Starting phenix.real_space_refine on Thu Mar 6 08:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a02_15045/03_2025/8a02_15045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a02_15045/03_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_15045/03_2025/8a02_15045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a02_15045/03_2025/8a02_15045.map" model { file = "/net/cci-nas-00/data/ceres_data/8a02_15045/03_2025/8a02_15045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a02_15045/03_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-5624/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: 4.04, per 1000 atoms: 0.73 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: 1.40 Conformation dependent library (CDL) restraints added in 676.7 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: 0.86 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: 1.89 Time building geometry restraints manager: 1.58 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: 0.550 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:3.090 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- 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 : 0.637 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: 0.1703 time to fit residues: 25.2395 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 : 0.647 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.104895 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: 3.81 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.639 Fit side-chains REVERT: F 100 GLU cc_start: 0.8237 (pt0) cc_final: 0.7853 (pt0) REVERT: F 155 ILE cc_start: 0.8715 (mt) cc_final: 0.8494 (mt) REVERT: F 160 ASP cc_start: 0.8020 (t0) cc_final: 0.7815 (t0) REVERT: E 1 MET cc_start: 0.8190 (pmm) cc_final: 0.7690 (ptt) REVERT: D 110 ILE cc_start: 0.9043 (mm) cc_final: 0.8638 (mt) REVERT: D 188 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8290 (t0) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.1620 time to fit residues: 22.5921 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 : 0.633 ------------------------------------------------------------------------------- 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: 7.9990 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 = 0.3176 r_free = 0.3176 target = 0.113189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101926 restraints weight = 7340.478| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.78 r_work: 0.2948 rms_B_bonded: 2.18 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: 0.8371 moved from start: 0.1474 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 5.900 7548 Z= 0.348 Chirality : 0.052 0.168 936 Planarity : 0.004 0.035 960 Dihedral : 4.843 16.565 750 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 : 15.71 % Favored : 81.59 % 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 : 0.663 Fit side-chains REVERT: E 1 MET cc_start: 0.8252 (pmm) cc_final: 0.7840 (ptt) REVERT: E 82 MET cc_start: 0.8455 (tmm) cc_final: 0.7906 (ttp) REVERT: E 136 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8682 (m) REVERT: D 110 ILE cc_start: 0.9048 (mm) cc_final: 0.8660 (mt) outliers start: 17 outliers final: 13 residues processed: 94 average time/residue: 0.1649 time to fit residues: 20.7268 Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 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 = 0.3220 r_free = 0.3220 target = 0.116967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.105527 restraints weight = 7276.737| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.80 r_work: 0.2994 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5571 Z= 0.161 Angle : 0.465 5.077 7548 Z= 0.256 Chirality : 0.047 0.150 936 Planarity : 0.003 0.029 960 Dihedral : 4.185 14.888 750 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.22 % Allowed : 17.14 % Favored : 80.63 % 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: -0.27 (0.31), residues: 711 helix: 0.34 (0.65), residues: 60 sheet: 0.49 (0.30), residues: 297 loop : -0.83 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 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 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: 0.8210 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: F 110 ILE cc_start: 0.8669 (mm) cc_final: 0.8423 (mm) REVERT: E 1 MET cc_start: 0.8193 (pmm) cc_final: 0.7830 (ptt) REVERT: E 140 GLU cc_start: 0.8687 (pp20) cc_final: 0.8122 (pp20) REVERT: D 110 ILE cc_start: 0.9128 (mm) cc_final: 0.8674 (mt) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.1609 time to fit residues: 20.9367 Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 overall best weight: 7.