Starting phenix.real_space_refine on Thu Jul 2 17:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bes_12158/07_2026/7bes_12158.cif" } resolution = 2.85 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 60 5.16 5 C 5870 2.51 5 N 1650 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 9446 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1182 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UTP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, E, F Time building chain proxies: 2.16, per 1000 atoms: 0.23 Number of scatterers: 9446 At special positions: 0 Unit cell: (87.316, 116.772, 87.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 24 15.00 O 1842 8.00 N 1650 7.00 C 5870 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: 0.86 Conformation dependent library (CDL) restraints added in 322.6 milliseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 49.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 92 through 117 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 164 through 176 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 221 through 231 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 50 through 67 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 92 through 117 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 50 through 67 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 92 through 117 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 50 through 67 Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 92 through 117 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'E' and resid 164 through 176 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 221 through 231 Processing helix chain 'E' and resid 244 through 252 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 50 through 67 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 92 through 117 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'F' and resid 164 through 177 Processing sheet with id=1, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.299A pdb=" N VAL A 181 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 238 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N MET A 183 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 207 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 135 through 136 removed outlier: 3.606A pdb=" N GLU B 135 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 71 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE B 154 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 73 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 207 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 135 through 136 removed outlier: 9.034A pdb=" N GLU C 135 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 124 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG C 32 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 182 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU C 34 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 135 through 136 removed outlier: 6.299A pdb=" N VAL D 181 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE D 238 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N MET D 183 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 207 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.606A pdb=" N GLU E 135 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 71 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE E 154 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL E 73 " --> pdb=" O PHE E 154 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL E 207 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'F' and resid 135 through 136 removed outlier: 9.034A pdb=" N GLU F 135 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL F 124 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG F 32 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU F 182 " --> pdb=" O ARG F 32 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LEU F 34 " --> pdb=" O LEU F 182 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3186 1.34 - 1.46: 1990 1.46 - 1.59: 4240 1.59 - 1.71: 8 1.71 - 