Starting phenix.real_space_refine on Fri Aug 22 12:36:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf4_37198/08_2025/8kf4_37198.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 978 2.51 5 N 252 2.21 5 O 264 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: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 250 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Restraints were copied for chains: C, E, A, F, B Time building chain proxies: 0.31, per 1000 atoms: 0.21 Number of scatterers: 1500 At special positions: 0 Unit cell: (68.8899, 70.5499, 36.52, 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 264 8.00 N 252 7.00 C 978 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: 0.06 Conformation dependent library (CDL) restraints added in 36.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 336 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 13 removed outlier: 6.387A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 17 through 20 removed outlier: 6.946A pdb=" N PHE D 20 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 24 through 25 removed outlier: 6.509A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 30 through 36 removed outlier: 6.548A pdb=" N ALA D 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLY E 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ILE D 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N MET E 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N LEU D 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.366A pdb=" N VAL D 40 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.400A pdb=" N VAL C 12 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.943A pdb=" N PHE C 20 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 17 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE B 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE C 19 " --> pdb=" O PHE B 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.503A pdb=" N VAL C 24 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.571A pdb=" N ALA C 30 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY A 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ILE C 32 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET A 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N LEU C 34 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET C 35 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 36 " --> pdb=" O MET C 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.365A pdb=" N VAL C 40 " --> pdb=" O ILE A 41 " (cutoff:3.500A) 18 hydrogen bonds defined for protein. 51 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: 0.13 Time building geometry restraints manager: 0.08 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: 486 1.33 - 1.45: 192 1.45 - 1.56: 834 1.56 - 1.67: 0 1.67 - 1.79: 12 Bond restraints: 1524 Sorted by residual: bond pdb=" CG1 ILE F 31 " pdb=" CD1 ILE F 31 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 bond pdb=" CG1 ILE D 31 " pdb=" CD1 ILE D 31 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.32e+00 bond pdb=" CG1 ILE B 31 " pdb=" CD1 ILE B 31 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.30e+00 bond pdb=" CG1 ILE A 31 " pdb=" CD1 ILE A 31 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.29e+00 bond pdb=" CG1 ILE E 31 " pdb=" CD1 ILE E 31 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.28e+00 ... (remaining 1519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 1603 0.78 - 1.56: 319 1.56 - 2.34: 100 2.34 - 3.12: 12 3.12 - 3.90: 12 Bond angle restraints: 2046 Sorted by residual: angle pdb=" C VAL B 12 " pdb=" N HIS B 13 " pdb=" CA HIS B 13 " ideal model delta sigma weight residual 121.75 117.85 3.90 1.73e+00 3.34e-01 5.07e+00 angle pdb=" C VAL E 12 " pdb=" N HIS E 13 " pdb=" CA HIS E 13 " ideal model delta sigma weight residual 121.75 117.86 3.89 1.73e+00 3.34e-01 5.06e+00 angle pdb=" C VAL C 12 " pdb=" N HIS C 13 " pdb=" CA HIS C 13 " ideal model delta sigma weight residual 121.75 117.86 3.89 1.73e+00 3.34e-01 5.05e+00 angle pdb=" C VAL A 12 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " ideal model delta sigma weight residual 121.75 117.87 3.88 1.73e+00 3.34e-01 5.02e+00 angle pdb=" C VAL D 12 " pdb=" N HIS D 13 " pdb=" CA HIS D 13 " ideal model delta sigma weight residual 121.75 117.88 3.87 1.73e+00 3.34e-01 5.01e+00 ... (remaining 2041 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 9.07: 672 9.07 - 18.11: 114 18.11 - 27.15: 36 27.15 - 36.19: 6 36.19 - 45.23: 18 Dihedral angle restraints: 846 sinusoidal: 306 harmonic: 540 Sorted by residual: dihedral pdb=" CA HIS A 14 " pdb=" C HIS A 14 " pdb=" N GLN A 15 " pdb=" CA GLN A 15 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 dihedral pdb=" CA HIS D 14 " pdb=" C HIS D 14 " pdb=" N GLN D 15 " pdb=" CA GLN D 15 " ideal model delta harmonic