Starting phenix.real_space_refine on Tue Aug 4 11:45:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.map" model { file = "/net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmq_66101/08_2026/9wmq_66101.cif" } resolution = 1.73 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1115 2.51 5 N 283 2.21 5 O 316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1719 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1486 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 169} Chain: "H" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 188 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain breaks: 1 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Time building chain proxies: 0.68, per 1000 atoms: 0.40 Number of scatterers: 1719 At special positions: 0 Unit cell: (75.65, 63.75, 73.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 316 8.00 N 283 7.00 C 1115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 63.0 milliseconds 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 392 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 39 through 49 removed outlier: 3.972A pdb=" N LYS F 85 " --> pdb=" O TRP F 207 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG F 209 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE F 83 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 39 through 49 removed outlier: 3.972A pdb=" N LYS F 85 " --> pdb=" O TRP F 207 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG F 209 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE F 83 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.686A pdb=" N THR F 119 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 104 " --> pdb=" O TYR F 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 50 through 51 68 hydrogen bonds defined for protein. 174 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: 0.22 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 508 1.34 - 1.46: 467 1.46 - 1.58: 792 1.58 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 1777 Sorted by residual: bond pdb=" N LYS F 194 " pdb=" CA LYS F 194 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.35e-02 5.49e+03 8.22e+00 bond pdb=" N MET F 135 " pdb=" CA MET F 135 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 6.01e+00 bond pdb=" N THR F 195 " pdb=" CA THR F 195 " ideal model delta sigma weight residual 1.455 1.477 -0.023 1.27e-02 6.20e+03 3.18e+00 bond pdb=" N ARG H 106 " pdb=" CA ARG H 106 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.23e-02 6.61e+03 3.11e+00 bond pdb=" N TYR H 54 " pdb=" CA TYR H 54 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.27e-02 6.20e+03 3.01e+00 ... (remaining 1772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 2249 1.41 - 2.83: 139 2.83 - 4.24: 27 4.24 - 5.66: 2 5.66 - 7.07: 1 Bond angle restraints: 2418 Sorted by residual: angle pdb=" CA THR F 195 " pdb=" C THR F 195 " pdb=" O THR F 195 " ideal model delta sigma weight residual 121.33 117.78 3.55 1.08e+00 8.57e-01 1.08e+01 angle pdb=" CA LYS F 194 " pdb=" C LYS F 194 " pdb=" O LYS F 194 " ideal model delta sigma weight residual 119.15 115.59 3.56 1.14e+00 7.69e-01 9.77e+00 angle pdb=" CA TYR H 54 " pdb=" C TYR H 54 " pdb=" O TYR H 54 " ideal model delta sigma weight residual 120.13 116.19 3.94 1.40e+00 5.10e-01 7.93e+00 angle pdb=" CA ARG F 168 " pdb=" C ARG F 168 " pdb=" N PRO F 169 " ideal model delta sigma weight residual 118.44 122.67 -4.23 1.59e+00 3.96e-01 7.07e+00 angle pdb=" N TYR H 54 " pdb=" CA TYR H 54 " pdb=" C TYR H 54 " ideal model delta sigma weight residual 112.68 109.51 3.17 1.33e+00 5.65e-01 5.68e+00 ... (remaining 2413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.05: 942 11.05 - 22.09: 62 22.09 - 33.14: 6 33.14 - 44.18: 6 44.18 - 55.23: 2 Dihedral angle restraints: 1018 sinusoidal: 405 harmonic: 613 Sorted by residual: dihedral pdb=" CA THR L 31 " pdb=" C THR L 31 " pdb=" N ASN L 32 " pdb=" CA ASN L 32 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLY F 183 " pdb=" C GLY F 183 " pdb=" N ALA F 184 " pdb=" CA ALA F 184 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PRO F 159 " pdb=" C PRO F 159 " pdb=" N GLY F 160 " pdb=" CA GLY F 160 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1015 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.042: 157 0.042 - 0.083: 59 0.083 - 0.124: 24 0.124 - 0.164: 8 0.164 - 0.205: 4 Chirality restraints: 252 Sorted by residual: chirality pdb=" CA ARG H 106 " pdb=" N ARG H 106 " pdb=" C ARG H 106 " pdb=" CB ARG H 106 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB THR F 117 " pdb=" CA THR F 117 " pdb=" OG1 THR F 117 " pdb=" CG2 THR F 117 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 249 not shown) Planarity restraints: 298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 54 " -0.028 2.00e-02 2.50e+03 1.55e-02 4.83e+00 pdb=" CG TYR H 54 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 