1.84: 136 Bond restraints: 9560 Sorted by residual: bond pdb=" O5' UDP C 301 " pdb=" PA UDP C 301 " ideal model delta sigma weight residual 1.581 1.838 -0.257 1.50e-02 4.44e+03 2.93e+02 bond pdb=" O5' UDP F 301 " pdb=" PA UDP F 301 " ideal model delta sigma weight residual 1.581 1.838 -0.257 1.50e-02 4.44e+03 2.93e+02 bond pdb=" O5' UDP E 301 " pdb=" PA UDP E 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.92e+02 bond pdb=" O5' UDP B 301 " pdb=" PA UDP B 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.92e+02 bond pdb=" O5' UDP D 301 " pdb=" PA UDP D 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.91e+02 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 12838 3.91 - 7.82: 74 7.82 - 11.73: 22 11.73 - 15.64: 16 15.64 - 19.55: 8 Bond angle restraints: 12958 Sorted by residual: angle pdb=" O2A UDP D 301 " pdb=" PA UDP D 301 " pdb=" O3A UDP D 301 " ideal model delta sigma weight residual 105.97 121.50 -15.53 1.00e+00 1.00e+00 2.41e+02 angle pdb=" O2A UDP A 301 " pdb=" PA UDP A 301 " pdb=" O3A UDP A 301 " ideal model delta sigma weight residual 105.97 121.50 -15.53 1.00e+00 1.00e+00 2.41e+02 angle pdb=" O5' UDP D 301 " pdb=" PA UDP D 301 " pdb=" O2A UDP D 301 " ideal model delta sigma weight residual 110.83 96.61 14.22 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O5' UDP A 301 " pdb=" PA UDP A 301 " pdb=" O2A UDP A 301 " ideal model delta sigma weight residual 110.83 96.61 14.22 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O5' UDP B 301 " pdb=" PA UDP B 301 " pdb=" O2A UDP B 301 " ideal model delta sigma weight residual 110.83 96.63 14.20 1.00e+00 1.00e+00 2.02e+02 ... (remaining 12953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.23: 5172 13.23 - 26.46: 392 26.46 - 39.69: 84 39.69 - 52.92: 36 52.92 - 66.15: 18 Dihedral angle restraints: 5702 sinusoidal: 2310 harmonic: 3392 Sorted by residual: dihedral pdb=" CA LEU D 34 " pdb=" CB LEU D 34 " pdb=" CG LEU D 34 " pdb=" CD1 LEU D 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LEU A 34 " pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " pdb=" CD1 LEU A 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LEU B 34 " pdb=" CB LEU B 34 " pdb=" CG LEU B 34 " pdb=" CD1 LEU B 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.96 56.04 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 5699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1292 0.056 - 0.112: 180 0.112 - 0.169: 28 0.169 - 0.225: 6 0.225 - 0.281: 10 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C1' UTP E 302 " pdb=" C2' UTP E 302 " pdb=" N1 UTP E 302 " pdb=" O4' UTP E 302 " both_signs ideal model delta sigma weight residual False 2.31 2.59 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1' UTP B 302 " pdb=" C2' UTP B 302 " pdb=" N1 UTP B 302 " pdb=" O4' UTP B 302 " both_signs ideal model delta sigma weight residual False 2.31 2.59 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C1' UTP C 302 " pdb=" C2' UTP C 302 " pdb=" N1 UTP C 302 " pdb=" O4' UTP C 302 " both_signs ideal model delta sigma weight residual False 2.31 2.59 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1513 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 233 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO B 234 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 233 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO E 234 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 160 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO D 161 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.017 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1612 2.77 - 3.30: 9174 3.30 - 3.83: 16545 3.83 - 4.37: 19945 4.37 - 4.90: 33621 Nonbonded interactions: 80897 Sorted by model distance: nonbonded pdb=" O MET A 101 " pdb=" OG1 THR A 104 " model vdw 2.236 3.040 nonbonded pdb=" O MET D 101 " pdb=" OG1 THR D 104 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR F 137 " pdb=" OE1 GLU F 175 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 137 " pdb=" OE1 GLU C 175 " model vdw 2.259 3.040 nonbonded pdb=" O MET F 101 " pdb=" OG1 THR F 104 " model