Starting phenix.real_space_refine on Wed Mar 5 14:17:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kf4_37198/03_2025/8kf4_37198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kf4_37198/03_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_37198/03_2025/8kf4_37198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kf4_37198/03_2025/8kf4_37198.map" model { file = "/net/cci-nas-00/data/ceres_data/8kf4_37198/03_2025/8kf4_37198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kf4_37198/03_2025/8kf4_37198.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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, B, E, D, F Time building chain proxies: 0.93, per 1000 atoms: 0.62 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: 0.74 Conformation dependent library (CDL) restraints added in 185.1 milliseconds 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: 0.27 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: 0.31 Time building geometry restraints manager: 0.82 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.020 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- 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= 0.667 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.002 HIS E 13 PHE 0.006 0.002 PHE A 20 TYR 0.003 0.001 TYR D 10 *********************** 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 : 0.131 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: 1.4022 time to fit residues: 28.5354 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 : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.096841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.080219 restraints weight = 1990.422| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.34 r_work: 0.2976 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1073 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= 0.123 Angle : 0.429 2.893 2046 Z= 0.259 Chirality : 0.059 0.134 234 Planarity : 0.001 0.004 258 Dihedral : 4.909 14.512 204 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.39), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.003 0.001 PHE C 19 TYR 0.001 0.000 TYR C 10 *********************** 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 : 0.150 Fit side-chains REVERT: D 28 LYS cc_start: 0.8561 (mttt) cc_final: 0.8240 (mttp) REVERT: A 11 GLU cc_start: 0.8679 (tt0) cc_final: 0.8471 (tt0) REVERT: F 28 LYS cc_start: 0.8598 (mttt) cc_final: 0.8309 (mttp) REVERT: B 28 LYS cc_start: 0.8620 (mttt) cc_final: 0.8277 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.7293 time to fit residues: 33.3330 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 : 0.159 ------------------------------------------------------------------------------- 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 9 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.095511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078934 restraints weight = 2017.621| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.33 r_work: 0.2961 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1201 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= 0.184 Angle : 0.441 3.163 2046 Z= 0.263 Chirality : 0.060 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.767 13.996 204 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.003 0.001 PHE C 19 TYR 0.002 0.000 TYR C 10 *********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.167 Fit side-chains REVERT: D 28 LYS cc_start: 0.8558 (mttt) cc_final: 0.8223 (mttp) REVERT: A 11 GLU cc_start: 0.8678 (tt0) cc_final: 0.8450 (tt0) REVERT: F 28 LYS cc_start: 0.8615 (mttt) cc_final: 0.8326 (mttp) REVERT: B 28 LYS cc_start: 0.8612 (mttt) cc_final: 0.8256 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.7543 time to fit residues: 33.8383 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 : 0.163 ------------------------------------------------------------------------------- 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 10 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.0070 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3404 r_free = 0.3404 target = 0.100891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084338 restraints weight = 1957.413| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.34 r_work: 0.3050 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.011 1524 Z= 0.096 Angle : 0.381 2.399 2046 Z= 0.231 Chirality : 0.058 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.413 12.947 204 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.002 0.000 PHE F 19 TYR 0.001 0.000 TYR C 10 *********************** 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 17 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.155 Fit side-chains REVERT: D 28 LYS cc_start: 0.8541 (mttt) cc_final: 0.8234 (mttp) REVERT: A 11 GLU cc_start: 0.8690 (tt0) cc_final: 0.8488 (tt0) REVERT: F 28 LYS cc_start: 0.8599 (mttt) cc_final: 0.8308 (mttp) REVERT: B 28 LYS cc_start: 0.8585 (mttt) cc_final: 0.8227 (mttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 2.1079 time to fit residues: 36.3234 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 : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.093520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076785 restraints weight = 1981.070| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.29 r_work: 0.2919 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 1524 Z= 0.305 Angle : 0.487 3.655 2046 Z= 0.286 Chirality : 0.061 0.135 234 Planarity : 0.001 0.004 258 Dihedral : 4.823 14.093 204 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 : 0.67 % Allowed : 11.33 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 14 PHE 0.005 0.001 PHE E 20 TYR 0.002 0.001 TYR B 10 *********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.192 Fit side-chains REVERT: D 28 LYS cc_start: 0.8587 (mttt) cc_final: 0.8225 (mttp) REVERT: A 11 GLU cc_start: 0.8729 (tt0) cc_final: 0.8515 (tt0) REVERT: F 28 LYS cc_start: 0.8646 (mttt) cc_final: 0.8371 (mttp) REVERT: B 28 LYS cc_start: 0.8642 (mttt) cc_final: 0.8289 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.9008 time to fit residues: 36.6053 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 : 0.170 ------------------------------------------------------------------------------- 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 12 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.099278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082155 restraints weight = 2006.768| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.38 r_work: 0.3022 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1524 Z= 0.108 Angle : 0.391 2.699 2046 Z= 0.238 Chirality : 0.059 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.507 13.791 204 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 : 0.