sigma weight residual 180.00 165.38 14.62 0 5.00e+00 4.00e-02 8.55e+00 dihedral pdb=" CA HIS C 14 " pdb=" C HIS C 14 " pdb=" N GLN C 15 " pdb=" CA GLN C 15 " ideal model delta harmonic sigma weight residual 180.00 165.39 14.61 0 5.00e+00 4.00e-02 8.54e+00 ... (remaining 843 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.031: 87 0.031 - 0.061: 59 0.061 - 0.091: 46 0.091 - 0.122: 24 0.122 - 0.152: 18 Chirality restraints: 234 Sorted by residual: chirality pdb=" CA HIS E 14 " pdb=" N HIS E 14 " pdb=" C HIS E 14 " pdb=" CB HIS E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA HIS B 14 " pdb=" N HIS B 14 " pdb=" C HIS B 14 " pdb=" CB HIS B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA HIS D 14 " pdb=" N HIS D 14 " pdb=" C HIS D 14 " pdb=" CB HIS D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 231 not shown) Planarity restraints: 258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 13 " -0.005 2.00e-02 2.50e+03 4.00e-03 2.40e-01 pdb=" CG HIS E 13 " 0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS E 13 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS E 13 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 13 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 13 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 13 " 0.005 2.00e-02 2.50e+03 3.91e-03 2.30e-01 pdb=" CG HIS B 13 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS B 13 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 13 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 13 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 13 " 0.004 2.00e-02 2.50e+03 3.86e-03 2.24e-01 pdb=" CG HIS A 13 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS A 13 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 13 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 13 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 13 " 0.001 2.00e-02 2.50e+03 ... (remaining 255 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 950 3.06 - 3.52: 1296 3.52 - 3.98: 2257 3.98 - 4.44: 2448 4.44 - 4.90: 4517 Nonbonded interactions: 11468 Sorted by model distance: nonbonded pdb=" OD1 ASN A 27 " pdb=" N GLY A 29 " model vdw 2.605 3.120 nonbonded pdb=" OD1 ASN E 27 " pdb=" N GLY E 29 " model vdw 2.605 3.120 nonbonded pdb=" OD1 ASN C 27 " pdb=" N GLY C 29 " model vdw 2.605 3.120 nonbonded pdb=" OD1 ASN D 27 " pdb=" N GLY D 29 " model vdw 2.606 3.120 nonbonded pdb=" OD1 ASN B 27 " pdb=" N GLY B 29 " model vdw 2.606 3.120 ... (remaining 11463 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 'D' selection = chain 'C' selection = chain 'E' selection = chain 'A' selection = chain 'F' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.720 Find NCS groups from input model: 0.010 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 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 0.045 1524 Z= 0.424 Angle : 0.766 3.896 2046 Z= 0.476 Chirality : 0.066 0.152 234 Planarity : 0.002 0.004 258 Dihedral : 12.823 45.231 510 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -4.40 (0.32), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.25), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR D 10 PHE 0.006 0.002 PHE A 20 HIS 0.003 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00998 ( 1524) covalent geometry : angle 0.76580 ( 2046) hydrogen bonds : bond 0.18158 ( 18) hydrogen bonds : angle 7.24854 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.034 Fit side-chains REVERT: D 28 LYS cc_start: 0.8393 (mttt) cc_final: 0.8043 (mttp) REVERT: F 28 LYS cc_start: 0.8420 (mttt) cc_final: 0.8168 (mttp) REVERT: B 28 LYS cc_start: 0.8436 (mttt) cc_final: 0.8149 (mttp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.4640 time to fit residues: 9.4168 Evaluate side-chains 20 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080096 restraints weight = 2006.887| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.40 r_work: 0.2973 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1524 Z= 0.074 Angle : 0.426 2.836 2046 Z= 0.258 Chirality : 0.059 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.906 14.469 204 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 8.67 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.39), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.30), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR C 10 PHE 0.003 0.001 PHE F 19 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00176 ( 1524) covalent geometry : angle 0.42632 ( 2046) hydrogen bonds : bond 0.02020 ( 18) hydrogen bonds : angle 5.31895 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.058 Fit side-chains REVERT: D 28 LYS cc_start: 0.8550 (mttt) cc_final: 0.8226 (mttp) REVERT: A 11 GLU cc_start: 0.8687 (tt0) cc_final: 0.8478 (tt0) REVERT: F 28 LYS cc_start: 0.8586 (mttt) cc_final: 0.8294 (mttp) REVERT: B 28 