Starting phenix.real_space_refine on Tue Feb 3 12:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.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 { model { file = "/net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hid_52186/02_2026/9hid_52186.map" } resolution = 3.2 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 462 2.51 5 N 108 2.21 5 O 120 1.98 5 H 798 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 1488 Number of models: 1 Model: "" Number of chains: 6 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} Time building chain proxies: 0.39, per 1000 atoms: 0.26 Number of scatterers: 1488 At special positions: 0 Unit cell: (41.75, 61.79, 34.235, 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 120 8.00 N 108 7.00 C 462 6.00 H 798 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: 0.12 Conformation dependent library (CDL) restraints added in 34.1 milliseconds 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 156 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 56.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 7.725A pdb=" N ILE A 56 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY E 57 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 53 removed outlier: 6.405A pdb=" N ASP B 47 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS F 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 49 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL F 52 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 7.637A pdb=" N ILE B 56 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 58 " --> pdb=" O GLY D 57 " (cutoff:3.500A) 23 hydrogen bonds defined for protein. 69 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: 0.32 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.08: 210 1.08 - 1.20: 588 1.20 - 1.32: 118 1.32 - 1.44: 128 1.44 - 1.56: 444 Bond restraints: 1488 Sorted by residual: bond pdb=" CE2 PHE B 46 " pdb=" HE2 PHE B 46 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE B 46 " pdb=" HD2 PHE B 46 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 PHE B 46 " pdb=" HD1 PHE B 46 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CZ PHE B 46 " pdb=" HZ PHE B 46 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ASP B 47 " pdb=" H ASP B 47 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 1483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 2680 6.67 - 13.34: 14 13.34 - 20.02: 8 20.02 - 26.69: 16 26.69 - 33.36: 24 Bond angle restraints: 2742 Sorted by residual: angle pdb=" CA VAL F 55 " pdb=" CB VAL F 55 " pdb=" CG1 VAL F 55 " ideal model delta sigma weight residual 110.40 135.28 -24.88 1.70e+00 3.46e-01 2.14e+02 angle pdb=" CA VAL D 55 " pdb=" CB VAL D 55 " pdb=" CG1 VAL D 55 " ideal model delta sigma weight residual 110.40 135.11 -24.71 1.70e+00 3.46e-01 2.11e+02 angle pdb=" CA VAL A 55 " pdb=" CB VAL A 55 " pdb=" CG1 VAL A 55 " ideal model delta sigma weight residual 110.40 134.54 -24.14 1.70e+00 3.46e-01 2.02e+02 angle pdb=" CA VAL B 55 " pdb=" CB VAL B 55 " pdb=" CG1 VAL B 55 " ideal model delta sigma weight residual 110.40 134.18 -23.78 1.70e+00 3.46e-01 1.96e+02 angle pdb=" CA VAL E 55 " pdb=" CB VAL E 55 " pdb=" CG1 VAL E 55 " ideal model delta sigma weight residual 110.40 134.03 -23.63 1.70e+00 3.46e-01 1.93e+02 ... (remaining 2737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 573 17.49 - 34.98: 41 34.98 - 52.47: 21 52.47 - 69.96: 4 69.96 - 87.45: 9 Dihedral angle restraints: 648 sinusoidal: 372 harmonic: 276 Sorted by residual: dihedral pdb=" CA ILE A 56 " pdb=" C ILE A 56 " pdb=" N GLY A 57 " pdb=" CA GLY A 57 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE B 56 " pdb=" C ILE B 56 " pdb=" N GLY B 57 " pdb=" CA GLY B 57 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA SER A 54 " pdb=" C SER A 54 " pdb=" N VAL A 55 " pdb=" CA VAL A 55 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 106 0.240 - 0.480: 2 0.480 - 0.720: 0 0.720 - 0.960: 1 0.960 - 1.200: 11 Chirality restraints: 120 Sorted by residual: chirality pdb=" CB VAL C 55 " pdb=" CA VAL C 55 " pdb=" CG1 VAL C 55 " pdb=" CG2 VAL C 55 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+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 -1.45 -1.18 2.00e-01 2.50e+01 3.49e+01 chirality pdb=" CB VAL A 52 " pdb=" CA VAL A 52 " pdb=" CG1 VAL A 52 " pdb=" CG2 VAL A 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.45 -1.18 2.00e-01 2.50e+01 3.49e+01 ... (remaining 117 not shown) Planarity restraints: 198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 57 " -0.025 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" N GLY C 58 " 0.079 2.00e-02 2.50e+03 pdb=" CA GLY C 58 " -0.023 2.00e-02 2.50e+03 pdb=" H GLY C 58 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 57 " 