vdw 2.287 3.040 ... (remaining 80892 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' 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: 1.350 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.270 Find NCS groups from input model: 0.070 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.010 0.257 9560 Z= 0.727 Angle : 1.044 19.550 12958 Z= 0.670 Chirality : 0.049 0.281 1516 Planarity : 0.003 0.031 1656 Dihedral : 11.049 66.148 3558 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.85 % Allowed : 4.24 % Favored : 94.92 % 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: 0.37 (0.24), residues: 1214 helix: 1.82 (0.21), residues: 596 sheet: -1.15 (0.30), residues: 216 loop : -1.33 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 123 TYR 0.006 0.001 TYR B 98 PHE 0.006 0.001 PHE A 154 HIS 0.003 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00985 / 0.73 ( 9560) covalent geometry : angle 1.04383 / 0.67 (12958) hydrogen bonds : bond 0.08712 / 6.21 ( 544) hydrogen bonds : angle 4.67886 / 3.31 ( 1590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 276 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7626 (mtt180) REVERT: B 99 MET cc_start: 0.8540 (mtp) cc_final: 0.8268 (mtm) REVERT: C 99 MET cc_start: 0.8800 (mtp) cc_final: 0.8561 (mtp) REVERT: C 141 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7723 (mmt180) REVERT: C 174 LEU cc_start: 0.7031 (mt) cc_final: 0.6739 (pp) REVERT: D 215 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7627 (mtt180) REVERT: E 99 MET cc_start: 0.8538 (mtp) cc_final: 0.8268 (mtm) REVERT: F 99 MET cc_start: 0.8802 (mtp) cc_final: 0.8564 (mtp) REVERT: F 141 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7719 (mmt180) REVERT: F 174 LEU cc_start: 0.7033 (mt) cc_final: 0.6740 (pp) outliers start: 8 outliers final: 0 residues processed: 278 average time/residue: 0.5659 time to fit residues: 167.1236 Evaluate side-chains 182 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 56 GLN A 87 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 46 GLN D 56 GLN D 87 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118387 restraints weight = 10887.248| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.72 r_work: 0.3276 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9560 Z= 0.130 Angle : 0.500 11.989 12958 Z= 0.252 Chirality : 0.041 0.137 1516 Planarity : 0.004 0.032 1656 Dihedral : 6.184 57.856 1490 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.97 % Allowed : 12.71 % Favored : 84.32 % 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: 0.51 (0.24), residues: 1214 helix: 1.83 (0.21), residues: 600 sheet: -0.77 (0.29), residues: 220 loop : -1.32 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.008 0.001 TYR D 137 PHE 0.005 0.001 PHE D 80 HIS 0.003 0.001 HIS E 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9560) covalent geometry : angle 0.49991 / 0.25 (12958) hydrogen bonds : bond 0.04416 / 3.00 ( 544) hydrogen bonds : angle 4.51094 / 3.19 ( 1590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 135 GLU cc_start: 0.8497 (pt0) cc_final: 0.8296 (tt0) REVERT: A 215 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7678 (mtt180) REVERT: B 56 GLN cc_start: 0.8290 (pt0) cc_final: 0.8076 (pt0) REVERT: B 99 MET cc_start: 0.8798 (mtp) cc_final: 0.8570 (mtm) REVERT: B 135 GLU cc_start: 0.8370 (pt0) cc_final: 0.8144 (pt0) REVERT: B 211 GLU cc_start: 0.7571 (mp0) cc_final: 0.7184 (mt-10) REVERT: C 40 GLU cc_start: 0.7980 (pm20) cc_final: 0.7685 (mp0) REVERT: C 99 MET cc_start: 0.8838 (mtp) cc_final: 0.8619 (mtp) REVERT: C 141 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7822 (mmt180) REVERT: C 182 LEU cc_start: 0.7922 (mt) cc_final: 0.7674 (mp) REVERT: D 118 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: D 135 GLU cc_start: 0.8502 (pt0) cc_final: 0.8300 (tt0) REVERT: D 215 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7676 (mtt180) REVERT: E 56 GLN cc_start: 0.8302 (pt0) cc_final: 0.8091 (pt0) REVERT: E 99 MET cc_start: 0.8814 (mtp) cc_final: 0.8587 (mtm) REVERT: E 135 GLU cc_start: 0.8374 (pt0) cc_final: 0.8148 (pt0) REVERT: E 211 GLU cc_start: 0.7572 (mp0) cc_final: 0.7176 (mt-10) REVERT: F 40 GLU cc_start: 0.7976 (pm20) cc_final: 0.7684 (mp0) REVERT: F 99 MET cc_start: 0.8833 (mtp) cc_final: 0.8612 (mtp) REVERT: F 141 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7831 (mmt180) REVERT: F 182 LEU cc_start: 0.7923 (mt) cc_final: 0.7679 (mp) outliers start: 28 outliers final: 2 residues processed: 242 average time/residue: 0.5967 time to fit residues: 152.9315 Evaluate side-chains 208 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 204 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115752 restraints weight = 11013.057| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.60 r_work: 0.3221 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9560 Z= 0.148 Angle : 0.515 11.627 12958 Z= 0.262 Chirality : 0.042 0.147 1516 Planarity : 0.003 0.032 1656 Dihedral : 5.396 41.913 1490 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.33 % Allowed : 15.89 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.24), residues: 1214 helix: 1.81 (0.21), residues: 600 sheet: -0.58 (0.30), residues: 220 loop : -1.32 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 144 TYR 0.009 0.001 TYR B 98 PHE 0.009 0.001 PHE F 114 HIS 0.002 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9560) covalent geometry : angle 0.51543 / 0.26 (12958) hydrogen bonds : bond 0.04759 / 3.24 ( 544) hydrogen bonds : angle 4.51245 / 3.20 ( 1590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 130 MET cc_start: 0.8608 (ptp) cc_final: 0.8361 (ptm) REVERT: A 137 TYR cc_start: 0.8869 (t80) cc_final: 0.8648 (t80) REVERT: A 215 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7599 (mtt180) REVERT: A 230 ASP cc_start: 0.7646 (t0) cc_final: 0.7417 (t0) REVERT: B 99 MET cc_start: 0.8832 (mtp) cc_final: 0.8588 (mtm) REVERT: B 135 GLU cc_start: 0.8378 (pt0) cc_final: 0.8174 (pt0) REVERT: B 211 GLU cc_start: 0.7572 (mp0) cc_final: 0.7128 (mt-10) REVERT: C 40 GLU cc_start: 0.7995 (pm20) cc_final: 0.7719 (mp0) REVERT: C 99 MET cc_start: 0.8863 (mtp) cc_final: 0.8634 (mtp) REVERT: C 141 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7897 (mmt180) REVERT: D 118 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: D 130 MET cc_start: 0.8617 (ptp) cc_final: 0.8368 (ptm) REVERT: D 137 TYR cc_start: 0.8871 (t80) cc_final: 0.8647 (t80) REVERT: D 215 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7599 (mtt180) REVERT: D 230 ASP cc_start: 0.7636 (t0) cc_final: 0.7412 (t0) REVERT: E 99 MET cc_start: 0.8848 (mtp) cc_final: 0.8602 (mtm) REVERT: E 135 GLU cc_start: 0.8373 (pt0) cc_final: 0.8172 (pt0) REVERT: E 211 GLU cc_start: 0.7575 (mp0) cc_final: 0.7121 (mt-10) REVERT: F 40 GLU cc_start: 0.7997 (pm20) cc_final: 0.7719 (mp0) REVERT: F 99 MET cc_start: 0.8866 (mtp) cc_final: 0.8639 (mtp) REVERT: F 141 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7908 (mmt180) outliers start: 22 outliers final: 8 residues processed: 234 average time/residue: 0.6584 time to fit residues: 162.4379 Evaluate side-chains 216 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 87 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 10 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 113 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 239 ASN C 87 GLN C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN E 239 ASN F 87 GLN F 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114513 restraints weight = 10979.353| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.73 r_work: 0.3219 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9560 Z= 0.139 Angle : 0.518 11.357 12958 Z= 0.260 Chirality : 0.042 0.132 1516 Planarity : 0.003 0.032 1656 Dihedral : 5.317 37.336 1490 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 2.75 % Allowed : 17.16 % Favored : 80.08 % 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: 0.58 (0.24), residues: 1214 helix: 1.77 (0.21), residues: 600 sheet: -0.45 (0.30), residues: 220 loop : -1.29 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 144 TYR 0.009 0.001 TYR E 98 PHE 0.007 