LYS cc_start: 0.8606 (mttt) cc_final: 0.8261 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.7108 time to fit residues: 13.6677 Evaluate side-chains 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.095619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078980 restraints weight = 2058.951| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.34 r_work: 0.2958 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1524 Z= 0.112 Angle : 0.438 3.173 2046 Z= 0.262 Chirality : 0.060 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.762 14.098 204 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.33), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 10 PHE 0.003 0.001 PHE C 19 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 1524) covalent geometry : angle 0.43835 ( 2046) hydrogen bonds : bond 0.02079 ( 18) hydrogen bonds : angle 5.00508 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.057 Fit side-chains REVERT: D 28 LYS cc_start: 0.8555 (mttt) cc_final: 0.8221 (mttp) REVERT: A 11 GLU cc_start: 0.8685 (tt0) cc_final: 0.8453 (tt0) REVERT: F 28 LYS cc_start: 0.8618 (mttt) cc_final: 0.8328 (mttp) REVERT: B 28 LYS cc_start: 0.8611 (mttt) cc_final: 0.8259 (mttp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 1.1346 time to fit residues: 20.6491 Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.9724 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.096569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079881 restraints weight = 2037.300| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.34 r_work: 0.2980 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1524 Z= 0.100 Angle : 0.420 2.950 2046 Z= 0.252 Chirality : 0.059 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.627 13.726 204 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR C 10 PHE 0.002 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 1524) covalent geometry : angle 0.41983 ( 2046) hydrogen bonds : bond 0.01821 ( 18) hydrogen bonds : angle 4.87555 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.057 Fit side-chains REVERT: D 28 LYS cc_start: 0.8569 (mttt) cc_final: 0.8195 (mttp) REVERT: E 11 GLU cc_start: 0.8754 (tt0) cc_final: 0.8542 (tt0) REVERT: A 11 GLU cc_start: 0.8723 (tt0) cc_final: 0.8516 (tt0) REVERT: F 28 LYS cc_start: 0.8656 (mttt) cc_final: 0.8368 (mttp) REVERT: B 28 LYS cc_start: 0.8620 (mttt) cc_final: 0.8260 (mttp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.9896 time to fit residues: 18.0165 Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 9 optimal weight: 5.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.095654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078981 restraints weight = 2015.619| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.32 r_work: 0.2963 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1524 Z= 0.119 Angle : 0.433 3.277 2046 Z= 0.260 Chirality : 0.059 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.663 13.964 204 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 10.00 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR D 10 PHE 0.003 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 1524) covalent geometry : angle 0.43269 ( 2046) hydrogen bonds : bond 0.01883 ( 18) hydrogen bonds : angle 4.95800 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.062 Fit side-chains REVERT: D 28 LYS cc_start: 0.8595 (mttt) cc_final: 0.8228 (mttp) REVERT: F 28 LYS cc_start: 0.8681 (mttt) cc_final: 0.8401 (mttp) REVERT: B 28 LYS cc_start: 0.8653 (mttt) cc_final: 0.8301 (mttp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 1.0125 time to fit residues: 18.4358 Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.096244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079551 restraints weight = 1994.324| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1524 Z= 0.104 Angle : 0.418 3.049 2046 Z= 0.252 Chirality : 0.059 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.616 13.995 204 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR D 10 PHE 0.003 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 1524) covalent geometry : angle 0.41831 ( 2046) hydrogen bonds : bond 0.01759 ( 18) hydrogen bonds : angle 4.93461 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.061 Fit side-chains REVERT: D 28 LYS cc_start: 0.8566 (mttt) cc_final: 0.8193 (mttp) REVERT: E 11 GLU cc_start: 0.8783 (tt0) cc_final: 0.8563 (tt0) REVERT: F 28 LYS cc_start: 0.8665 (mttt) cc_final: 0.8381 (mttp) REVERT: B 28 LYS cc_start: 0.8644 (mttt) cc_final: 0.8295 (mttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0544 time to fit residues: 18.1390 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.097803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081117 restraints weight = 1966.606| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.32 