Starting phenix.real_space_refine on Fri Aug 22 12:37:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8otf_17177/08_2025/8otf_17177.map" } resolution = 3.3 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 S 6 5.16 5 C 882 2.51 5 N 234 2.21 5 O 228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1350 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 225 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 0.39, per 1000 atoms: 0.29 Number of scatterers: 1350 At special positions: 0 Unit cell: (57.68, 78.28, 29.664, 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 6 16.00 O 228 8.00 N 234 7.00 C 882 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: 0.31 Conformation dependent library (CDL) restraints added in 40.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 27 removed outlier: 8.682A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.390A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.305A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 20 removed outlier: 6.617A pdb=" N PHE B 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 24 through 27 removed outlier: 8.676A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER F 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN B 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.407A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.265A pdb=" N VAL B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.11 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 338 1.33 - 1.45: 255 1.45 - 1.56: 763 1.56 - 1.68: 0 1.68 - 1.79: 12 Bond restraints: 1368 Sorted by residual: bond pdb=" CG HIS F 14 " pdb=" CD2 HIS F 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.43e+00 bond pdb=" CG HIS B 14 " pdb=" CD2 HIS B 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.42e+00 bond pdb=" CG HIS D 14 " pdb=" CD2 HIS D 14 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.41e+00 bond pdb=" CG HIS A 14 " pdb=" CD2 HIS A 14 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.17e+00 bond pdb=" CG HIS E 14 " pdb=" CD2 HIS E 14 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.14e+00 ... (remaining 1363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 1417 1.57 - 3.15: 338 3.15 - 4.72: 63 4.72 - 6.29: 6 6.29 - 7.87: 12 Bond angle restraints: 1836 Sorted by residual: angle pdb=" CA ASP E 23 " pdb=" CB ASP E 23 " pdb=" CG ASP E 23 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" CA ASP C 23 " pdb=" CB ASP C 23 " pdb=" CG ASP C 23 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" CA ASP A 23 " pdb=" CB ASP A 23 " pdb=" CG ASP A 23 " ideal model delta sigma weight residual 112.60 120.46 -7.86 1.00e+00 1.00e+00 6.18e+01 angle pdb=" CA ASP F 23 " pdb=" CB ASP F 23 " pdb=" CG ASP F 23 " ideal model delta sigma weight residual 112.60 120.29 -7.69 1.00e+00 1.00e+00 5.91e+01 angle pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " ideal model delta sigma weight residual 112.60 120.27 -7.67 1.00e+00 1.00e+00 5.89e+01 ... (remaining 1831 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.15: 654 13.15 - 26.29: 75 26.29 - 39.43: 15 39.43 - 52.57: 12 52.57 - 65.71: 12 Dihedral angle restraints: 768 sinusoidal: 276 harmonic: 492 Sorted by residual: dihedral pdb=" CA GLY B 38 " pdb=" C GLY B 38 " pdb=" N VAL B 39 " pdb=" CA VAL B 39 " ideal model delta harmonic sigma weight residual -180.00 -157.14 -22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY D 38 " pdb=" C GLY D 38 " pdb=" N VAL D 39 " pdb=" CA VAL D 39 " ideal model delta harmonic sigma weight residual -180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLY F 38 " pdb=" C GLY F 38 " pdb=" N VAL F 39 " pdb=" CA VAL F 39 " ideal model delta harmonic sigma weight residual 180.00 -157.18 -22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 765 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.048: 71 0.048 - 0.092: 67 0.092 - 0.137: 36 0.137 - 0.181: 36 0.181 - 0.226: 12 Chirality restraints: 222 Sorted by residual: chirality pdb=" CA ASP C 23 " pdb=" N ASP C 23 " pdb=" C ASP C 23 " pdb=" CB ASP C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP A 23 " pdb=" N ASP A 23 " pdb=" C ASP A 23 " pdb=" CB ASP A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP E 23 " pdb=" N ASP E 23 " pdb=" C ASP E 23 " pdb=" CB ASP E 23 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 219 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C VAL A 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 40 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 39 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL C 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL C 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL C 40 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 39 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C VAL E 39 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL E 39 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL E 40 " -0.009 2.00e-02 2.50e+03 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 835 3.07 - 3.53: 1302 3.53 - 3.99: 2108 3.99 - 4.44: 2436 4.44 - 4.90: 4177 Nonbonded interactions: 10858 Sorted by model distance: nonbonded pdb=" N GLU E 22 " pdb=" O GLU E 22 " model vdw 2.614 2.496 nonbonded pdb=" N GLU A 22 " pdb=" O GLU A 22 " model vdw 2.614 2.496 nonbonded pdb=" N GLU C 22 " pdb=" O GLU C 22 " model vdw 2.614 2.496 nonbonded pdb=" N VAL F 18 " pdb=" O VAL F 18 " model vdw 2.657 2.496 nonbonded pdb=" N VAL B 18 " pdb=" O VAL B 18 " model vdw 2.658 2.496 ... (remaining 10853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 2.980 Find NCS groups from input model: 0.010 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:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 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 : 0.010 0.047 1368 Z= 0.628 Angle : 1.525 7.866 1836 Z= 1.025 Chirality : 0.102 0.226 222 Planarity : 0.006 0.016 228 Dihedral : 16.154 65.711 456 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.35 % Allowed : 4.35 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.33), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.005 