B 200 ASN cc_start: 0.8826 (m-40) cc_final: 0.8573 (t0) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.0966 time to fit residues: 6.7797 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 : 0.223 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.5442 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.139075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105700 restraints weight = 7340.730| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.49 r_work: 0.3252 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0653 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= 0.139 Angle : 0.511 5.408 9108 Z= 0.280 Chirality : 0.042 0.137 1002 Planarity : 0.004 0.035 1032 Dihedral : 21.573 84.371 1275 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.66 % Allowed : 17.02 % 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: 0.91 (0.34), residues: 672 helix: 1.79 (0.32), residues: 288 sheet: -0.82 (0.70), residues: 52 loop : -0.16 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 152 TYR 0.010 0.001 TYR A 5 PHE 0.009 0.001 PHE B 3 TRP 0.012 0.001 TRP B 117 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6564) covalent geometry : angle 0.51084 / 0.28 ( 9108) hydrogen bonds : bond 0.04678 / 3.20 ( 281) hydrogen bonds : angle 3.92942 / 2.65 ( 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: 15 poor density : 44 time to evaluate : 0.249 Fit side-chains REVERT: A 64 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 333 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7648 (tpt90) REVERT: B 121 MET cc_start: 0.7650 (mtp) cc_final: 0.7381 (mmm) REVERT: B 169 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 176 ARG cc_start: 0.8354 (mmm160) cc_final: 0.7922 (tpt90) REVERT: B 200 ASN cc_start: 0.8797 (m-40) cc_final: 0.8545 (t0) outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 0.0970 time to fit residues: 7.1253 Evaluate side-chains 52 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 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 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 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: 10.0000 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102773 restraints weight = 7379.607| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.49 r_work: 0.3214 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6564 Z= 0.199 Angle : 0.557 6.182 9108 Z= 0.300 Chirality : 0.044 0.145 1002 Planarity : 0.004 0.034 1032 Dihedral : 21.719 83.265 1275 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 0.76 (0.34), residues: 672 helix: 1.62 (0.32), residues: 288 sheet: -1.00 (0.67), residues: 52 loop : -0.17 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.014 0.002 TYR A 5 PHE 0.012 0.001 PHE B 3 TRP 0.012 0.002 TRP B 117 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 6564) covalent geometry : angle 0.55672 / 0.30 ( 9108) hydrogen bonds : bond 0.05318 / 3.65 ( 281) hydrogen bonds : angle 3.94090 / 2.68 ( 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 62 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.206 Fit side-chains REVERT: A 64 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8380 (t80) REVERT: A 231 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8106 (mm-40) REVERT: A 333 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7655 (tpt90) REVERT: B 169 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 176 ARG cc_start: 0.8389 (mmm160) cc_final: 0.7930 (tpt90) REVERT: B 200 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8437 (t0) REVERT: B 229 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8314 (mmt-90) outliers start: 18 outliers final: 12 residues processed: 54 average time/residue: 0.0982 time to fit residues: 6.8656 Evaluate side-chains 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 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 = 0.3851 r_free = 0.3851 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104867 restraints weight = 7472.121| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.50 r_work: 0.3241 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6564 Z= 0.146 Angle : 0.514 5.782 9108 Z= 0.279 Chirality : 0.042 0.145 1002 Planarity : 0.004 0.033 1032 Dihedral : 21.665 83.749 1275 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.70 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: 0.93 (0.34), residues: 672 helix: 1.78 (0.32), residues: 288 sheet: -1.00 (0.68), residues: 52 loop : -0.08 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.012 0.001 TYR A 5 PHE 0.008 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 0.00330 / 0.15 ( 6564) covalent geometry : angle 0.51438 / 0.28 ( 9108) hydrogen bonds : bond 0.04657 / 3.19 ( 281) hydrogen bonds : angle 3.79845 / 2.58 ( 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 58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.228 Fit side-chains REVERT: A 64 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.8362 (t80) REVERT: A 333 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7687 (tpt90) REVERT: B 169 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7931 (mm-30) REVERT: B 176 ARG cc_start: 0.8382 (mmm160) cc_final: 0.7936 (tpt90) REVERT: B 200 ASN cc_start: 0.8845 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 229 