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.112590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101277 restraints weight = 7252.309| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.77 r_work: 0.2935 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 5571 Z= 0.574 Angle : 0.698 5.977 7548 Z= 0.372 Chirality : 0.054 0.173 936 Planarity : 0.004 0.037 960 Dihedral : 4.985 16.717 750 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 4.13 % Allowed : 17.94 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 711 helix: -0.45 (0.63), residues: 60 sheet: 0.17 (0.30), residues: 297 loop : -1.14 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 118 PHE 0.013 0.002 PHE F 63 TYR 0.020 0.002 TYR E 43 ARG 0.003 0.001 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 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.055 Fit side-chains REVERT: F 107 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: E 1 MET cc_start: 0.8244 (pmm) cc_final: 0.7853 (ptt) REVERT: E 59 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8571 (mp) REVERT: E 82 MET cc_start: 0.8464 (tmm) cc_final: 0.7956 (ttp) REVERT: E 136 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8664 (m) REVERT: D 110 ILE cc_start: 0.9121 (mm) cc_final: 0.8756 (mt) outliers start: 26 outliers final: 18 residues processed: 94 average time/residue: 0.1792 time to fit residues: 22.6476 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 91 GLU 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 201 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 164 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.0000 chunk 29 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.116383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104930 restraints weight = 7171.163| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.79 r_work: 0.2988 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5571 Z= 0.180 Angle : 0.469 4.903 7548 Z= 0.259 Chirality : 0.047 0.149 936 Planarity : 0.003 0.032 960 Dihedral : 4.220 14.873 750 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.97 % 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: -0.48 (0.31), residues: 711 helix: 0.05 (0.64), residues: 60 sheet: 0.35 (0.30), residues: 297 loop : -0.94 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 118 PHE 0.008 0.001 PHE D 63 TYR 0.013 0.001 TYR E 43 ARG 0.004 0.000 ARG D 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 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.625 Fit side-chains REVERT: F 107 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: E 1 MET cc_start: 0.8193 (pmm) cc_final: 0.7884 (ptt) REVERT: E 82 MET cc_start: 0.8340 (tmm) cc_final: 0.7787 (ttp) REVERT: D 1 MET cc_start: 0.7588 (pmm) cc_final: 0.5099 (tpt) REVERT: D 110 ILE cc_start: 0.9107 (mm) cc_final: 0.8668 (mt) outliers start: 18 outliers final: 15 residues processed: 92 average time/residue: 0.1444 time to fit residues: 18.1778 Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 99 LYS 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 206 THR Chi-restraints excluded: chain F residue 238 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 Chi-restraints excluded: chain D residue 117 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.114389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.102834 restraints weight = 7291.599| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.82 r_work: 0.2954 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5571 Z= 0.327 Angle : 0.547 5.978 7548 Z= 0.297 Chirality : 0.049 0.159 936 Planarity : 0.004 0.032 960 Dihedral : 4.478 15.086 750 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.95 % Favored : 96.91 % Rotamer: Outliers : 3.81 % Allowed : 18.57 % 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: -0.58 (0.31), residues: 711 helix: -0.10 (0.63), residues: 60 sheet: 0.27 (0.30), residues: 297 loop : -0.98 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.010 0.001 PHE D 231 TYR 0.019 0.002 TYR E 43 ARG 0.004 0.000 ARG D 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 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.602 Fit side-chains REVERT: F 107 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: E 1 MET cc_start: 0.8215 (pmm) cc_final: 0.7883 (ptt) REVERT: E 82 MET cc_start: 0.8377 (tmm) cc_final: 0.7809 (ttp) REVERT: D 110 ILE cc_start: 0.9079 (mm) cc_final: 0.8669 (mt) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1521 time to fit residues: 19.7750 Evaluate side-chains 95 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 170 SER 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 165 LEU 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 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103133 restraints weight = 7241.538| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.80 r_work: 0.2958 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5571 Z= 0.304 Angle : 0.538 6.057 7548 Z= 0.292 Chirality : 0.049 0.157 936 Planarity : 0.004 0.033 960 Dihedral : 4.465 15.094 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.53 % Favored : 97.19 % Rotamer: Outliers : 3.81 % Allowed : 18.89 % Favored : 77.30 % 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: -0.59 (0.31), residues: 711 helix: -0.12 (0.63), residues: 60 sheet: 0.25 (0.30), residues: 297 loop : -0.97 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 118 PHE 0.009 0.001 PHE D 231 TYR 0.018 0.002 TYR E 43 ARG 0.004 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 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.641 Fit side-chains REVERT: F 107 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: E 1 MET cc_start: 0.8216 (pmm) cc_final: 0.7884 (ptt) REVERT: D 1 MET cc_start: 0.7631 (pmm) cc_final: 0.5076 (tpt) REVERT: D 110 ILE cc_start: 0.9081 (mm) cc_final: 0.8680 (mt) outliers start: 24 outliers final: 20 residues processed: 94 average time/residue: 0.1534 time to fit residues: 19.9125 Evaluate side-chains 97 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 170 SER 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 136 SER Chi-restraints excluded: chain E residue 165 LEU 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 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: 4.