r_work: 0.3106 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1524 Z= 0.084 Angle : 0.403 2.857 2046 Z= 0.243 Chirality : 0.059 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.517 13.797 204 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.67 % Allowed : 10.67 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR D 10 PHE 0.002 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 1524) covalent geometry : angle 0.40262 ( 2046) hydrogen bonds : bond 0.01662 ( 18) hydrogen bonds : angle 4.91186 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.061 Fit side-chains REVERT: D 28 LYS cc_start: 0.8746 (mttt) cc_final: 0.8418 (mttp) REVERT: F 28 LYS cc_start: 0.8797 (mttt) cc_final: 0.8546 (mttp) REVERT: B 28 LYS cc_start: 0.8787 (mttt) cc_final: 0.8489 (mttp) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.9869 time to fit residues: 17.9724 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.097725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080883 restraints weight = 1997.483| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.33 r_work: 0.3008 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1524 Z= 0.091 Angle : 0.403 2.915 2046 Z= 0.244 Chirality : 0.059 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.488 13.490 204 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR D 10 PHE 0.002 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 1524) covalent geometry : angle 0.40282 ( 2046) hydrogen bonds : bond 0.01681 ( 18) hydrogen bonds : angle 4.87405 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.064 Fit side-chains REVERT: D 28 LYS cc_start: 0.8591 (mttt) cc_final: 0.8253 (mttp) REVERT: F 28 LYS cc_start: 0.8688 (mttt) cc_final: 0.8412 (mttp) REVERT: B 28 LYS cc_start: 0.8654 (mttt) cc_final: 0.8318 (mttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0377 time to fit residues: 17.8378 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.0370 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.097489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080822 restraints weight = 1962.829| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.31 r_work: 0.2999 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1524 Z= 0.100 Angle : 0.410 2.976 2046 Z= 0.247 Chirality : 0.059 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.504 13.645 204 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR D 10 PHE 0.003 0.001 PHE E 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 1524) covalent geometry : angle 0.40963 ( 2046) hydrogen bonds : bond 0.01739 ( 18) hydrogen bonds : angle 4.88429 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.039 Fit side-chains REVERT: D 28 LYS cc_start: 0.8572 (mttt) cc_final: 0.8195 (mttp) REVERT: F 28 LYS cc_start: 0.8653 (mttt) cc_final: 0.8373 (mttp) REVERT: B 28 LYS cc_start: 0.8647 (mttt) cc_final: 0.8304 (mttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0235 time to fit residues: 17.6007 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.095501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078173 restraints weight = 2013.265| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.37 r_work: 0.2956 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1524 Z= 0.135 Angle : 0.437 3.271 2046 Z= 0.262 Chirality : 0.060 0.134 234 Planarity : 0.001 0.004 258 Dihedral : 4.651 13.874 204 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR D 10 PHE 0.004 0.001 PHE E 20 HIS 0.003 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 1524) covalent geometry : angle 0.43715 ( 2046) hydrogen bonds : bond 0.01980 ( 18) hydrogen bonds : angle 4.98338 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.060 Fit side-chains REVERT: D 28 LYS cc_start: 0.8597 (mttt) cc_final: 0.8240 (mttp) REVERT: F 28 LYS cc_start: 0.8638 (mttt) cc_final: 0.8369 (mttp) REVERT: B 28 LYS cc_start: 0.8644 (mttt) cc_final: 0.8301 (mttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 1.0775 time to fit residues: 18.5301 Evaluate side-chains 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.095720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078583 restraints weight = 1985.335| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.37 r_work: 0.2974 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1524 Z= 0.132 Angle : 0.437 3.263 2046 Z= 0.262 Chirality : 0.060 0.134 234 Planarity : 0.001 0.004 258 Dihedral : 4.647 13.757 204 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR D 10 PHE 0.004 0.001 PHE E 20 HIS 0.002 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 1524) covalent geometry : angle 0.43672 ( 2046) hydrogen bonds : bond 0.01937 ( 18) hydrogen bonds : angle 4.98879 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 845.30 seconds wall clock time: 15 minutes 25.06 seconds (925.06 seconds total)