54 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 54 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 54 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR H 54 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 54 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 54 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 58 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO F 59 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 59 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 59 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 177 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO F 178 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 178 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 178 " 0.020 5.00e-02 4.00e+02 ... (remaining 295 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 567 2.87 - 3.38: 1205 3.38 - 3.88: 2675 3.88 - 4.39: 2762 4.39 - 4.90: 5163 Nonbonded interactions: 12372 Sorted by model distance: nonbonded pdb=" O THR F 34 " pdb=" OG1 THR F 37 " model vdw 2.359 3.040 nonbonded pdb=" OD1 ASP F 56 " pdb=" NE2 HIS H 59 " model vdw 2.403 3.120 nonbonded pdb=" O SER F 129 " pdb=" NH1 ARG F 132 " model vdw 2.482 3.120 nonbonded pdb=" OG1 THR F 154 " pdb=" O HIS F 158 " model vdw 2.494 3.040 nonbonded pdb=" N ASP F 112 " pdb=" OD1 ASP F 112 " model vdw 2.559 3.120 ... (remaining 12367 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 29.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.050 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 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 : 0.004 0.039 1777 Z= 0.228 Angle : 0.764 7.070 2418 Z= 0.456 Chirality : 0.056 0.205 252 Planarity : 0.007 0.048 298 Dihedral : 8.595 55.226 626 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.50), residues: 202 helix: None (None), residues: 0 sheet: -1.05 (0.55), residues: 76 loop : -2.21 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 143 TYR 0.029 0.003 TYR H 54 PHE 0.015 0.003 PHE F 165 TRP 0.017 0.002 TRP F 187 HIS 0.004 0.001 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.23 ( 1777) covalent geometry : angle 0.76439 / 0.46 ( 2418) hydrogen bonds : bond 0.29050 / 19.08 ( 49) hydrogen bonds : angle 9.28716 / 6.02 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.072 Fit side-chains REVERT: F 170 THR cc_start: 0.7409 (m) cc_final: 0.7206 (p) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.5768 time to fit residues: 25.8415 Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 57 ASN L 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105374 restraints weight = 1860.637| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.01 r_work: 0.3492 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1777 Z= 0.126 Angle : 0.562 4.487 2418 Z= 0.315 Chirality : 0.047 0.132 252 Planarity : 0.005 0.037 298 Dihedral : 5.044 18.232 229 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 6.49 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.55), residues: 202 helix: None (None), residues: 0 sheet: -0.12 (0.54), residues: 84 loop : -1.44 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 132 TYR 0.015 0.002 TYR F 80 PHE 0.009 0.001 PHE F 65 TRP 0.018 0.001 TRP F 187 HIS 0.001 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 1777) covalent geometry : angle 0.56208 / 0.32 ( 2418) hydrogen bonds : bond 0.04468 / 3.07 ( 49) hydrogen bonds : angle 5.08662 / 3.30 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.072 Fit side-chains REVERT: F 46 MET cc_start: 0.8649 (tmm) cc_final: 0.8378 (tmm) REVERT: F 128 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8327 (mp0) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.5849 time to fit residues: 22.0004 Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104957 restraints weight = 1890.148| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.02 r_work: 0.3486 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1777 Z= 0.114 Angle : 0.528 4.403 2418 Z= 0.295 Chirality : 0.046 0.132 252 Planarity : 0.005 0.034 298 Dihedral : 4.789 16.996 229 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.08 % Allowed : 10.27 % Favored : 88.65 % 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 (0.57), residues: 202 helix: None (None), residues: 0 sheet: 0.09 (0.54), residues: 82 loop : -1.13 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 132 TYR 0.010 0.001 TYR F 80 PHE 0.008 0.001 PHE F 65 TRP 0.013 0.001 TRP F 187 HIS 0.002 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 1777) covalent geometry : angle 0.52762 / 0.30 ( 2418) hydrogen bonds : bond 0.03972 / 2.74 ( 49) hydrogen bonds : angle 4.71845 / 3.06 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.053 Fit side-chains REVERT: F 128 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8319 (mp0) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.5726 