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8329 (mmt-90) outliers start: 15 outliers final: 11 residues processed: 54 average time/residue: 0.0836 time to fit residues: 5.9970 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 : 0.143 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.140945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107850 restraints weight = 7302.212| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.48 r_work: 0.3296 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6564 Z= 0.119 Angle : 0.490 6.282 9108 Z= 0.266 Chirality : 0.041 0.144 1002 Planarity : 0.003 0.032 1032 Dihedral : 21.646 84.103 1275 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.66 % Allowed : 16.49 % 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: 1.16 (0.35), residues: 672 helix: 1.92 (0.32), residues: 288 sheet: -0.80 (0.72), residues: 48 loop : 0.07 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.010 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 A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6564) covalent geometry : angle 0.48977 / 0.27 ( 9108) hydrogen bonds : bond 0.04189 / 2.87 ( 281) hydrogen bonds : angle 3.65107 / 2.48 ( 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 : 0.230 Fit side-chains REVERT: A 64 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8432 (t80) REVERT: A 333 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7689 (tpt90) REVERT: B 169 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 176 ARG cc_start: 0.8359 (mmm160) cc_final: 0.7904 (tpt90) REVERT: B 200 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8569 (t0) REVERT: B 229 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8255 (mmt-90) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.0954 time to fit residues: 6.8545 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 : 0.222 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.134464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100865 restraints weight = 7419.660| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.50 r_work: 0.3186 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 6564 Z= 0.284 Angle : 0.613 6.039 9108 Z= 0.327 Chirality : 0.047 0.151 1002 Planarity : 0.005 0.034 1032 Dihedral : 21.812 81.699 1275 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.37 % Allowed : 15.60 % 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: 0.69 (0.34), residues: 672 helix: 1.50 (0.31), residues: 288 sheet: -1.40 (0.65), residues: 54 loop : -0.06 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 29 TYR 0.029 0.002 TYR B 5 PHE 0.013 0.002 PHE B 3 TRP 0.011 0.002 TRP B 156 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.28 ( 6564) covalent geometry : angle 0.61296 / 0.33 ( 9108) hydrogen bonds : bond 0.05955 / 4.08 ( 281) hydrogen bonds : angle 3.94514 / 2.70 ( 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 61 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.237 Fit side-chains REVERT: A 64 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8422 (t80) REVERT: A 231 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8139 (mm-40) REVERT: A 333 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7750 (tpt90) REVERT: B 176 ARG cc_start: 0.8443 (mmm160) cc_final: 0.7956 (tpt90) REVERT: B 200 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8558 (t0) REVERT: B 229 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8366 (mmt-90) outliers start: 19 outliers final: 14 residues processed: 56 average time/residue: 0.0932 time to fit residues: 6.8356 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 : 0.215 ------------------------------------------------------------------------------- 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: 0.0570 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.137370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103969 restraints weight = 7401.050| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.48 r_work: 0.3232 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1007 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= 0.156 Angle : 0.529 5.660 9108 Z= 0.285 Chirality : 0.042 0.151 1002 Planarity : 0.004 0.032 1032 Dihedral : 21.691 82.756 1275 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.84 % Allowed : 15.96 % Favored : 81.21 % 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: 0.92 (0.34), residues: 672 helix: 1.73 (0.32), residues: 288 sheet: -1.15 (0.66), residues: 52 loop : -0.02 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.021 0.001 TYR B 5 PHE 0.007 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 0.00356 / 0.16 ( 6564) covalent geometry : angle 0.52913 / 0.29 ( 9108) hydrogen bonds : bond 0.04779 / 3.29 ( 281) hydrogen bonds : angle 3.77086 / 2.57 ( 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 57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.190 Fit side-chains REVERT: A 64 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8392 (t80) REVERT: A 231 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8173 (mm-40) REVERT: A 333 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7746 (tpt90) REVERT: B 169 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 176 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7916 (tpt90) REVERT: B 200 