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.52), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.002 0.000 PHE F 19 TYR 0.001 0.000 TYR C 10 *********************** 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 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.238 Fit side-chains REVERT: D 28 LYS cc_start: 0.8561 (mttt) cc_final: 0.8221 (mttp) REVERT: A 11 GLU cc_start: 0.8729 (tt0) cc_final: 0.8521 (tt0) REVERT: F 28 LYS cc_start: 0.8664 (mttt) cc_final: 0.8378 (mttp) REVERT: B 28 LYS cc_start: 0.8609 (mttt) cc_final: 0.8263 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 2.1983 time to fit residues: 40.1769 Evaluate side-chains 18 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.0170 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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 = 0.095382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078690 restraints weight = 2001.672| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.31 r_work: 0.2957 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1514 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= 0.225 Angle : 0.453 3.386 2046 Z= 0.266 Chirality : 0.060 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.663 13.804 204 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 : 0.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.003 0.001 PHE E 20 TYR 0.002 0.001 TYR D 10 *********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.161 Fit side-chains REVERT: D 28 LYS cc_start: 0.8584 (mttt) cc_final: 0.8214 (mttp) REVERT: A 11 GLU cc_start: 0.8750 (tt0) cc_final: 0.8549 (tt0) REVERT: F 28 LYS cc_start: 0.8659 (mttt) cc_final: 0.8381 (mttp) REVERT: B 28 LYS cc_start: 0.8630 (mttt) cc_final: 0.8280 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.7990 time to fit residues: 34.6772 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 : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.095288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.078651 restraints weight = 1992.557| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.31 r_work: 0.2955 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1530 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= 0.215 Angle : 0.449 3.659 2046 Z= 0.264 Chirality : 0.060 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.685 13.937 204 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 : 0.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.54), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.003 0.001 PHE E 20 TYR 0.001 0.001 TYR D 10 *********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.189 Fit side-chains REVERT: D 28 LYS cc_start: 0.8614 (mttt) cc_final: 0.8254 (mttp) REVERT: F 28 LYS cc_start: 0.8674 (mttt) cc_final: 0.8398 (mttp) REVERT: B 28 LYS cc_start: 0.8643 (mttt) cc_final: 0.8304 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.7994 time to fit residues: 34.7052 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 : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER 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 17 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.095467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.078333 restraints weight = 1984.124| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.36 r_work: 0.2951 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1563 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= 0.230 Angle : 0.465 4.723 2046 Z= 0.269 Chirality : 0.060 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.724 13.910 204 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 : 0.67 % Allowed : 11.33 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS E 14 PHE 0.003 0.001 PHE E 20 TYR 0.002 0.001 TYR D 10 *********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.171 Fit side-chains REVERT: D 28 LYS cc_start: 0.8612 (mttt) cc_final: 0.8257 (mttp) REVERT: F 28 LYS cc_start: 0.8656 (mttt) cc_final: 0.8383 (mttp) REVERT: B 28 LYS cc_start: 0.8648 (mttt) cc_final: 0.8315 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.8962 time to fit residues: 36.5442 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 : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.100193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082784 restraints weight = 1988.466| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.42 r_work: 0.3058 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1524 Z= 0.106 Angle : 0.412 5.661 2046 Z= 0.240 Chirality : 0.058 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.460 13.301 204 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 : 0.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.57), 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 HIS 0.002 0.001 HIS E 14 PHE 0.002 0.000 PHE F 19 TYR 0.001 0.000 TYR C 10 ********************** 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 19 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.164 Fit side-chains REVERT: D 28 LYS cc_start: 0.8590 (mttt) cc_final: 0.8257 (mttp) REVERT: F 28 LYS cc_start: 0.8661 (mttt) cc_final: 0.8383 (mttp) REVERT: B 28 LYS cc_start: 0.8640 (mttt) cc_final: 0.8307 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.8257 time to fit residues: 35.1841 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 : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.0030 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- 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 = 0.097682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080488 restraints weight = 2032.166| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.40 r_work: 0.3006 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1751 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= 0.178 Angle : 0.462 7.614 2046 Z= 0.258 Chirality : 0.059 0.134 234 Planarity : 0.001 0.004 258 Dihedral : 4.528 13.359 204 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 : 12.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.57), 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 HIS 0.002 0.001 HIS E 14 PHE 0.003 0.001 PHE E 20 TYR 0.001 0.000 TYR D 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.87 seconds wall clock time: 29 minutes 27.79 seconds (1767.79 seconds total)