time to fit residues: 21.5280 Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101877 restraints weight = 1831.044| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.00 r_work: 0.3432 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1777 Z= 0.149 Angle : 0.596 4.422 2418 Z= 0.334 Chirality : 0.048 0.145 252 Planarity : 0.005 0.036 298 Dihedral : 5.122 17.222 229 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.62 % Allowed : 9.73 % Favored : 88.65 % 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: -0.70 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.07 (0.53), residues: 89 loop : -0.76 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 132 TYR 0.010 0.002 TYR F 201 PHE 0.008 0.001 PHE F 65 TRP 0.014 0.001 TRP F 187 HIS 0.003 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 1777) covalent geometry : angle 0.59599 / 0.33 ( 2418) hydrogen bonds : bond 0.04371 / 3.01 ( 49) hydrogen bonds : angle 4.70637 / 3.06 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.073 Fit side-chains REVERT: F 128 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8235 (mp0) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.5313 time to fit residues: 20.5600 Evaluate side-chains 39 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099717 restraints weight = 1827.748| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 0.99 r_work: 0.3392 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1777 Z= 0.193 Angle : 0.665 4.738 2418 Z= 0.376 Chirality : 0.051 0.155 252 Planarity : 0.005 0.038 298 Dihedral : 5.547 19.420 229 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.62 % Allowed : 9.19 % Favored : 89.19 % 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: -0.71 (0.58), residues: 202 helix: None (None), residues: 0 sheet: 0.04 (0.56), residues: 81 loop : -0.82 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 68 TYR 0.012 0.002 TYR F 210 PHE 0.010 0.002 PHE F 65 TRP 0.014 0.002 TRP F 187 HIS 0.003 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 1777) covalent geometry : angle 0.66541 / 0.38 ( 2418) hydrogen bonds : bond 0.04994 / 3.42 ( 49) hydrogen bonds : angle 4.83635 / 3.15 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.083 Fit side-chains REVERT: F 128 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8225 (mp0) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.5473 time to fit residues: 20.0688 Evaluate side-chains 37 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102318 restraints weight = 1839.272| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.99 r_work: 0.3436 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1777 Z= 0.134 Angle : 0.581 6.419 2418 Z= 0.321 Chirality : 0.047 0.143 252 Planarity : 0.005 0.034 298 Dihedral : 5.004 17.243 229 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.62 % Allowed : 10.27 % Favored : 88.11 % 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: -0.66 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.03 (0.53), residues: 87 loop : -0.73 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 132 TYR 0.009 0.002 TYR F 144 PHE 0.008 0.001 PHE F 65 TRP 0.010 0.001 TRP F 187 HIS 0.002 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 1777) covalent geometry : angle 0.58093 / 0.32 ( 2418) hydrogen bonds : bond 0.04052 / 2.80 ( 49) hydrogen bonds : angle 4.72134 / 3.07 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.041 Fit side-chains REVERT: F 128 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8238 (mp0) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.3474 time to fit residues: 13.0746 Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101929 restraints weight = 1779.050| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 0.99 r_work: 0.3430 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1777 Z= 0.142 Angle : 0.594 7.009 2418 Z= 0.328 Chirality : 0.048 0.146 252 Planarity : 0.005 0.034 298 Dihedral : 5.022 17.034 229 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 9.19 % Favored : 88.65 % 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 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.03 (0.54), residues: 87 loop : -0.70 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 132 TYR 0.010 0.002 TYR F 210 PHE 0.008 0.001 PHE F 65 TRP 0.011 0.001 TRP F 187 HIS 0.002 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 1777) covalent geometry : angle 0.59423 / 0.33 ( 2418) hydrogen bonds : bond 0.04212 / 2.91 ( 49) hydrogen bonds : angle 4.71870 / 3.07 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.039 Fit side-chains REVERT: F 128 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8244 (mp0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.3557 time to fit residues: 13.7382 Evaluate side-chains 40 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 0.0020 chunk 2 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105345 