Starting phenix.real_space_refine on Tue Feb 3 12:40:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgt_52167/02_2026/9hgt_52167.map" } resolution = 3.0 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: 0.53, per 1000 atoms: 0.24 Number of scatterers: 2232 At special positions: 0 Unit cell: (74.315, 78.49, 29.225, 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: 0.19 Conformation dependent library (CDL) restraints added in 48.8 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 3 sheets defined 0.0% alpha, 50.0% 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 'D' and resid 48 through 56 removed outlier: 6.332A pdb=" N ILE A 48 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS G 51 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 50 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA G 53 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 52 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL G 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER A 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 56 removed outlier: 6.411A pdb=" N ILE B 48 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LYS H 51 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS B 50 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA H 53 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL H 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER B 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 48 through 56 removed outlier: 6.422A pdb=" N ILE C 48 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LYS I 51 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 50 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ALA I 53 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL I 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER C 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.42 Time building geometry restraints manager: 0.28 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: 269 1.08 - 1.20: 928 1.20 - 1.33: 198 1.33 - 1.45: 175 1.45 - 1.57: 662 Bond restraints: 2232 Sorted by residual: bond pdb=" CD1 PHE E 46 " pdb=" HD1 PHE E 46 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE A 48 " pdb=" H ILE A 48 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD1 PHE B 46 " pdb=" HD1 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=" CZ PHE C 46 " pdb=" HZ PHE C 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 ILE D 48 " pdb=" H ILE D 48 " 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 - 6.68: 4044 6.68 - 13.37: 33 13.37 - 20.05: 9 20.05 - 26.74: 9 26.74 - 33.42: 18 Bond angle restraints: 4113 Sorted by residual: angle pdb=" CA VAL I 52 " pdb=" CB VAL I 52 " pdb=" CG1 VAL I 52 " ideal model delta sigma weight residual 110.40 130.37 -19.97 1.70e+00 3.46e-01 1.38e+02 angle pdb=" CA VAL B 52 " pdb=" CB VAL B 52 " pdb=" CG1 VAL B 52 " ideal model delta sigma weight residual 110.40 130.15 -19.75 1.70e+00 3.46e-01 1.35e+02 angle pdb=" CA VAL H 52 " pdb=" CB VAL H 52 " pdb=" CG1 VAL H 52 " ideal model delta sigma weight residual 110.40 130.08 -19.68 1.70e+00 3.46e-01 1.34e+02 angle pdb=" CA VAL E 52 " pdb=" CB VAL E 52 " pdb=" CG1 VAL E 52 " ideal model delta sigma weight residual 110.40 129.75 -19.35 1.70e+00 3.46e-01 1.29e+02 angle pdb=" CA VAL G 52 " pdb=" CB VAL G 52 " pdb=" CG1 VAL G 52 " ideal model delta sigma weight residual 110.40 129.54 -19.14 1.70e+00 3.46e-01 1.27e+02 ... (remaining 4108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.72: 790 11.72 - 23.44: 130 23.44 - 35.16: 17 35.16 - 46.88: 9 46.88 - 58.59: 26 Dihedral angle restraints: 972 sinusoidal: 558 harmonic: 414 Sorted by residual: dihedral pdb=" CA ASP C 47 " pdb=" C ASP C 47 " pdb=" N ILE C 48 " pdb=" CA ILE C 48 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ASP A 47 " pdb=" C ASP A 47 " pdb=" N ILE A 48 " pdb=" CA ILE A 48 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP H 47 " pdb=" C ASP H 47 " pdb=" N ILE H 48 " pdb=" CA ILE H 48 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 969 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.254: 171 0.254 - 0.504: 0 0.504 - 0.754: 0 0.754 - 1.004: 5 1.004 - 1.253: 4 Chirality restraints: 180 Sorted by residual: chirality pdb=" CB VAL C 52 " pdb=" CA VAL C 52 " pdb=" CG1 VAL C 52 " pdb=" CG2 VAL C 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.38 -1.25 2.00e-01 2.50e+01 3.93e+01 chirality pdb=" CB VAL B 52 " pdb=" CA VAL B 52 " pdb=" CG1 VAL B 52 " pdb=" CG2 VAL B 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.40 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" CB VAL F 52 " pdb=" CA VAL F 52 " pdb=" CG1 VAL F 52 " pdb=" CG2 VAL F 52 " both_signs ideal model delta sigma weight residual False -2.63 -1.48 -1.15 2.00e-01 2.50e+01 3.30e+01 ... (remaining 177 not shown) Planarity restraints: 297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 46 " 0.026 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" N ASP C 47 " -0.082 2.00e-02 2.50e+03 pdb=" CA ASP C 47 " 0.024 2.00e-02 2.50e+03 pdb=" H ASP C 47 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 46 " 0.026 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" N ASP D 47 " -0.081 2.00e-02 2.50e+03 pdb=" CA ASP D 47 " 0.023 2.00e-02 2.50e+03 pdb=" H ASP D 47 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 46 " 0.024 