Starting phenix.real_space_refine on Tue Feb 11 11:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.map" model { file = "/net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a02_15045/02_2025/8a02_15045.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "E" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "D" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 3.86, per 1000 atoms: 0.70 Number of scatterers: 5511 At special positions: 0 Unit cell: (94.24, 96.72, 63.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 885 7.00 C 3495 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: 1.31 Conformation dependent library (CDL) restraints added in 635.7 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 19 sheets defined 9.5% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.922A pdb=" N LEU F 35 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 178 through 187 removed outlier: 3.565A pdb=" N ARG F 187 " --> pdb=" O GLN F 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 60 through 66 Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 178 through 187 Processing sheet with id=AA1, first strand: chain 'F' and resid 2 through 7 removed outlier: 5.892A pdb=" N LYS F 2 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY F 119 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 4 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 23 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 15 through 17 removed outlier: 7.190A pdb=" N ILE F 42 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASN F 56 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE F 44 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU F 54 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ARG F 46 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL F 52 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 93 through 94 removed outlier: 5.967A pdb=" N SER F 93 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 128 through 137 removed outlier: 5.517A pdb=" N ASN F 230 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU F 153 " --> pdb=" O ARG F 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 143 through 146 removed outlier: 6.601A pdb=" N GLN F 168 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 219 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER F 166 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE F 221 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP F 164 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS F 223 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 162 " --> pdb=" O LYS F 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 7 removed outlier: 5.694A pdb=" N LYS E 2 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 119 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA E 4 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA E 23 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 15 through 17 removed outlier: 3.695A pdb=" N SER E 101 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE E 40 " --> pdb=" O ASN E 56 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN E 56 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 42 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 94 removed outlier: 5.751A pdb=" N SER E 93 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 128 through 137 removed outlier: 5.192A pdb=" N ASN E 230 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU E 153 " --> pdb=" O ARG E 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 143 through 146 removed outlier: 3.937A pdb=" N LEU E 165 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 7 removed outlier: 6.654A pdb=" N LEU D 117 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR D 5 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 115 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 27 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 5.657A pdb=" N SER D 93 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 128 through 137 removed outlier: 5.268A pdb=" N ASN D 230 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 153 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 143 through 146 removed outlier: 3.601A pdb=" N GLY D 218 " --> pdb=" O GLN D 168 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 194 through 195 224 hydrogen bonds defined for protein. 