Starting phenix.real_space_refine on Tue Feb 3 12:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.map" model { file = "/net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgl_52151/02_2026/9hgl_52151.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 C 693 2.51 5 N 162 2.21 5 O 180 1.98 5 H 1197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2232 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "E" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Time building chain proxies: 0.51, per 1000 atoms: 0.23 Number of scatterers: 2232 At special positions: 0 Unit cell: (73.1, 73.95, 30.6, 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) O 180 8.00 N 162 7.00 C 693 6.00 H 1197 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 49.8 milliseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 234 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 95.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 3.682A pdb=" N SER C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.594A pdb=" N LEU B 45 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE C 48 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 47 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS C 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 49 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 52 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LYS B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N SER C 54 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ALA B 53 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ILE C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL B 55 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.366A pdb=" N PHE D 46 " --> pdb=" O ASP F 47 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE F 49 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 48 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS F 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LYS D 50 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA F 53 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.366A pdb=" N PHE D 46 " --> pdb=" O ASP F 47 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE F 49 " --> pdb=" O PHE D 46 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 48 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LYS F 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LYS D 50 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA F 53 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 45 " --> pdb=" O PHE F 46 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE F 48 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP E 47 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS F 50 " --> pdb=" O ASP E 47 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 49 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL F 52 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LYS E 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N SER F 54 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ALA E 53 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ILE F 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL E 55 " --> pdb=" O ILE F 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 45 through 50 removed outlier: 3.730A pdb=" N SER I 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.569A pdb=" N LEU H 45 " --> pdb=" O PHE I 46 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE I 48 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP H 47 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LYS I 50 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE H 49 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL I 52 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS H 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N SER I 54 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ALA H 53 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N ILE I 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL H 55 " --> pdb=" O ILE I 56 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 90 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: 0.39 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.08: 307 1.08 - 1.20: 890 1.20 - 1.32: 172 1.32 - 1.45: 197 1.45 - 1.57: 666 Bond restraints: 2232 Sorted by residual: bond pdb=" CE1 PHE B 46 " pdb=" HE1 PHE B 46 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LEU C 59 " pdb=" H LEU C 59 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD1 PHE C 46 " pdb=" HD1 PHE C 46 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 PHE I 46 " pdb=" HE2 PHE I 46 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASP I 47 " pdb=" H ASP I 47 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 2227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.61: 4016 6.61 - 13.21: 61 13.21 - 19.82: 7 19.82 - 26.43: 11 26.43 - 33.03: 18 Bond angle restraints: 4113 Sorted by residual: angle pdb=" CA VAL H 52 " pdb=" CB VAL H 52 " pdb=" CG1 VAL H 52 " ideal model delta sigma weight residual 110.40 130.57 -20.17 1.70e+00 3.46e-01 1.41e+02 angle pdb=" CA VAL I 52 " pdb=" CB VAL I 52 " pdb=" CG1 VAL I 52 " ideal model delta sigma weight residual 110.40 130.43 -20.03 1.70e+00 3.46e-01 1.39e+02 angle pdb=" CA VAL F 52 " pdb=" CB VAL F 52 " pdb=" CG1 VAL F 52 " ideal model delta sigma weight residual 110.40 129.96 -19.56 1.70e+00 3.46e-01 1.32e+02 angle pdb=" CA VAL G 52 " pdb=" CB VAL G 52 " pdb=" CG1 VAL G 52 " ideal model delta sigma weight residual 110.40 129.84 -19.44 1.70e+00 3.46e-01 1.31e+02 angle pdb=" CA VAL B 52 " pdb=" CB VAL B 52 " pdb=" CG1 VAL B 52 " ideal model delta sigma weight residual 110.40 129.75 -19.35 1.70e+00 3.46e-01 1.30e+02 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.90: 883 17.90 - 35.80: 23 35.80 - 53.69: 40 53.69 - 71.58: 14 71.58 - 89.48: 12 Dihedral angle restraints: 972 sinusoidal: 558 harmonic: 414 Sorted by residual: dihedral pdb=" C LEU C 59 " pdb=" N LEU C 59 " pdb=" CA LEU C 59 " pdb=" CB LEU C 59 " ideal model delta harmonic sigma weight residual -122.60 -135.11 12.51 0 2.50e+00 1.60e-01 2.50e+01 dihedral pdb=" C LEU I 59 " pdb=" N LEU I 59 " pdb=" CA LEU I 59 " pdb=" CB LEU I 59 " ideal model delta harmonic sigma weight residual -122.60 -134.29 11.69 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" C LEU F 59 " pdb=" N LEU F 59 " pdb=" CA LEU F 59 " pdb=" CB LEU F 59 " ideal model delta harmonic sigma weight residual -122.60 -134.18 11.58 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 969 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.221: 153 0.221 - 0.441: 18 0.441 - 0.662: 0 0.662 - 0.882: 1 0.882 - 1.102: 8 Chirality restraints: 180 