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" N ASP A 47 " -0.076 2.00e-02 2.50e+03 pdb=" CA ASP A 47 " 0.022 2.00e-02 2.50e+03 pdb=" H ASP A 47 " 0.030 2.00e-02 2.50e+03 ... (remaining 294 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.29: 363 2.29 - 2.84: 4466 2.84 - 3.39: 5109 3.39 - 3.95: 7511 3.95 - 4.50: 9086 Nonbonded interactions: 26535 Sorted by model distance: nonbonded pdb=" O ILE B 56 " pdb=" H GLY H 57 " model vdw 1.732 2.450 nonbonded pdb=" O ILE A 56 " pdb=" H GLY G 57 " model vdw 1.736 2.450 nonbonded pdb=" H GLY A 57 " pdb=" O ILE D 56 " model vdw 1.745 2.450 nonbonded pdb=" H GLY B 57 " pdb=" O ILE E 56 " model vdw 1.751 2.450 nonbonded pdb=" HA VAL E 52 " pdb=" HB VAL E 52 " model vdw 1.757 1.952 ... (remaining 26530 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: 2.820 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: 0.020 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.580 Find NCS groups from input model: 0.030 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 0.066 1035 Z= 0.622 Angle : 2.532 19.968 1377 Z= 1.544 Chirality : 0.247 1.253 180 Planarity : 0.007 0.021 162 Dihedral : 11.219 31.762 369 Min Nonbonded Distance : 2.696 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.85 % Allowed : 11.11 % Favored : 87.04 % 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: -0.64 (0.73), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.004 PHE G 46 Details of bonding type rmsd covalent geometry : bond 0.01162 ( 1035) covalent geometry : angle 2.53190 ( 1377) hydrogen bonds : bond 0.19179 ( 24) hydrogen bonds : angle 10.87570 ( 72) *********************** 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 50 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.064 Fit side-chains REVERT: G 46 PHE cc_start: 0.8452 (t80) cc_final: 0.7928 (p90) REVERT: H 46 PHE cc_start: 0.8446 (t80) cc_final: 0.7963 (p90) REVERT: I 46 PHE cc_start: 0.8466 (t80) cc_final: 0.7949 (p90) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.1166 time to fit residues: 6.4200 Evaluate side-chains 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.062 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2488 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.134611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.112767 restraints weight = 6794.544| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 4.79 r_work: 0.4239 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 1035 Z= 0.182 Angle : 1.352 10.795 1377 Z= 0.685 Chirality : 0.326 1.462 180 Planarity : 0.002 0.006 162 Dihedral : 10.295 44.106 144 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.78 % Allowed : 45.37 % Favored : 51.85 % 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: -0.52 (0.76), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE B 46 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 1035) covalent geometry : angle 1.35177 ( 1377) hydrogen bonds : bond 0.02566 ( 24) hydrogen bonds : angle 7.90352 ( 72) *********************** 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 37 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.041 Fit side-chains REVERT: F 46 PHE cc_start: 0.8411 (t80) cc_final: 0.8150 (t80) REVERT: G 46 PHE cc_start: 0.8610 (t80) cc_final: 0.7423 (p90) REVERT: H 46 PHE cc_start: 0.8611 (t80) cc_final: 0.7507 (p90) REVERT: I 46 PHE cc_start: 0.8663 (t80) cc_final: 0.7617 (p90) outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.1017 time to fit residues: 3.8081 Evaluate side-chains 33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 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 = 0.4429 r_free = 0.4429 target = 0.131215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.109127 restraints weight = 6712.549| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 4.64 r_work: 0.4175 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6624 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= 0.164 Angle : 1.269 10.730 1377 Z= 0.651 Chirality : 0.318 1.407 180 Planarity : 0.001 0.005 162 Dihedral : 8.977 39.214 144 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.63 % Allowed : 40.74 % Favored : 54.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.84 (0.71), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 1035) covalent geometry : angle 1.26910 ( 1377) hydrogen bonds : bond 0.02627 ( 24) hydrogen bonds : angle 6.55714 ( 72) *********************** 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 35 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.068 Fit side-chains REVERT: G 46 PHE cc_start: 0.8817 (t80) cc_final: 0.7437 (p90) REVERT: H 46 PHE cc_start: 0.8796 (t80) cc_final: 0.7452 (p90) REVERT: I 46 PHE cc_start: 0.8826 (t80) cc_final: 0.7383 (p90) outliers start: 5 outliers final: 0 residues processed: 33 average time/residue: 0.1315 time to fit residues: 4.7709 Evaluate side-chains 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.0070 overall best weight: 1.2508 ------------------------------------------------------------------------------- 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 = 0.4497 r_free = 0.4497 target = 0.140106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.116219 restraints weight = 7009.236| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 4.76 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6777 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= 0.149 Angle : 1.262 10.790 1377 Z= 0.640 Chirality : 0.320 1.416 180 Planarity : 0.001 0.005 162 Dihedral : 8.101 34.846 144 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.85 % Allowed : 45.37 % Favored : 52.