594 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: 1.66 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1818 1.34 - 1.46: 866 1.46 - 1.57: 2863 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" N GLY F 49 " pdb=" CA GLY F 49 " ideal model delta sigma weight residual 1.449 1.465 -0.015 1.45e-02 4.76e+03 1.14e+00 bond pdb=" CG LEU F 117 " pdb=" CD2 LEU F 117 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.89e-01 bond pdb=" N GLY E 119 " pdb=" CA GLY E 119 " ideal model delta sigma weight residual 1.449 1.457 -0.008 1.14e-02 7.69e+03 4.54e-01 bond pdb=" CG LEU F 26 " pdb=" CD2 LEU F 26 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.08e-01 bond pdb=" CG1 ILE E 155 " pdb=" CD1 ILE E 155 " ideal model delta sigma weight residual 1.513 1.489 0.024 3.90e-02 6.57e+02 3.82e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 7320 1.15 - 2.30: 188 2.30 - 3.44: 34 3.44 - 4.59: 4 4.59 - 5.74: 2 Bond angle restraints: 7548 Sorted by residual: angle pdb=" C LEU F 26 " pdb=" N SER F 27 " pdb=" CA SER F 27 " ideal model delta sigma weight residual 122.73 119.59 3.14 1.62e+00 3.81e-01 3.77e+00 angle pdb=" C GLY F 47 " pdb=" N ASN F 48 " pdb=" CA ASN F 48 " ideal model delta sigma weight residual 123.25 120.28 2.97 1.69e+00 3.50e-01 3.09e+00 angle pdb=" C GLY F 49 " pdb=" N SER F 50 " pdb=" CA SER F 50 " ideal model delta sigma weight residual 121.54 124.68 -3.14 1.91e+00 2.74e-01 2.71e+00 angle pdb=" CA LEU F 153 " pdb=" CB LEU F 153 " pdb=" CG LEU F 153 " ideal model delta sigma weight residual 116.30 122.04 -5.74 3.50e+00 8.16e-02 2.69e+00 angle pdb=" C ILE F 42 " pdb=" N TYR F 43 " pdb=" CA TYR F 43 " ideal model delta sigma weight residual 122.11 119.58 2.53 1.59e+00 3.96e-01 2.54e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3090 17.88 - 35.76: 259 35.76 - 53.64: 52 53.64 - 71.52: 11 71.52 - 89.40: 8 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA ASP F 198 " pdb=" CB ASP F 198 " pdb=" CG ASP F 198 " pdb=" OD1 ASP F 198 " ideal model delta sinusoidal sigma weight residual -30.00 -88.02 58.02 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU D 45 " pdb=" CG GLU D 45 " pdb=" CD GLU D 45 " pdb=" OE1 GLU D 45 " ideal model delta sinusoidal sigma weight residual 0.00 -84.79 84.79 1 3.00e+01 1.11e-03 9.70e+00 dihedral pdb=" CG ARG E 114 " pdb=" CD ARG E 114 " pdb=" NE ARG E 114 " pdb=" CZ ARG E 114 " ideal model delta sinusoidal sigma weight residual -90.00 -131.38 41.38 2 1.50e+01 4.44e-03 9.32e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 579 0.031 - 0.063: 204 0.063 - 0.094: 60 0.094 - 0.125: 82 0.125 - 0.156: 11 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE F 42 " pdb=" N ILE F 42 " pdb=" C ILE F 42 " pdb=" CB ILE F 42 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE F 83 " pdb=" N ILE F 83 " pdb=" C ILE F 83 " pdb=" CB ILE F 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE E 42 " pdb=" N ILE E 42 " pdb=" C ILE E 42 " pdb=" CB ILE E 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 178 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO E 179 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 179 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 179 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 178 " -0.004 2.00e-02 2.50e+03 8.06e-03 6.50e-01 pdb=" C LEU E 178 " 0.014 2.00e-02 2.50e+03 pdb=" O LEU E 178 " -0.005 2.00e-02 2.50e+03 pdb=" N PRO E 179 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 122 " 0.013 5.00e-02 4.00e+02 1.99e-02 6.31e-01 pdb=" N PRO F 123 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO F 123 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 123 " 0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1162 2.79 - 3.32: 4453 3.32 - 3.85: 8367 3.85 - 4.37: 9799 4.37 - 4.90: 18508 Nonbonded interactions: 42289 Sorted by model distance: nonbonded pdb=" NZ LYS E 2 " pdb=" OG1 THR E 5 " model vdw 2.264 3.120 nonbonded pdb=" OD1 ASN F 80 " pdb=" NH2 ARG F 114 " model vdw 2.395 3.120 nonbonded pdb=" N GLY D 22 " pdb=" O ILE D 120 " model vdw 2.406 3.120 nonbonded pdb=" O GLU D 140 " pdb=" NE2 GLN D 225 " model vdw 2.409 3.120 nonbonded pdb=" OG SER F 76 " pdb=" N ASP F 77 " model vdw 2.443 3.120 ... (remaining 42284 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 