0.001 PHE F 114 HIS 0.003 0.001 HIS E 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 9560) covalent geometry : angle 0.51759 / 0.26 (12958) hydrogen bonds : bond 0.04611 / 3.13 ( 544) hydrogen bonds : angle 4.49953 / 3.19 ( 1590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 130 MET cc_start: 0.8606 (ptp) cc_final: 0.8355 (ptm) REVERT: A 137 TYR cc_start: 0.8866 (t80) cc_final: 0.8635 (t80) REVERT: A 215 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7679 (mtt180) REVERT: A 230 ASP cc_start: 0.7669 (t0) cc_final: 0.7431 (t0) REVERT: B 99 MET cc_start: 0.8781 (mtp) cc_final: 0.8539 (mtm) REVERT: B 135 GLU cc_start: 0.8370 (pt0) cc_final: 0.8167 (pt0) REVERT: B 166 ASP cc_start: 0.8571 (m-30) cc_final: 0.8126 (t0) REVERT: B 211 GLU cc_start: 0.7499 (mp0) cc_final: 0.7062 (mt-10) REVERT: C 40 GLU cc_start: 0.7967 (pm20) cc_final: 0.7719 (mp0) REVERT: C 99 MET cc_start: 0.8838 (mtp) cc_final: 0.8611 (mtp) REVERT: D 118 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: D 130 MET cc_start: 0.8611 (ptp) cc_final: 0.8360 (ptm) REVERT: D 137 TYR cc_start: 0.8865 (t80) cc_final: 0.8632 (t80) REVERT: D 215 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7678 (mtt180) REVERT: D 230 ASP cc_start: 0.7668 (t0) cc_final: 0.7449 (t0) REVERT: E 99 MET cc_start: 0.8786 (mtp) cc_final: 0.8543 (mtm) REVERT: E 135 GLU cc_start: 0.8360 (pt0) cc_final: 0.8152 (pt0) REVERT: E 166 ASP cc_start: 0.8567 (m-30) cc_final: 0.8120 (t0) REVERT: E 211 GLU cc_start: 0.7506 (mp0) cc_final: 0.7064 (mt-10) REVERT: F 40 GLU cc_start: 0.7976 (pm20) cc_final: 0.7722 (mp0) REVERT: F 99 MET cc_start: 0.8839 (mtp) cc_final: 0.8610 (mtp) outliers start: 26 outliers final: 7 residues processed: 226 average time/residue: 0.5960 time to fit residues: 142.2471 Evaluate side-chains 199 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 190 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111736 restraints weight = 10900.321| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.75 r_work: 0.3183 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9560 Z= 0.168 Angle : 0.540 11.573 12958 Z= 0.275 Chirality : 0.042 0.137 1516 Planarity : 0.003 0.034 1656 Dihedral : 5.586 39.248 1490 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.97 % Allowed : 17.16 % Favored : 79.87 % 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: 0.48 (0.24), residues: 1214 helix: 1.67 (0.21), residues: 600 sheet: -0.41 (0.31), residues: 220 loop : -1.36 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.010 0.001 TYR E 98 PHE 0.006 0.001 PHE B 225 HIS 0.002 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9560) covalent geometry : angle 0.54030 / 0.27 (12958) hydrogen bonds : bond 0.05046 / 3.44 ( 544) hydrogen bonds : angle 4.59604 / 3.25 ( 1590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 137 TYR cc_start: 0.8869 (t80) cc_final: 0.8669 (t80) REVERT: A 215 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7515 (mtt180) REVERT: A 230 ASP cc_start: 0.7664 (t0) cc_final: 0.7447 (t0) REVERT: B 135 GLU cc_start: 0.8443 (pt0) cc_final: 0.8240 (pt0) REVERT: B 211 GLU cc_start: 0.7558 (mp0) cc_final: 0.7138 (mt-10) REVERT: C 40 GLU cc_start: 0.7986 (pm20) cc_final: 0.7771 (mp0) REVERT: C 99 MET cc_start: 0.8835 (mtp) cc_final: 0.8592 (mtp) REVERT: D 118 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 137 TYR cc_start: 0.8867 (t80) cc_final: 0.8665 (t80) REVERT: D 215 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7515 (mtt180) REVERT: D 230 ASP cc_start: 0.7637 (t0) cc_final: 0.7418 (t0) REVERT: E 135 GLU cc_start: 0.8433 (pt0) cc_final: 0.8231 (pt0) REVERT: E 211 GLU cc_start: 0.7577 (mp0) cc_final: 0.7147 (mt-10) REVERT: F 40 GLU cc_start: 0.7994 (pm20) cc_final: 0.7775 (mp0) REVERT: F 99 MET cc_start: 0.8829 (mtp) cc_final: 0.8586 (mtp) outliers start: 28 outliers final: 8 residues processed: 213 average time/residue: 0.6817 time to fit residues: 153.3053 Evaluate side-chains 198 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113496 restraints weight = 10747.451| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.74 