PHE F 19 HIS 0.005 0.003 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00983 ( 1368) covalent geometry : angle 1.52505 ( 1836) hydrogen bonds : bond 0.14287 ( 12) hydrogen bonds : angle 5.81484 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.028 Fit side-chains REVERT: A 23 ASP cc_start: 0.8334 (p0) cc_final: 0.8108 (p0) REVERT: A 35 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8845 (tpt) REVERT: D 16 LYS cc_start: 0.8968 (mttp) cc_final: 0.8203 (mmtt) REVERT: E 22 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.6818 (pt0) REVERT: E 23 ASP cc_start: 0.8576 (p0) cc_final: 0.8324 (p0) REVERT: F 22 GLU cc_start: 0.8889 (mm-30) cc_final: 0.7005 (pt0) outliers start: 6 outliers final: 0 residues processed: 36 average time/residue: 0.0395 time to fit residues: 1.5803 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain E residue 22 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080383 restraints weight = 2046.652| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.96 r_work: 0.3164 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1368 Z= 0.113 Angle : 0.439 2.718 1836 Z= 0.245 Chirality : 0.055 0.132 222 Planarity : 0.001 0.005 228 Dihedral : 8.358 57.110 186 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.35 % Allowed : 6.52 % Favored : 89.13 % 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 aren not related in a simple way. whole: -3.00 (0.42), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 19 HIS 0.002 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 1368) covalent geometry : angle 0.43866 ( 1836) hydrogen bonds : bond 0.00760 ( 12) hydrogen bonds : angle 4.84971 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.030 Fit side-chains REVERT: D 22 GLU cc_start: 0.8451 (tp30) cc_final: 0.8211 (tp30) REVERT: E 22 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6164 (pt0) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 0.0398 time to fit residues: 1.5533 Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.100015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080180 restraints weight = 2072.397| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.99 r_work: 0.3129 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 1368 Z= 0.172 Angle : 0.455 3.223 1836 Z= 0.244 Chirality : 0.054 0.131 222 Planarity : 0.001 0.004 228 Dihedral : 7.116 60.259 183 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.90 % Allowed : 6.52 % Favored : 90.58 % 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 aren not related in a simple way. whole: -2.30 (0.48), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 19 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 1368) covalent geometry : angle 0.45454 ( 1836) hydrogen bonds : bond 0.00997 ( 12) hydrogen bonds : angle 4.88807 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.031 Fit side-chains REVERT: D 22 GLU cc_start: 0.8555 (tp30) cc_final: 0.8092 (mm-30) REVERT: E 22 GLU cc_start: 0.8244 (mm-30) cc_final: 0.6277 (pt0) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.0423 time to fit residues: 1.6486 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077510 restraints weight = 2121.154| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.04 r_work: 0.3074 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.022 1368 Z= 0.271 Angle : 0.520 3.711 1836 Z= 0.275 Chirality : 0.056 0.132 222 Planarity : 0.002 0.006 228 Dihedral : 4.611 10.653 180 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.62 % Allowed : 6.52 % Favored : 89.86 % 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 aren not related in a simple way. whole: -1.86 (0.51), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.39), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE B 19 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00618 ( 1368) covalent geometry : angle 0.51986 ( 1836) hydrogen bonds : bond 0.01026 ( 12) hydrogen bonds : angle 4.99913 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.062 Fit side-chains REVERT: D 22 GLU cc_start: 0.8630 (tp30) cc_final: 0.8168 (mm-30) REVERT: E 22 GLU cc_start: 0.8303 (mm-30) cc_final: 0.6296 (pt0) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0974 time to fit residues: 3.9175 Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.102644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082249 restraints weight = 2030.014| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.06 r_work: 0.3169 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1368 Z= 0.097 Angle : 0.392 2.848 1836 Z= 0.212 Chirality : 0.054 0.129 222 Planarity : 0.001 0.006 228 Dihedral : 4.108 9.925 180 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.17 % Allowed : 8.70 % Favored : 89.13 % 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 aren not related in a simple way. whole: -1.62 (0.55), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 19 HIS 0.001 0.000 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 1368) covalent geometry : angle 0.39237 ( 1836) hydrogen bonds : bond 0.00702 ( 12) hydrogen bonds : angle 4.71325 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.054 Fit side-chains REVERT: D 22 GLU cc_start: 0.8437 (tp30) cc_final: 0.8018 (mm-30) REVERT: E 22 GLU cc_start: 0.8209 (mm-30) cc_final: 0.6254 (pt0) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0741 time to fit residues: 3.0257 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 16 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.0010 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.4170 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.100885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081106 restraints weight = 2034.639| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.98 r_work: 0.3159 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1368 Z= 0.144 Angle : 0.423 3.079 1836 Z= 0.227 Chirality : 0.054 0.130 222 Planarity : 0.001 0.005 228 Dihedral : 4.076 10.236 180 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 10.87 % Favored : 86.96 % 