Sorted by residual: chirality pdb=" CB VAL G 52 " pdb=" CA VAL G 52 " pdb=" CG1 VAL G 52 " pdb=" CG2 VAL G 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.53 -1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CB VAL I 52 " pdb=" CA VAL I 52 " pdb=" CG1 VAL I 52 " pdb=" CG2 VAL I 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.60 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CB VAL E 52 " pdb=" CA VAL E 52 " pdb=" CG1 VAL E 52 " pdb=" CG2 VAL E 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.62 -1.01 2.00e-01 2.50e+01 2.55e+01 ... (remaining 177 not shown) Planarity restraints: 297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 49 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" N LYS D 50 " 0.062 2.00e-02 2.50e+03 pdb=" CA LYS D 50 " -0.018 2.00e-02 2.50e+03 pdb=" H LYS D 50 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 49 " 0.019 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" N LYS I 50 " -0.061 2.00e-02 2.50e+03 pdb=" CA LYS I 50 " 0.017 2.00e-02 2.50e+03 pdb=" H LYS I 50 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 49 " -0.019 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" N LYS F 50 " 0.061 2.00e-02 2.50e+03 pdb=" CA LYS F 50 " -0.017 2.00e-02 2.50e+03 pdb=" H LYS F 50 " -0.024 2.00e-02 2.50e+03 ... (remaining 294 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.29: 349 2.29 - 2.85: 4337 2.85 - 3.40: 5148 3.40 - 3.95: 7059 3.95 - 4.50: 9171 Nonbonded interactions: 26064 Sorted by model distance: nonbonded pdb=" OXT LEU A 59 " pdb=" HZ2 LYS G 51 " model vdw 1.742 2.450 nonbonded pdb=" O LEU A 59 " pdb=" HZ3 LYS I 51 " model vdw 1.744 2.450 nonbonded pdb=" HZ2 LYS E 51 " pdb=" OXT LEU H 59 " model vdw 1.745 2.450 nonbonded pdb=" HZ3 LYS F 51 " pdb=" O LEU G 59 " model vdw 1.749 2.450 nonbonded pdb=" OXT LEU B 59 " pdb=" HZ2 LYS H 51 " model vdw 1.749 2.450 ... (remaining 26059 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 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 : 0.012 0.030 1035 Z= 0.663 Angle : 2.566 20.173 1377 Z= 1.528 Chirality : 0.251 1.102 180 Planarity : 0.008 0.023 162 Dihedral : 14.722 89.304 369 Min Nonbonded Distance : 2.707 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 5.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.44), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.34), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.005 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.01158 ( 1035) covalent geometry : angle 2.56615 ( 1377) hydrogen bonds : bond 0.16668 ( 21) hydrogen bonds : angle 6.63637 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.4013 time to fit residues: 16.5266 Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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 = 0.5125 r_free = 0.5125 target = 0.181634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.150117 restraints weight = 5770.497| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 6.06 r_work: 0.4672 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 1035 Z= 0.187 Angle : 1.300 11.387 1377 Z= 0.676 Chirality : 0.327 1.461 180 Planarity : 0.002 0.008 162 Dihedral : 16.082 83.606 144 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.56 % Allowed : 15.74 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.55), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.42), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 1035) covalent geometry : angle 1.29985 ( 1377) hydrogen bonds : bond 0.03251 ( 21) hydrogen bonds : angle 4.35939 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.069 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 22 average time/residue: 0.1868 time to fit residues: 4.4260 Evaluate side-chains 15 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.2490 ------------------------------------------------------------------------------- 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 = 0.5096 r_free = 0.5096 target = 0.177730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.144776 restraints weight = 5868.790| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 6.02 r_work: 0.4639 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1035 Z= 0.164 Angle : 1.287 11.146 1377 Z= 0.672 Chirality : 0.330 1.476 180 Planarity : 0.002 0.007 162 Dihedral : 15.455 88.577 144 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.33 % Allowed : 10.19 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.57), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE I 46 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 1035) covalent geometry : angle 1.28744 ( 1377) hydrogen bonds : bond 0.03823 ( 21) hydrogen bonds : angle 4.41475 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 12 time to evaluate : 0.071 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 19 average time/residue: 0.0636 time to fit residues: 1.5123 Evaluate side-chains 12 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.5066 r_free = 0.5066 target = 0.174314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.141356 restraints weight = 5960.725| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 6.06 r_work: 0.4590 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 1035 Z= 0.168 Angle : 1.277 11.247 1377 Z= 0.664 Chirality : 0.331 1.480 180 Planarity : 0.002 0.006 162 Dihedral : 14.165 84.733 144 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.70 % Allowed : 13.89 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.61), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 1035) covalent geometry : angle 1.27706 ( 1377) hydrogen bonds : bond 0.02512 ( 21) hydrogen bonds : angle 3.80962 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.067 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 14 average time/residue: 0.0944 time to fit residues: 1.5526 Evaluate side-chains 12 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7488 ------------------------------------------------------------------------------- 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 = 0.5093 r_free = 0.5093 target = 0.176812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.142829 restraints weight = 5849.513| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 6.12 r_work: 0.4614 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1035 Z= 0.141 Angle : 1.252 11.123 1377 Z= 0.650 Chirality : 0.327 1.471 180 Planarity : 0.002 0.005 162 Dihedral : 13.729 89.573 144 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 14.81 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.64), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 1035) covalent geometry : angle 1.25229 ( 1377) hydrogen bonds : bond 0.01952 ( 21) hydrogen bonds : angle 3.57321 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.039 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0821 time to fit residues: 1.1610 Evaluate side-chains 11 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.7238 ------------------------------------------------------------------------------- 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 = 0.5036 r_free = 0.5036 target = 0.173493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.139190 restraints weight = 5734.730| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 5.92 r_work: 0.4552 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1035 Z= 0.158 Angle : 1.266 11.155 1377 Z= 0.656 Chirality : 0.329 1.505 180 Planarity : 0.002 0.005 162 Dihedral : 12.485 69.723 144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.70 % Allowed : 15.74 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.65), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 1035) covalent geometry : angle 1.26570 ( 1377) hydrogen bonds : bond 0.02022 ( 21) hydrogen bonds : angle 3.45776 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.065 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 10 average time/residue: 0.1040 time to fit residues: 1.2288 Evaluate side-chains 10 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 1.4983 ------------------------------------------------------------------------------- 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 = 0.5066 r_free = 0.5066 target = 0.175937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.141403 restraints weight = 5592.856| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 5.83 r_work: 0.4595 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1035 Z= 0.134 Angle : 1.235 11.026 1377 Z= 0.640 Chirality : 0.324 1.451 180 Planarity : 0.001 0.005 162 Dihedral : 11.878 69.522 144 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.70 % Allowed : 13.89 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.67), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 1035) covalent geometry : angle 1.23550 ( 1377) hydrogen bonds : bond 0.02044 ( 21) hydrogen bonds : angle 3.33530 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.039 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 11 average time/residue: 0.0588 time to fit residues: 0.7759 Evaluate side-chains 9 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 1.9488 ------------------------------------------------------------------------------- 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 = 0.5051 r_free = 0.5051 target = 0.174409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.140372 restraints weight = 5733.619| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 5.96 r_work: 0.4595 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1035 Z= 0.140 Angle : 1.243 11.095 1377 Z= 0.644 Chirality : 0.326 1.481 180 Planarity : 0.001 0.004 162 Dihedral : 11.543 68.452 144 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.69), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 1035) covalent geometry : angle 1.24256 ( 1377) hydrogen bonds : bond 0.02059 ( 21) hydrogen bonds : angle 3.60350 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.039 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 9 average time/residue: 0.0663 time to fit residues: 0.7099 Evaluate side-chains 8 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.2490 ------------------------------------------------------------------------------- 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 = 0.5037 r_free = 0.5037 target = 0.172583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.138260 restraints weight = 5759.073| |-----------------------------------------------------------------------------| r_work (start): 0.4644 rms_B_bonded: 5.93 r_work: 0.4569 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1035 Z= 0.143 Angle : 1.241 11.047 1377 Z= 0.643 Chirality : 0.325 1.456 180 Planarity : 0.001 0.005 162 Dihedral : 11.445 68.316 144 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.71), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 1035) covalent geometry : angle 1.24117 ( 1377) hydrogen bonds : bond 0.01789 ( 21) hydrogen bonds : angle 3.40384 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 5 time to evaluate : 0.064 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 8 average time/residue: 0.1225 time to fit residues: 1.1633 Evaluate side-chains 7 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 1.6733 ------------------------------------------------------------------------------- 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 = 0.5055 r_free = 0.5055 target = 0.174635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.139909 restraints weight = 5642.277| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 5.91 r_work: 0.4565 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1035 Z= 0.135 Angle : 1.232 11.034 1377 Z= 0.638 Chirality : 0.325 1.463 180 Planarity : 0.001 0.004 162 Dihedral : 11.197 68.722 144 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.73), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.000 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 1035) covalent geometry : angle 1.23178 ( 1377) hydrogen bonds : bond 0.01700 ( 21) hydrogen bonds : angle 3.48071 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.062 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 7 average time/residue: 0.1417 time to fit residues: 1.1491 Evaluate side-chains 7 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain G residue 56 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 2.7488 ------------------------------------------------------------------------------- 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 = 0.5027 r_free = 0.5027 target = 0.172839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.138665 restraints weight = 5858.258| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 5.91 r_work: 0.4566 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1035 Z= 0.150 Angle : 1.250 11.138 1377 Z= 0.647 Chirality : 0.328 1.467 180 Planarity : 0.001 0.005 162 Dihedral : 11.346 69.407 144 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.78 % Allowed : 13.89 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.75), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 1035) covalent geometry : angle 1.24978 ( 1377) hydrogen bonds : bond 0.01844 ( 21) hydrogen bonds : angle 3.54871 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 871.90 seconds wall clock time: 15 minutes 31.86 seconds (931.86 seconds total)