restraints weight = 1858.589| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 0.99 r_work: 0.3490 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1777 Z= 0.104 Angle : 0.520 6.427 2418 Z= 0.283 Chirality : 0.045 0.133 252 Planarity : 0.005 0.031 298 Dihedral : 4.492 16.336 229 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.08 % Allowed : 10.81 % Favored : 88.11 % 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: -0.57 (0.59), residues: 202 helix: None (None), residues: 0 sheet: 0.05 (0.53), residues: 87 loop : -0.67 (0.60), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 50 TYR 0.008 0.001 TYR F 144 PHE 0.007 0.001 PHE F 65 TRP 0.008 0.001 TRP F 187 HIS 0.001 0.000 HIS F 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 1777) covalent geometry : angle 0.52010 / 0.28 ( 2418) hydrogen bonds : bond 0.03432 / 2.39 ( 49) hydrogen bonds : angle 4.63606 / 3.00 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.042 Fit side-chains REVERT: F 128 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8231 (mp0) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.4443 time to fit residues: 16.2193 Evaluate side-chains 36 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 128 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100351 restraints weight = 1817.169| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.99 r_work: 0.3397 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1777 Z= 0.200 Angle : 0.683 8.036 2418 Z= 0.379 Chirality : 0.051 0.157 252 Planarity : 0.005 0.037 298 Dihedral : 5.399 19.236 229 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.08 % Allowed : 11.35 % Favored : 87.57 % 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 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.01 (0.53), residues: 89 loop : -0.57 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.012 0.002 TYR F 210 PHE 0.010 0.002 PHE F 65 TRP 0.011 0.002 TRP F 187 HIS 0.003 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 1777) covalent geometry : angle 0.68323 / 0.38 ( 2418) hydrogen bonds : bond 0.04892 / 3.36 ( 49) hydrogen bonds : angle 4.83290 / 3.14 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.042 Fit side-chains REVERT: F 128 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8216 (mp0) outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.4109 time to fit residues: 15.4275 Evaluate side-chains 38 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101406 restraints weight = 1807.875| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.00 r_work: 0.3421 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1777 Z= 0.157 Angle : 0.629 8.830 2418 Z= 0.344 Chirality : 0.049 0.148 252 Planarity : 0.005 0.034 298 Dihedral : 5.138 17.120 229 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.54 % Allowed : 11.35 % Favored : 88.11 % 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: -0.53 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.04 (0.53), residues: 89 loop : -0.54 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.010 0.002 TYR F 210 PHE 0.008 0.001 PHE F 65 TRP 0.009 0.001 TRP F 187 HIS 0.002 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 1777) covalent geometry : angle 0.62929 / 0.34 ( 2418) hydrogen bonds : bond 0.04353 / 3.00 ( 49) hydrogen bonds : angle 4.78096 / 3.10 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 404 Ramachandran restraints generated. 202 Oldfield, 0 Emsley, 202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.070 Fit side-chains REVERT: F 128 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8203 (mp0) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.4694 time to fit residues: 16.2696 Evaluate side-chains 34 residues out of total 185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 128 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100443 restraints weight = 1829.890| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.01 r_work: 0.3405 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1777 Z= 0.178 Angle : 0.673 10.090 2418 Z= 0.367 Chirality : 0.050 0.152 252 Planarity : 0.005 0.036 298 Dihedral : 5.295 17.822 229 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.62 % Allowed : 10.81 % Favored : 87.57 % 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: -0.54 (0.58), residues: 202 helix: None (None), residues: 0 sheet: -0.03 (0.53), residues: 89 loop : -0.56 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 50 TYR 0.012 0.002 TYR F 210 PHE 0.009 0.002 PHE F 65 TRP 0.010 0.001 TRP F 187 HIS 0.002 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 1777) covalent geometry : angle 0.67269 / 0.37 ( 2418) hydrogen bonds : bond 0.04685 / 3.23 ( 49) hydrogen bonds : angle 4.79797 / 3.11 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.38 seconds wall clock time: 28 minutes 19.66 seconds (1699.66 seconds total)