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 aren not related in a simple way. whole: -1.40 (0.57), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 19 HIS 0.006 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 1368) covalent geometry : angle 0.42309 ( 1836) hydrogen bonds : bond 0.00757 ( 12) hydrogen bonds : angle 4.56697 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.055 Fit side-chains REVERT: D 22 GLU cc_start: 0.8502 (tp30) cc_final: 0.8097 (mm-30) REVERT: E 22 GLU cc_start: 0.8236 (mm-30) cc_final: 0.6288 (pt0) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.0704 time to fit residues: 2.7510 Evaluate side-chains 37 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.0170 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 0.0000 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085394 restraints weight = 1962.372| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.97 r_work: 0.3237 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1368 Z= 0.076 Angle : 0.364 2.910 1836 Z= 0.200 Chirality : 0.053 0.127 222 Planarity : 0.001 0.004 228 Dihedral : 3.732 9.846 180 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % 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 aren not related in a simple way. whole: -1.32 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE D 19 HIS 0.005 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00164 ( 1368) covalent geometry : angle 0.36405 ( 1836) hydrogen bonds : bond 0.00607 ( 12) hydrogen bonds : angle 4.26619 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.054 Fit side-chains REVERT: D 22 GLU cc_start: 0.8287 (tp30) cc_final: 0.7861 (mm-30) REVERT: E 22 GLU cc_start: 0.8231 (mm-30) cc_final: 0.6231 (pt0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0787 time to fit residues: 3.1199 Evaluate side-chains 32 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.094967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076084 restraints weight = 2108.468| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.97 r_work: 0.3074 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 1368 Z= 0.316 Angle : 0.598 8.741 1836 Z= 0.303 Chirality : 0.057 0.146 222 Planarity : 0.002 0.005 228 Dihedral : 4.324 10.849 180 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.45 % Allowed : 13.04 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 19 HIS 0.005 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00727 ( 1368) covalent geometry : angle 0.59791 ( 1836) hydrogen bonds : bond 0.01134 ( 12) hydrogen bonds : angle 4.63368 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.055 Fit side-chains REVERT: D 22 GLU cc_start: 0.8594 (tp30) cc_final: 0.8185 (mm-30) REVERT: E 22 GLU cc_start: 0.8363 (mm-30) cc_final: 0.6315 (pt0) outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.0652 time to fit residues: 2.4873 Evaluate side-chains 35 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080909 restraints weight = 2019.906| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.96 r_work: 0.3155 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1368 Z= 0.147 Angle : 0.493 8.709 1836 Z= 0.246 Chirality : 0.054 0.129 222 Planarity : 0.001 0.005 228 Dihedral : 4.134 10.406 180 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.72 % Allowed : 13.04 % Favored : 86.23 % 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 aren not related in a simple way. whole: -1.24 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 19 HIS 0.005 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 1368) covalent geometry : angle 0.49346 ( 1836) hydrogen bonds : bond 0.00847 ( 12) hydrogen bonds : angle 4.48101 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.056 Fit side-chains REVERT: D 22 GLU cc_start: 0.8482 (tp30) cc_final: 0.8041 (mm-30) REVERT: E 22 GLU cc_start: 0.8339 (mm-30) cc_final: 0.6398 (pt0) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0659 time to fit residues: 2.5241 Evaluate side-chains 35 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.105641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085214 restraints weight = 1966.931| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.97 r_work: 0.3249 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1368 Z= 0.090 Angle : 0.450 8.249 1836 Z= 0.226 Chirality : 0.053 0.127 222 Planarity : 0.001 0.004 228 Dihedral : 3.791 9.974 180 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % 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 aren not related in a simple way. whole: -1.20 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE D 19 HIS 0.005 0.000 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 1368) covalent geometry : angle 0.44993 ( 1836) hydrogen bonds : bond 0.00659 ( 12) hydrogen bonds : angle 4.23570 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 348 Ramachandran restraints generated. 174 Oldfield, 0 Emsley, 174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.052 Fit side-chains REVERT: D 22 GLU cc_start: 0.8282 (tp30) cc_final: 0.7834 (mm-30) REVERT: E 22 GLU cc_start: 0.8294 (mm-30) cc_final: 0.6294 (pt0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0597 time to fit residues: 2.3557 Evaluate side-chains 34 residues out of total 138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.082873 restraints weight = 1991.824| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.11 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1368 Z= 0.116 Angle : 0.463 8.242 1836 Z= 0.233 Chirality : 0.053 0.127 222 Planarity : 0.001 0.005 228 Dihedral : 3.776 10.106 180 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.72 % Allowed : 13.77 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.58), residues: 174 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 19 HIS 0.006 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 1368) covalent geometry : angle 0.46340 ( 1836) hydrogen bonds : bond 0.00758 ( 12) hydrogen bonds : angle 4.34751 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 606.13 seconds wall clock time: 11 minutes 39.35 seconds (699.35 seconds total)