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3178 r_free = 0.3178 target = 0.113633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102170 restraints weight = 7296.591| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.81 r_work: 0.2948 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5571 Z= 0.387 Angle : 0.587 6.001 7548 Z= 0.317 Chirality : 0.050 0.162 936 Planarity : 0.004 0.036 960 Dihedral : 4.640 15.263 750 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.52 % Favored : 96.20 % Rotamer: Outliers : 4.29 % Allowed : 19.21 % Favored : 76.51 % 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: -0.72 (0.31), residues: 711 helix: -0.33 (0.63), residues: 60 sheet: 0.16 (0.30), residues: 297 loop : -1.02 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 118 PHE 0.010 0.002 PHE D 231 TYR 0.019 0.002 TYR E 43 ARG 0.005 0.001 ARG D 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 105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.718 Fit side-chains REVERT: F 107 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: E 1 MET cc_start: 0.8226 (pmm) cc_final: 0.7881 (ptt) REVERT: E 59 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8536 (mp) REVERT: E 136 SER cc_start: 0.9012 (m) cc_final: 0.8663 (m) REVERT: E 209 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8232 (tp) REVERT: D 110 ILE cc_start: 0.9089 (mm) cc_final: 0.8714 (mt) outliers start: 27 outliers final: 20 residues processed: 98 average time/residue: 0.1532 time to fit residues: 20.6154 Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 170 SER 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 165 LEU Chi-restraints excluded: chain E residue 209 LEU 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 164 ASP Chi-restraints excluded: chain D residue 165 LEU 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: 5.9990 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.115295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.103771 restraints weight = 7268.781| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.82 r_work: 0.2969 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5571 Z= 0.245 Angle : 0.511 5.766 7548 Z= 0.280 Chirality : 0.048 0.154 936 Planarity : 0.003 0.033 960 Dihedral : 4.374 17.141 750 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.53 % Favored : 97.19 % Rotamer: Outliers : 3.65 % Allowed : 20.00 % Favored : 76.35 % 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: -0.58 (0.31), residues: 711 helix: -0.08 (0.64), residues: 60 sheet: 0.23 (0.30), residues: 297 loop : -0.94 (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 0.004 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 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.622 Fit side-chains REVERT: F 107 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: E 1 MET cc_start: 0.8204 (pmm) cc_final: 0.7883 (ptt) REVERT: E 59 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8514 (mp) REVERT: E 209 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8242 (tp) REVERT: D 1 MET cc_start: 0.7593 (pmm) cc_final: 0.5128 (tpt) REVERT: D 110 ILE cc_start: 0.9081 (mm) cc_final: 0.8667 (mt) outliers start: 23 outliers final: 19 residues processed: 96 average time/residue: 0.1481 time to fit residues: 19.5842 Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 170 SER 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 209 LEU Chi-restraints excluded: chain D residue 117 LEU 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 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.114959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103493 restraints weight = 7296.220| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.81 r_work: 0.2963 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5571 Z= 0.267 Angle : 0.522 5.875 7548 Z= 0.285 Chirality : 0.048 0.155 936 Planarity : 0.003 0.033 960 Dihedral : 4.389 17.076 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.67 % Favored : 97.05 % Rotamer: Outliers : 3.81 % Allowed : 19.68 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.31), residues: 711 helix: -0.07 (0.64), residues: 60 sheet: 0.23 (0.30), residues: 297 loop : -0.91 (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 0.017 0.001 TYR E 43 ARG 0.004 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.89 seconds wall clock time: 45 minutes 37.08 seconds (2737.08 seconds total)