r_work: 0.3204 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9560 Z= 0.142 Angle : 0.524 11.307 12958 Z= 0.266 Chirality : 0.042 0.135 1516 Planarity : 0.003 0.035 1656 Dihedral : 5.312 39.932 1490 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.18 % Allowed : 17.69 % Favored : 79.13 % 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: 0.56 (0.24), residues: 1214 helix: 1.73 (0.21), residues: 602 sheet: -0.35 (0.31), residues: 220 loop : -1.34 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 144 TYR 0.008 0.001 TYR B 98 PHE 0.006 0.001 PHE E 225 HIS 0.002 0.001 HIS E 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9560) covalent geometry : angle 0.52365 / 0.27 (12958) hydrogen bonds : bond 0.04662 / 3.17 ( 544) hydrogen bonds : angle 4.52009 / 3.20 ( 1590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 118 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: A 137 TYR cc_start: 0.8854 (t80) cc_final: 0.8636 (t80) REVERT: A 215 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7605 (mtt180) REVERT: B 135 GLU cc_start: 0.8437 (pt0) cc_final: 0.8235 (pt0) REVERT: C 99 MET cc_start: 0.8825 (mtp) cc_final: 0.8602 (mtp) REVERT: D 47 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8711 (p) REVERT: D 118 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: D 137 TYR cc_start: 0.8852 (t80) cc_final: 0.8634 (t80) REVERT: D 215 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7659 (mtt180) REVERT: E 135 GLU cc_start: 0.8415 (pt0) cc_final: 0.8212 (pt0) REVERT: F 99 MET cc_start: 0.8814 (mtp) cc_final: 0.8590 (mtp) outliers start: 30 outliers final: 11 residues processed: 216 average time/residue: 0.6779 time to fit residues: 155.1349 Evaluate side-chains 197 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 87 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 86 optimal weight: 0.0980 chunk 104 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 46 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109876 restraints weight = 10846.422| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.73 r_work: 0.3154 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9560 Z= 0.201 Angle : 0.589 11.648 12958 Z= 0.299 Chirality : 0.044 0.136 1516 Planarity : 0.004 0.039 1656 Dihedral : 5.811 39.692 1490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.28 % Allowed : 19.07 % Favored : 77.65 % 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: 0.41 (0.24), residues: 1214 helix: 1.59 (0.21), residues: 600 sheet: -0.42 (0.30), residues: 220 loop : -1.35 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 93 TYR 0.013 0.002 TYR E 98 PHE 0.009 0.001 PHE B 225 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 9560) covalent geometry : angle 0.58932 / 0.30 (12958) hydrogen bonds : bond 0.05397 / 3.67 ( 544) hydrogen bonds : angle 4.65472 / 3.29 ( 1590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 137 TYR cc_start: 0.8901 (t80) cc_final: 0.8660 (t80) REVERT: A 215 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7492 (mtt180) REVERT: B 135 GLU cc_start: 0.8457 (pt0) cc_final: 0.8228 (pt0) REVERT: B 193 GLU cc_start: 0.7106 (tp30) cc_final: 0.6767 (tm-30) REVERT: B 241 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7446 (mm) REVERT: C 99 MET cc_start: 0.8859 (mtp) cc_final: 0.8630 (mtp) REVERT: D 118 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: D 137 TYR cc_start: 0.8895 (t80) cc_final: 0.8653 (t80) REVERT: D 215 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7467 (mtt180) REVERT: E 135 GLU cc_start: 0.8444 (pt0) cc_final: 0.8216 (pt0) REVERT: E 193 GLU cc_start: 0.7101 (tp30) cc_final: 0.6760 (tm-30) REVERT: E 241 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7444 (mm) REVERT: F 99 MET cc_start: 0.8846 (mtp) cc_final: 0.8617 (mtp) outliers start: 31 outliers final: 17 residues processed: 206 average time/residue: 0.7215 time to fit residues: 157.0884 Evaluate side-chains 218 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 174 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 87 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111467 