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8539 (t0) REVERT: B 229 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8255 (mmt-90) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.0830 time to fit residues: 5.8107 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 : 0.224 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.136400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102830 restraints weight = 7469.768| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.50 r_work: 0.3215 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6564 Z= 0.181 Angle : 0.545 5.778 9108 Z= 0.292 Chirality : 0.043 0.152 1002 Planarity : 0.004 0.032 1032 Dihedral : 21.723 82.352 1275 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.01 % Allowed : 15.78 % Favored : 81.21 % 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: 0.91 (0.34), residues: 672 helix: 1.71 (0.32), residues: 288 sheet: -1.12 (0.67), residues: 52 loop : -0.02 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.022 0.002 TYR B 5 PHE 0.008 0.001 PHE B 3 TRP 0.012 0.002 TRP B 156 HIS 0.002 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 6564) covalent geometry : angle 0.54490 / 0.29 ( 9108) hydrogen bonds : bond 0.04979 / 3.42 ( 281) hydrogen bonds : angle 3.78641 / 2.58 ( 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 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.186 Fit side-chains REVERT: A 64 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8383 (t80) REVERT: A 231 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8181 (mm-40) REVERT: A 333 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7771 (tpt90) REVERT: B 169 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7852 (mm-30) REVERT: B 176 ARG cc_start: 0.8411 (mmm160) cc_final: 0.7923 (tpt90) REVERT: B 200 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8536 (t0) REVERT: B 229 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8283 (mmt-90) outliers start: 17 outliers final: 13 residues processed: 52 average time/residue: 0.1048 time to fit residues: 7.1724 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 : 0.211 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 33 optimal weight: 30.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.141309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108395 restraints weight = 7276.536| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.47 r_work: 0.3309 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6564 Z= 0.108 Angle : 0.498 5.909 9108 Z= 0.270 Chirality : 0.040 0.152 1002 Planarity : 0.003 0.033 1032 Dihedral : 21.628 83.272 1275 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.13 % Allowed : 16.84 % 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: 1.23 (0.35), residues: 672 helix: 1.94 (0.32), residues: 290 sheet: -0.80 (0.73), residues: 48 loop : 0.14 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.013 0.001 TYR B 5 PHE 0.005 0.001 PHE A 171 TRP 0.013 0.001 TRP B 156 HIS 0.001 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 6564) covalent geometry : angle 0.49767 / 0.27 ( 9108) hydrogen bonds : bond 0.04078 / 2.79 ( 281) hydrogen bonds : angle 3.64439 / 2.48 ( 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 56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.182 Fit side-chains REVERT: A 64 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8436 (t80) REVERT: A 231 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8175 (mm-40) REVERT: A 260 MET cc_start: 0.8940 (ttm) cc_final: 0.8735 (ttt) REVERT: A 333 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7763 (tpt90) REVERT: B 169 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7894 (mm-30) REVERT: B 176 ARG cc_start: 0.8395 (mmm160) cc_final: 0.7936 (tpt90) REVERT: B 200 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8548 (t0) REVERT: B 229 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8242 (mmt-90) outliers start: 12 outliers final: 8 residues processed: 54 average time/residue: 0.0949 time to fit residues: 6.6722 Evaluate side-chains 54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 B residue 64 TYR Chi-restraints excluded: chain B residue 161 VAL 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 297 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.137939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104349 restraints weight = 7382.265| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.50 r_work: 0.3243 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6564 Z= 0.152 Angle : 0.523 6.644 9108 Z= 0.281 Chirality : 0.042 0.152 1002 Planarity : 0.004 0.032 1032 Dihedral : 21.642 82.421 1272 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.48 % Allowed : 16.67 % 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: 1.90 (0.32), residues: 290 sheet: -0.84 (0.71), residues: 48 loop : 0.14 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.020 0.001 TYR B 5 PHE 0.007 0.001 PHE B 3 TRP 0.013 0.002 TRP B 156 HIS 0.001 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 6564) covalent geometry : angle 0.52306 / 0.28 ( 9108) hydrogen bonds : bond 0.04527 / 3.12 ( 281) hydrogen bonds : angle 3.67693 / 2.52 ( 759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.76 seconds wall clock time: 28 minutes 42.70 seconds (1722.70 seconds total)