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.830 Find NCS groups from input model: 0.210 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5571 Z= 0.167 Angle : 0.469 5.739 7548 Z= 0.257 Chirality : 0.047 0.156 936 Planarity : 0.003 0.026 960 Dihedral : 14.611 89.400 2064 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.32), residues: 711 helix: 0.95 (0.67), residues: 60 sheet: 0.70 (0.30), residues: 300 loop : -0.53 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 118 PHE 0.009 0.001 PHE D 231 TYR 0.012 0.001 TYR E 43 ARG 0.002 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.648 Fit side-chains REVERT: F 155 ILE cc_start: 0.8606 (mt) cc_final: 0.8355 (mt) REVERT: D 110 ILE cc_start: 0.9032 (mm) cc_final: 0.8752 (mt) REVERT: D 147 ASP cc_start: 0.7550 (t70) cc_final: 0.7279 (t70) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1615 time to fit residues: 23.8104 Evaluate side-chains 87 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104896 restraints weight = 7223.465| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.78 r_work: 0.2993 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5571 Z= 0.315 Angle : 0.552 5.810 7548 Z= 0.297 Chirality : 0.049 0.164 936 Planarity : 0.003 0.030 960 Dihedral : 4.295 14.863 750 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.75 % Allowed : 10.16 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 711 helix: 0.64 (0.66), residues: 60 sheet: 0.54 (0.30), residues: 300 loop : -0.62 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.017 0.002 TYR E 43 ARG 0.003 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.721 Fit side-chains REVERT: F 100 GLU cc_start: 0.8225 (pt0) cc_final: 0.7840 (pt0) REVERT: F 155 ILE cc_start: 0.8713 (mt) cc_final: 0.8493 (mt) REVERT: F 160 ASP cc_start: 0.8015 (t0) cc_final: 0.7807 (t0) REVERT: E 1 MET cc_start: 0.8193 (pmm) cc_final: 0.7690 (ptt) REVERT: D 110 ILE cc_start: 0.9057 (mm) cc_final: 0.8652 (mt) REVERT: D 188 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (t0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.1623 time to fit residues: 22.5581 Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 188 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101838 restraints weight = 7340.061| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.78 r_work: 0.2949 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 5571 Z= 0.481 Angle : 0.651 5.924 7548 Z= 0.348 Chirality : 0.052 0.169 936 Planarity : 0.004 0.035 960 Dihedral : 4.843 16.569 750 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 2.70 % Allowed : 15.87 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.31), residues: 711 helix: -0.07 (0.64), residues: 60 sheet: 0.30 (0.30), residues: 297 loop : -0.94 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 118 PHE 0.012 0.002 PHE F 63 TYR 0.020 0.002 TYR E 43 ARG 0.004 0.001 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.683 Fit side-chains REVERT: E 1 MET cc_start: 0.8254 (pmm) cc_final: 0.7841 (ptt) REVERT: E 82 MET cc_start: 0.8450 (tmm) cc_final: 0.7901 (ttp) REVERT: E 136 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8680 (m) REVERT: D 110 ILE cc_start: 0.9054 (mm) cc_final: 0.8667 (mt) outliers start: 17 outliers final: 13 residues processed: 94 average time/residue: 0.1583 time to fit residues: 19.8009 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106046 restraints weight = 7259.074| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.80 r_work: 0.3003 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5571 Z= 0.160 Angle : 0.456 4.875 7548 Z= 0.251 Chirality : 0.047 0.149 936 Planarity : 0.003 0.029 960 Dihedral : 4.119 14.740 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.22 % Allowed : 17.30 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.31), residues: 711 helix: 0.40 (0.65), residues: 60 sheet: 0.51 (0.30), residues: 297 loop : -0.82 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.013 0.001 TYR E 43 ARG 0.002 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.669 Fit side-chains REVERT: F 107 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: F 110 ILE cc_start: 0.8660 (mm) cc_final: 0.8416 (mm) REVERT: E 1 MET cc_start: 0.8186 (pmm) cc_final: 0.7829 (ptt) REVERT: E 140 GLU cc_start: 0.8694 (pp20) cc_final: 0.8132 (pp20) REVERT: D 110 ILE cc_start: 0.9123 (mm) cc_final: 0.8663 (mt) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.1626 time to fit residues: 20.9940 Evaluate side-chains 91 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.116773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.105336 restraints weight = 7120.514| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.77 r_work: 0.2991 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5571 Z= 0.212 Angle : 0.480 5.240 7548 Z= 0.263 Chirality : 0.047 0.155 936 Planarity : 0.003 0.029 960 Dihedral : 4.155 14.736 750 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.17 % Allowed : 17.78 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.31), residues: 711 helix: 0.40 (0.64), residues: 60 sheet: 0.52 (0.30), residues: 297 loop : -0.80 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.016 0.001 TYR E 43 ARG 0.001 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.657 Fit side-chains REVERT: F 107 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: F 110 ILE cc_start: 0.8653 (mm) cc_final: 0.8419 (mm) REVERT: E 1 MET cc_start: 0.8184 (pmm) cc_final: 0.7826 (ptt) REVERT: D 1 MET cc_start: 0.7727 (pmm) cc_final: 0.5212 (tpt) REVERT: D 110 ILE cc_start: 0.9103 (mm) cc_final: 0.8648 (mt) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.1385 time to fit residues: 18.8859 Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 188 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.113303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.101866 restraints weight = 7251.761| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.80 r_work: 0.2942 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 5571 Z= 0.464 Angle : 0.628 5.943 7548 Z= 0.337 Chirality : 0.051 0.167 936 Planarity : 0.004 0.034 960 Dihedral : 4.741 15.629 750 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 4.13 % Allowed : 18.25 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.31), residues: 711 helix: -0.28 (0.62), residues: 60 sheet: 0.27 (0.30), residues: 297 loop : -1.02 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 118 PHE 0.011 0.002 PHE D 231 TYR 0.019 0.002 TYR E 43 ARG 0.003 0.001 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.647 Fit side-chains REVERT: F 107 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: E 1 MET cc_start: 0.8235 (pmm) cc_final: 0.7858 (ptt) REVERT: E 59 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (mp) REVERT: E 82 MET cc_start: 0.8395 (tmm) cc_final: 0.7823 (ttp) REVERT: E 136 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8651 (m) REVERT: D 110 ILE cc_start: 0.9117 (mm) cc_final: 0.8736 (mt) outliers start: 26 outliers final: 17 residues processed: 96 average time/residue: 0.1611 time to fit residues: 20.7471 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.117061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105556 restraints weight = 7231.370| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.80 r_work: 0.2995 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5571 Z= 0.162 Angle : 0.458 5.160 7548 Z= 0.253 Chirality : 0.047 0.148 936 Planarity : 0.003 0.031 960 Dihedral : 4.110 16.577 750 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.70 % Allowed : 19.68 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.31), residues: 711 helix: 0.18 (0.64), residues: 60 sheet: 0.45 (0.30), residues: 297 loop : -0.85 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 118 PHE 0.008 0.001 PHE D 231 TYR 0.013 0.001 TYR E 43 ARG 0.001 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.671 Fit side-chains REVERT: F 107 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: F 110 ILE cc_start: 0.8706 (mm) cc_final: 0.8428 (mm) REVERT: E 1 MET cc_start: 0.8184 (pmm) cc_final: 0.7863 (ptt) REVERT: D 1 MET cc_start: 0.7555 (pmm) cc_final: 0.5092 (tpt) REVERT: D 110 ILE cc_start: 0.9078 (mm) cc_final: 0.8633 (mt) outliers start: 17 outliers final: 16 residues processed: 91 average time/residue: 0.1484 time to fit residues: 18.4582 Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 0.0010 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105979 restraints weight = 7166.666| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.80 r_work: 0.2998 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5571 Z= 0.163 Angle : 0.453 5.220 7548 Z= 0.250 