restraints weight = 10814.570| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.74 r_work: 0.3181 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9560 Z= 0.166 Angle : 0.569 11.379 12958 Z= 0.289 Chirality : 0.043 0.134 1516 Planarity : 0.004 0.037 1656 Dihedral : 5.503 40.600 1490 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 3.60 % Allowed : 19.39 % Favored : 77.01 % 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: 0.47 (0.24), residues: 1214 helix: 1.61 (0.21), residues: 600 sheet: -0.38 (0.30), residues: 218 loop : -1.29 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 144 TYR 0.010 0.001 TYR B 98 PHE 0.007 0.001 PHE B 225 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9560) covalent geometry : angle 0.56854 / 0.29 (12958) hydrogen bonds : bond 0.04990 / 3.40 ( 544) hydrogen bonds : angle 4.61620 / 3.26 ( 1590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (p) REVERT: A 118 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 137 TYR cc_start: 0.8855 (t80) cc_final: 0.8066 (t80) REVERT: A 175 GLU cc_start: 0.8324 (tt0) cc_final: 0.7938 (tt0) REVERT: A 215 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7527 (mtt180) REVERT: B 135 GLU cc_start: 0.8452 (pt0) cc_final: 0.8221 (pt0) REVERT: B 166 ASP cc_start: 0.8609 (m-30) cc_final: 0.8103 (t0) REVERT: B 193 GLU cc_start: 0.7113 (tp30) cc_final: 0.6785 (tm-30) REVERT: B 241 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7316 (mm) REVERT: C 141 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7447 (tpt-90) REVERT: D 47 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8754 (p) REVERT: D 118 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: D 137 TYR cc_start: 0.8854 (t80) cc_final: 0.8061 (t80) REVERT: D 175 GLU cc_start: 0.8309 (tt0) cc_final: 0.7925 (tt0) REVERT: D 215 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7594 (mtt180) REVERT: E 135 GLU cc_start: 0.8440 (pt0) cc_final: 0.8207 (pt0) REVERT: E 166 ASP cc_start: 0.8620 (m-30) cc_final: 0.8115 (t0) REVERT: E 193 GLU cc_start: 0.7108 (tp30) cc_final: 0.6780 (tm-30) REVERT: E 241 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7320 (mm) REVERT: F 141 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7455 (tpt-90) outliers start: 34 outliers final: 13 residues processed: 220 average time/residue: 0.6635 time to fit residues: 154.6418 Evaluate side-chains 201 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 141 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 113 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113729 restraints weight = 10815.386| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.74 r_work: 0.3213 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9560 Z= 0.135 Angle : 0.555 10.629 12958 Z= 0.283 Chirality : 0.042 0.137 1516 Planarity : 0.003 0.037 1656 Dihedral : 5.243 40.100 1490 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.22 % Allowed : 20.97 % Favored : 76.80 % 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: 0.55 (0.24), residues: 1214 helix: 1.67 (0.21), residues: 602 sheet: -0.33 (0.31), residues: 218 loop : -1.25 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 59 TYR 0.007 0.001 TYR D 98 PHE 0.006 0.001 PHE B 225 HIS 0.002 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9560) covalent geometry : angle 0.55491 / 0.28 (12958) hydrogen bonds : bond 0.04537 / 3.10 ( 544) hydrogen bonds : angle 4.57960 / 3.23 ( 1590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 118 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 137 TYR cc_start: 0.8823 (t80) cc_final: 0.8022 (t80) REVERT: A 175 GLU cc_start: 0.8269 (tt0) cc_final: 0.7824 (tt0) REVERT: A 215 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7591 (mtt180) REVERT: B 135 GLU cc_start: 0.8417 (pt0) cc_final: 0.8183 (pt0) REVERT: B 193 GLU cc_start: 0.7099 (tp30) cc_final: 0.6791 (tm-30) REVERT: B 241 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7199 (mm) REVERT: D 47 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8762 (p) REVERT: D 118 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: D 137 TYR cc_start: 0.8815 (t80) cc_final: 0.8010 (t80) REVERT: D 175 GLU cc_start: 0.8263 (tt0) cc_final: 0.7820 (tt0) REVERT: D 215 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7644 (mtt180) REVERT: E 135 GLU cc_start: 0.8407 (pt0) cc_final: 0.8171 (pt0) REVERT: E 193 GLU cc_start: 0.7090 (tp30) cc_final: 0.6784 (tm-30) REVERT: E 241 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7206 (mm) outliers start: 21 outliers final: 8 residues processed: 197 average time/residue: 0.6539 time to fit residues: 136.4820 Evaluate side-chains 196 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 87 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 46 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113988 restraints weight = 10839.731| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.74 r_work: 0.3217 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9560 Z= 0.138 Angle : 0.567 10.449 12958 Z= 0.288 Chirality : 0.042 0.138 1516 Planarity : 0.003 0.036 1656 Dihedral : 5.247 39.988 1490 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.12 % Allowed : 22.14 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.24), residues: 1214 helix: 1.66 (0.21), residues: 602 sheet: -0.31 (0.31), residues: 218 loop : -1.23 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.008 0.001 TYR B 98 PHE 0.006 0.001 PHE B 225 HIS 0.002 0.001 HIS E 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9560) covalent geometry : angle 0.56723 / 0.29 (12958) hydrogen bonds : bond 0.04524 / 3.09 ( 544) hydrogen bonds : angle 4.58637 / 3.23 ( 1590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8711 (p) REVERT: A 118 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: A 215 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7638 (mtt180) REVERT: B 99 MET cc_start: 0.8731 (mtp) cc_final: 0.8498 (mtm) REVERT: B 135 GLU cc_start: 0.8414 (pt0) cc_final: 0.8180 (pt0) REVERT: B 166 ASP cc_start: 0.8494 (m-30) cc_final: 0.7989 (t0) REVERT: B 193 GLU cc_start: 0.7091 (tp30) cc_final: 0.6770 (tm-30) REVERT: B 241 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7195 (mm) REVERT: D 47 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8713 (p) REVERT: D 118 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: D 137 TYR cc_start: 0.8811 (t80) cc_final: 0.8017 (t80) REVERT: D 175 GLU cc_start: 0.8268 (tt0) cc_final: 0.7805 (tt0) REVERT: D 215 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7657 (mtt180) REVERT: E 99 MET cc_start: 0.8738 (mtp) cc_final: 0.8504 (mtm) REVERT: E 135 GLU cc_start: 0.8404 (pt0) cc_final: 0.8169 (pt0) REVERT: E 166 ASP cc_start: 0.8491 (m-30) cc_final: 0.7986 (t0) REVERT: E 193 GLU cc_start: 0.7078 (tp30) cc_final: 0.6761 (tm-30) REVERT: E 241 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7202 (mm) outliers start: 20 outliers final: 6 residues processed: 198 average time/residue: 0.6343 time to fit residues: 133.0962 Evaluate side-chains 183 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 0.8980 chunk 82 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115091 restraints weight = 10731.515| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.73 r_work: 0.3230 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9560 Z= 0.133 Angle : 0.562 10.589 12958 Z= 0.287 Chirality : 0.042 0.140 1516 Planarity : 0.003 0.035 1656 Dihedral : 5.164 39.827 1490 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.12 % Allowed : 22.35 % Favored : 75.53 % 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: 0.57 (0.24), residues: 1214 helix: 1.64 (0.21), residues: 606 sheet: -0.29 (0.31), residues: 218 loop : -1.20 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 59 TYR 0.008 0.001 TYR D 98 PHE 0.006 0.001 PHE F 114 HIS 0.002 0.001 HIS E 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9560) covalent geometry : angle 0.56155 / 0.29 (12958) hydrogen bonds : bond 0.04372 / 2.98 ( 544) hydrogen bonds : angle 4.57337 / 3.22 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.03 seconds wall clock time: 62 minutes 34.86 seconds (3754.86 seconds total)