0.022 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" N GLY D 58 " -0.071 2.00e-02 2.50e+03 pdb=" CA GLY D 58 " 0.020 2.00e-02 2.50e+03 pdb=" H GLY D 58 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 54 " -0.020 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" N VAL A 55 " 0.062 2.00e-02 2.50e+03 pdb=" CA VAL A 55 " -0.018 2.00e-02 2.50e+03 pdb=" H VAL A 55 " -0.025 2.00e-02 2.50e+03 ... (remaining 195 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.15: 127 2.15 - 2.73: 2194 2.73 - 3.32: 3639 3.32 - 3.91: 4914 3.91 - 4.50: 6549 Nonbonded interactions: 17423 Sorted by model distance: nonbonded pdb="HG23 VAL B 55 " pdb=" HA VAL F 55 " model vdw 1.556 2.440 nonbonded pdb="HG21 VAL A 55 " pdb=" HA VAL E 55 " model vdw 1.589 2.440 nonbonded pdb=" HA VAL B 55 " pdb=" HB VAL B 55 " model vdw 1.694 1.952 nonbonded pdb=" HZ1 LYS B 50 " pdb=" OXT LEU E 59 " model vdw 1.695 2.450 nonbonded pdb=" HA VAL F 55 " pdb=" HB VAL F 55 " model vdw 1.702 1.952 ... (remaining 17418 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' } 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: 4.380 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.011 0.043 690 Z= 0.571 Angle : 3.045 24.881 918 Z= 1.805 Chirality : 0.360 1.200 120 Planarity : 0.008 0.018 108 Dihedral : 12.562 87.449 246 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 8.33 % Allowed : 0.00 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.75), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.005 PHE F 46 Details of bonding type rmsd covalent geometry : bond 0.01142 ( 690) covalent geometry : angle 3.04522 ( 918) hydrogen bonds : bond 0.16804 ( 23) hydrogen bonds : angle 7.17563 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 PHE cc_start: 0.7996 (p90) cc_final: 0.6403 (m-10) REVERT: D 46 PHE cc_start: 0.7804 (p90) cc_final: 0.6471 (m-80) outliers start: 6 outliers final: 0 residues processed: 34 average time/residue: 0.0880 time to fit residues: 3.2945 Evaluate side-chains 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.9313 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.118743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.100012 restraints weight = 3540.258| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 3.10 r_work: 0.3853 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 690 Z= 0.220 Angle : 1.688 11.114 918 Z= 0.879 Chirality : 0.444 1.458 120 Planarity : 0.002 0.009 108 Dihedral : 10.440 69.779 96 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.56 % Allowed : 8.33 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.78), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00621 ( 690) covalent geometry : angle 1.68808 ( 918) hydrogen bonds : bond 0.05265 ( 23) hydrogen bonds : angle 4.77444 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.026 Fit side-chains REVERT: C 46 PHE cc_start: 0.7925 (p90) cc_final: 0.5963 (m-80) REVERT: D 45 LEU cc_start: 0.8225 (mt) cc_final: 0.7982 (mt) REVERT: D 46 PHE cc_start: 0.7745 (p90) cc_final: 0.6091 (m-80) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 0.0223 time to fit residues: 0.5975 Evaluate side-chains 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 1.2317 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.120565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.101829 restraints weight = 3562.431| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.07 r_work: 0.3853 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 690 Z= 0.207 Angle : 1.672 10.973 918 Z= 0.867 Chirality : 0.447 1.441 120 Planarity : 0.002 0.007 108 Dihedral : 8.153 48.670 96 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.94 % Allowed : 12.50 % 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: -0.97 (0.82), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 690) covalent geometry : angle 1.67214 ( 918) hydrogen bonds : bond 0.04555 ( 23) hydrogen bonds : angle 4.02770 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.047 Fit side-chains REVERT: C 46 PHE cc_start: 0.8009 (p90) cc_final: 0.5800 (m-80) REVERT: D 46 PHE cc_start: 0.7697 (p90) cc_final: 0.5626 (m-80) outliers start: 5 outliers final: 2 residues processed: 20 average time/residue: 0.0304 time to fit residues: 0.7798 Evaluate side-chains 17 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 1.5987 ------------------------------------------------------------------------------- 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 = 0.4174 r_free = 0.4174 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.106993 restraints weight = 3543.142| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.06 r_work: 0.3891 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 690 Z= 0.211 Angle : 1.666 11.053 918 Z= 0.859 