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.70), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE F 46 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 1035) covalent geometry : angle 1.26236 ( 1377) hydrogen bonds : bond 0.01448 ( 24) hydrogen bonds : angle 5.41419 ( 72) *********************** 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 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.068 Fit side-chains REVERT: G 46 PHE cc_start: 0.8778 (t80) cc_final: 0.7310 (p90) REVERT: H 46 PHE cc_start: 0.8759 (t80) cc_final: 0.7403 (p90) REVERT: I 46 PHE cc_start: 0.8774 (t80) cc_final: 0.7425 (p90) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.0937 time to fit residues: 3.0097 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.9233 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.135604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.112934 restraints weight = 6571.243| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 4.54 r_work: 0.4233 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6962 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= 0.143 Angle : 1.252 10.773 1377 Z= 0.635 Chirality : 0.320 1.409 180 Planarity : 0.001 0.004 162 Dihedral : 7.269 31.542 144 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.93 % Allowed : 46.30 % Favored : 52.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.70), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 1035) covalent geometry : angle 1.25190 ( 1377) hydrogen bonds : bond 0.01158 ( 24) hydrogen bonds : angle 4.89362 ( 72) *********************** 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 30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.082 Fit side-chains REVERT: D 59 LEU cc_start: 0.8183 (mt) cc_final: 0.7949 (mt) REVERT: G 46 PHE cc_start: 0.8808 (t80) cc_final: 0.7291 (p90) REVERT: H 46 PHE cc_start: 0.8811 (t80) cc_final: 0.7430 (p90) REVERT: I 46 PHE cc_start: 0.8808 (t80) cc_final: 0.7400 (p90) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1428 time to fit residues: 4.5395 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9230 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.137077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.114798 restraints weight = 6561.278| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 4.49 r_work: 0.4255 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.7094 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= 0.142 Angle : 1.251 10.763 1377 Z= 0.632 Chirality : 0.321 1.413 180 Planarity : 0.001 0.004 162 Dihedral : 6.868 31.350 144 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 43.52 % Favored : 53.70 % 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: -1.58 (0.71), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.54), 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 0.00409 ( 1035) covalent geometry : angle 1.25089 ( 1377) hydrogen bonds : bond 0.00993 ( 24) hydrogen bonds : angle 4.58742 ( 72) *********************** 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 31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.063 Fit side-chains REVERT: B 46 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.8092 (t80) REVERT: D 59 LEU cc_start: 0.8238 (mt) cc_final: 0.8027 (mt) REVERT: G 46 PHE cc_start: 0.8773 (t80) cc_final: 0.7292 (p90) REVERT: H 46 PHE cc_start: 0.8781 (t80) cc_final: 0.7330 (p90) REVERT: I 46 PHE cc_start: 0.8799 (t80) cc_final: 0.7392 (p90) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.1398 time to fit residues: 4.2781 Evaluate side-chains 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain F residue 46 PHE 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: 6.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4485 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.111113 restraints weight = 6639.180| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 4.46 r_work: 0.4231 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.7270 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= 0.148 Angle : 1.243 10.800 1377 Z= 0.630 Chirality : 0.320 1.415 180 Planarity : 0.001 0.004 162 Dihedral : 7.016 30.273 144 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 45.37 % Favored : 54.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.78 (0.72), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE E 46 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 1035) covalent geometry : angle 1.24332 ( 1377) hydrogen bonds : bond 0.01133 ( 24) hydrogen bonds : angle 4.52213 ( 72) *********************** 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 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.068 Fit side-chains REVERT: D 59 LEU cc_start: 0.8188 (mt) cc_final: 0.7946 (mt) REVERT: G 46 PHE cc_start: 0.8822 (t80) cc_final: 0.7267 (p90) REVERT: H 46 PHE cc_start: 0.8813 (t80) cc_final: 0.7361 (p90) REVERT: I 46 PHE cc_start: 0.8818 (t80) cc_final: 0.7418 (p90) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1515 time to fit residues: 4.2952 Evaluate side-chains 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.2238 