Chirality : 0.047 0.150 936 Planarity : 0.003 0.030 960 Dihedral : 3.962 15.987 750 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.86 % Allowed : 19.37 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.31), residues: 711 helix: 0.36 (0.65), residues: 60 sheet: 0.54 (0.30), residues: 297 loop : -0.73 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.013 0.001 TYR E 43 ARG 0.002 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.658 Fit side-chains REVERT: F 107 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: F 110 ILE cc_start: 0.8559 (mm) cc_final: 0.8312 (mm) REVERT: E 1 MET cc_start: 0.8181 (pmm) cc_final: 0.7865 (ptt) REVERT: D 1 MET cc_start: 0.7498 (pmm) cc_final: 0.5076 (tpt) REVERT: D 110 ILE cc_start: 0.9069 (mm) cc_final: 0.8610 (mt) REVERT: D 140 GLU cc_start: 0.8420 (tt0) cc_final: 0.8100 (tp30) REVERT: D 189 ILE cc_start: 0.7954 (mm) cc_final: 0.7703 (mt) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 0.1494 time to fit residues: 19.3454 Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.103023 restraints weight = 7246.982| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.82 r_work: 0.2956 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5571 Z= 0.355 Angle : 0.560 5.703 7548 Z= 0.304 Chirality : 0.049 0.161 936 Planarity : 0.003 0.032 960 Dihedral : 4.459 16.559 750 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 4.44 % Allowed : 18.41 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 711 helix: 0.02 (0.63), residues: 60 sheet: 0.41 (0.30), residues: 297 loop : -0.86 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.011 0.002 PHE D 231 TYR 0.018 0.002 TYR E 43 ARG 0.002 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.651 Fit side-chains REVERT: F 107 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: E 1 MET cc_start: 0.8225 (pmm) cc_final: 0.7882 (ptt) REVERT: E 59 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8490 (mp) REVERT: D 1 MET cc_start: 0.7631 (pmm) cc_final: 0.5053 (tpt) REVERT: D 110 ILE cc_start: 0.9061 (mm) cc_final: 0.8656 (mt) outliers start: 28 outliers final: 21 residues processed: 102 average time/residue: 0.1384 time to fit residues: 19.5002 Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.115381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103763 restraints weight = 7264.602| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.83 r_work: 0.2968 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5571 Z= 0.258 Angle : 0.509 5.521 7548 Z= 0.279 Chirality : 0.048 0.153 936 Planarity : 0.003 0.032 960 Dihedral : 4.304 16.419 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.11 % Favored : 97.75 % Rotamer: Outliers : 3.17 % Allowed : 19.21 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 711 helix: 0.12 (0.64), residues: 60 sheet: 0.40 (0.30), residues: 297 loop : -0.83 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.015 0.001 TYR E 43 ARG 0.001 0.000 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.702 Fit side-chains REVERT: F 107 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: E 1 MET cc_start: 0.8216 (pmm) cc_final: 0.7881 (ptt) REVERT: E 82 MET cc_start: 0.8319 (tmm) cc_final: 0.7777 (ttp) REVERT: D 1 MET cc_start: 0.7578 (pmm) cc_final: 0.5111 (tpt) REVERT: D 110 ILE cc_start: 0.9044 (mm) cc_final: 0.8627 (mt) outliers start: 20 outliers final: 19 residues processed: 93 average time/residue: 0.1462 time to fit residues: 18.6225 Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.115286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103675 restraints weight = 7272.391| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.82 r_work: 0.2967 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5571 Z= 0.277 Angle : 0.519 5.679 7548 Z= 0.284 Chirality : 0.048 0.155 936 Planarity : 0.003 0.032 960 Dihedral : 4.355 16.482 750 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 3.81 % Allowed : 19.05 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.31), residues: 711 helix: 0.04 (0.63), residues: 60 sheet: 0.35 (0.30), residues: 297 loop : -0.84 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 118 PHE 0.010 0.001 PHE D 231 TYR 0.017 0.001 TYR E 43 ARG 0.005 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.89 seconds wall clock time: 45 minutes 4.40 seconds (2704.40 seconds total)