Chirality : 0.447 1.440 120 Planarity : 0.002 0.007 108 Dihedral : 6.014 17.387 96 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.94 % Allowed : 13.89 % Favored : 79.17 % 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: -1.24 (0.82), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 690) covalent geometry : angle 1.66601 ( 918) hydrogen bonds : bond 0.04173 ( 23) hydrogen bonds : angle 3.94441 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.048 Fit side-chains REVERT: C 46 PHE cc_start: 0.7994 (p90) cc_final: 0.5415 (m-80) REVERT: D 46 PHE cc_start: 0.7871 (p90) cc_final: 0.5690 (m-80) outliers start: 5 outliers final: 4 residues processed: 18 average time/residue: 0.0321 time to fit residues: 0.7424 Evaluate side-chains 18 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.3323 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.125709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.105273 restraints weight = 3623.272| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.97 r_work: 0.3836 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 690 Z= 0.237 Angle : 1.666 11.143 918 Z= 0.858 Chirality : 0.445 1.455 120 Planarity : 0.002 0.005 108 Dihedral : 5.640 13.979 96 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.56 % Allowed : 15.28 % Favored : 79.17 % 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: -1.56 (0.78), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 690) covalent geometry : angle 1.66612 ( 918) hydrogen bonds : bond 0.04135 ( 23) hydrogen bonds : angle 3.84791 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.045 Fit side-chains REVERT: A 45 LEU cc_start: 0.8663 (tp) cc_final: 0.8201 (tt) REVERT: C 46 PHE cc_start: 0.7944 (p90) cc_final: 0.5334 (m-80) REVERT: D 46 PHE cc_start: 0.7963 (p90) cc_final: 0.5563 (m-80) outliers start: 4 outliers final: 4 residues processed: 18 average time/residue: 0.0379 time to fit residues: 0.8690 Evaluate side-chains 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.2987 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.125909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.105397 restraints weight = 3625.746| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.03 r_work: 0.3859 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 690 Z= 0.234 Angle : 1.662 11.164 918 Z= 0.857 Chirality : 0.447 1.452 120 Planarity : 0.002 0.007 108 Dihedral : 5.550 13.674 96 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 6.94 % Allowed : 12.50 % 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: -1.62 (0.78), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 690) covalent geometry : angle 1.66233 ( 918) hydrogen bonds : bond 0.03853 ( 23) hydrogen bonds : angle 3.67491 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.027 Fit side-chains REVERT: A 45 LEU cc_start: 0.8747 (tp) cc_final: 0.8292 (tt) REVERT: C 46 PHE cc_start: 0.8040 (p90) cc_final: 0.5223 (m-80) REVERT: D 46 PHE cc_start: 0.7968 (p90) cc_final: 0.5470 (m-80) REVERT: F 46 PHE cc_start: 0.8175 (p90) cc_final: 0.7846 (p90) outliers start: 5 outliers final: 5 residues processed: 20 average time/residue: 0.0273 time to fit residues: 0.6923 Evaluate side-chains 19 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 14 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0317 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.128642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.108578 restraints weight = 3549.361| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.00 r_work: 0.3912 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 690 Z= 0.195 Angle : 1.655 11.062 918 Z= 0.852 Chirality : 0.451 1.441 120 Planarity : 0.001 0.005 108 Dihedral : 5.078 11.676 96 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.94 % Allowed : 9.72 % 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: -1.48 (0.81), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 690) covalent geometry : angle 1.65520 ( 918) hydrogen bonds : bond 0.02998 ( 23) hydrogen bonds : angle 3.35245 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.047 Fit side-chains REVERT: A 45 LEU cc_start: 0.8779 (tp) cc_final: 0.8310 (tt) REVERT: C 46 PHE cc_start: 0.7869 (p90) cc_final: 0.5163 (m-80) REVERT: D 46 PHE cc_start: 0.7938 (p90) cc_final: 0.5351 (m-80) REVERT: F 46 PHE cc_start: 0.8171 (p90) cc_final: 0.7873 (p90) outliers start: 5 outliers final: 5 residues processed: 22 average time/residue: 0.0237 time to fit residues: 0.6823 Evaluate side-chains 23 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 1.8987 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.127559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.107559 restraints weight = 3565.826| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.99 r_work: 0.3862 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.6856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 690 Z= 0.215 Angle : 1.661 11.149 918 Z= 0.855 Chirality : 0.449 1.449 120 Planarity : 0.001 0.005 108 Dihedral : 5.199 12.845 96 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.94 % Allowed : 11.