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.138723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.114254 restraints weight = 6871.445| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 4.73 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7358 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 : 1.247 10.793 1377 Z= 0.630 Chirality : 0.320 1.415 180 Planarity : 0.001 0.004 162 Dihedral : 6.751 28.609 144 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 40.74 % Favored : 56.48 % 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: -1.89 (0.72), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE H 46 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 1035) covalent geometry : angle 1.24712 ( 1377) hydrogen bonds : bond 0.00918 ( 24) hydrogen bonds : angle 4.27945 ( 72) *********************** 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 31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.069 Fit side-chains REVERT: B 46 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8086 (t80) REVERT: D 59 LEU cc_start: 0.8097 (mt) cc_final: 0.7821 (mt) REVERT: G 46 PHE cc_start: 0.8799 (t80) cc_final: 0.7258 (p90) REVERT: H 46 PHE cc_start: 0.8795 (t80) cc_final: 0.7350 (p90) REVERT: I 46 PHE cc_start: 0.8825 (t80) cc_final: 0.7403 (p90) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.1422 time to fit residues: 4.3556 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 46 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.4990 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.138006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.113473 restraints weight = 6930.980| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 4.69 r_work: 0.4196 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.7600 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= 0.148 Angle : 1.240 10.782 1377 Z= 0.628 Chirality : 0.320 1.412 180 Planarity : 0.001 0.003 162 Dihedral : 6.879 29.054 144 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 45.37 % Favored : 54.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.93 (0.73), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE F 46 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 1035) covalent geometry : angle 1.23992 ( 1377) hydrogen bonds : bond 0.01008 ( 24) hydrogen bonds : angle 4.26102 ( 72) *********************** 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 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.066 Fit side-chains REVERT: D 59 LEU cc_start: 0.8149 (mt) cc_final: 0.7878 (mt) REVERT: G 46 PHE cc_start: 0.8835 (t80) cc_final: 0.7275 (p90) REVERT: H 46 PHE cc_start: 0.8813 (t80) cc_final: 0.7328 (p90) REVERT: I 46 PHE cc_start: 0.8811 (t80) cc_final: 0.7348 (p90) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1531 time to fit residues: 4.3399 Evaluate side-chains 26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.110966 restraints weight = 6622.647| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 4.43 r_work: 0.4222 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7620 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= 0.140 Angle : 1.248 10.766 1377 Z= 0.629 Chirality : 0.320 1.416 180 Planarity : 0.001 0.003 162 Dihedral : 6.228 24.746 144 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.78 % Allowed : 42.59 % Favored : 54.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.92 (0.74), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE H 46 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 1035) covalent geometry : angle 1.24848 ( 1377) hydrogen bonds : bond 0.00695 ( 24) hydrogen bonds : angle 3.95365 ( 72) ********************** 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 29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.038 Fit side-chains REVERT: B 46 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.8095 (t80) REVERT: G 46 PHE cc_start: 0.8831 (t80) cc_final: 0.7234 (p90) REVERT: H 46 PHE cc_start: 0.8808 (t80) cc_final: 0.7320 (p90) REVERT: I 46 PHE cc_start: 0.8826 (t80) cc_final: 0.7343 (p90) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.0940 time to fit residues: 2.6693 Evaluate side-chains 28 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 46 PHE 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: 7.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1985 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.136509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.113256 restraints weight = 6886.739| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 4.53 r_work: 0.4224 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.7796 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= 0.145 Angle : 1.266 10.786 1377 Z= 0.633 Chirality : 0.320 1.413 180 Planarity : 0.001 0.004 162 Dihedral : 6.373 26.007 144 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.85 % Allowed : 42.59 % Favored : 55.56 % 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: -1.96 (0.73), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.000 PHE F 46 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 1035) covalent geometry : angle 1.26568 ( 1377) hydrogen bonds : bond 0.00832 ( 24) hydrogen bonds : angle 3.95121 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 931.50 seconds wall clock time: 16 minutes 29.06 seconds (989.06 seconds total)