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.78), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE D 46 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 690) covalent geometry : angle 1.66144 ( 918) hydrogen bonds : bond 0.03465 ( 23) hydrogen bonds : angle 3.28301 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.044 Fit side-chains REVERT: A 45 LEU cc_start: 0.8848 (tp) cc_final: 0.8411 (tt) REVERT: C 46 PHE cc_start: 0.8089 (p90) cc_final: 0.5147 (m-80) REVERT: D 46 PHE cc_start: 0.8001 (p90) cc_final: 0.5384 (m-80) REVERT: F 46 PHE cc_start: 0.8225 (p90) cc_final: 0.7913 (p90) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0395 time to fit residues: 1.0585 Evaluate side-chains 21 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 2.2653 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.125771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.105724 restraints weight = 3689.270| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 3.10 r_work: 0.3777 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 690 Z= 0.224 Angle : 1.659 11.154 918 Z= 0.854 Chirality : 0.449 1.450 120 Planarity : 0.001 0.004 108 Dihedral : 5.286 12.474 96 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.33 % Allowed : 8.33 % 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: -1.84 (0.77), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 690) covalent geometry : angle 1.65882 ( 918) hydrogen bonds : bond 0.03335 ( 23) hydrogen bonds : angle 3.29993 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.045 Fit side-chains REVERT: A 45 LEU cc_start: 0.8728 (tp) cc_final: 0.8274 (tt) REVERT: C 46 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.5287 (m-80) REVERT: F 46 PHE cc_start: 0.8079 (p90) cc_final: 0.7660 (p90) outliers start: 6 outliers final: 5 residues processed: 20 average time/residue: 0.0359 time to fit residues: 0.9173 Evaluate side-chains 22 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.9653 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.125904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.106428 restraints weight = 3610.659| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.05 r_work: 0.3860 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 690 Z= 0.216 Angle : 1.665 11.138 918 Z= 0.858 Chirality : 0.449 1.446 120 Planarity : 0.002 0.005 108 Dihedral : 5.321 13.210 96 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.33 % Allowed : 12.50 % Favored : 79.17 % 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 (0.76), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.58), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 690) covalent geometry : angle 1.66501 ( 918) hydrogen bonds : bond 0.03757 ( 23) hydrogen bonds : angle 3.25584 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 168 Ramachandran restraints generated. 84 Oldfield, 0 Emsley, 84 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.046 Fit side-chains REVERT: A 45 LEU cc_start: 0.8879 (tp) cc_final: 0.8470 (tt) REVERT: C 46 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: D 46 PHE cc_start: 0.8050 (p90) cc_final: 0.5213 (m-80) REVERT: F 46 PHE cc_start: 0.8217 (p90) cc_final: 0.7897 (p90) outliers start: 6 outliers final: 5 residues processed: 21 average time/residue: 0.0372 time to fit residues: 1.0003 Evaluate side-chains 23 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain F residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.126630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.106888 restraints weight = 3636.451| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 3.10 r_work: 0.3854 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 690 Z= 0.218 Angle : 1.662 11.164 918 Z= 0.855 Chirality : 0.449 1.449 120 Planarity : 0.001 0.004 108 Dihedral : 5.246 12.565 96 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.33 % Allowed : 11.11 % 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: -1.98 (0.76), residues: 84 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.58), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.002 PHE C 46 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 690) covalent geometry : angle 1.66183 ( 918) hydrogen bonds : bond 0.03784 ( 23) hydrogen bonds : angle 3.17794 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 683.14 seconds wall clock time: 12 minutes 28.89 seconds (748.89 seconds total)