Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_37198.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_37198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_37198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_37198.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kf4_37198/09_2024/8kf4_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-5461/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: 0.91, per 1000 atoms: 0.61 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: 0.96 Conformation dependent library (CDL) restraints added in 196.6 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: 0.30 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: 0.32 Time building geometry restraints manager: 1.02 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.060 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.176 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: 1.2999 time to fit residues: 26.5019 Evaluate side-chains 20 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1072 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 fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.167 Fit side-chains REVERT: D 28 LYS cc_start: 0.8431 (mttt) cc_final: 0.8118 (mttp) REVERT: F 28 LYS cc_start: 0.8465 (mttt) cc_final: 0.8179 (mttp) REVERT: B 28 LYS cc_start: 0.8479 (mttt) cc_final: 0.8152 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 1.7190 time to fit residues: 33.1634 Evaluate side-chains 19 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 4 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.0040 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1379 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= 0.141 Angle : 0.416 2.893 2046 Z= 0.250 Chirality : 0.059 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.638 13.567 204 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 1.66 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: -2.45 (0.44), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.002 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.166 Fit side-chains REVERT: D 28 LYS cc_start: 0.8427 (mttt) cc_final: 0.8091 (mttp) REVERT: F 28 LYS cc_start: 0.8495 (mttt) cc_final: 0.8201 (mttp) REVERT: B 28 LYS cc_start: 0.8434 (mttt) cc_final: 0.8094 (mttp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 1.9373 time to fit residues: 35.3684 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1523 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= 0.133 Angle : 0.402 2.790 2046 Z= 0.243 Chirality : 0.059 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.511 13.543 204 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.66 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: -1.98 (0.48), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.002 0.001 PHE C 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.165 Fit side-chains REVERT: D 28 LYS cc_start: 0.8431 (mttt) cc_final: 0.8086 (mttp) REVERT: F 28 LYS cc_start: 0.8532 (mttt) cc_final: 0.8243 (mttp) REVERT: B 28 LYS cc_start: 0.8447 (mttt) cc_final: 0.8111 (mttp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 1.9461 time to fit residues: 35.5634 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 15 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.0050 chunk 8 optimal weight: 0.0370 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 1524 Z= 0.088 Angle : 0.374 2.489 2046 Z= 0.228 Chirality : 0.058 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.324 12.936 204 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 1.99 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: -1.52 (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 0.001 0.000 HIS A 14 PHE 0.002 0.000 PHE F 19 TYR 0.001 0.000 TYR D 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.168 Fit side-chains REVERT: D 28 LYS cc_start: 0.8410 (mttt) cc_final: 0.8117 (mttp) REVERT: F 28 LYS cc_start: 0.8478 (mttt) cc_final: 0.8192 (mttp) REVERT: B 28 LYS cc_start: 0.8439 (mttt) cc_final: 0.8097 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.9439 time to fit residues: 35.4921 Evaluate side-chains 17 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.0020 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1875 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 : 0.383 3.678 2046 Z= 0.228 Chirality : 0.058 0.132 234 Planarity : 0.001 0.004 258 Dihedral : 4.211 12.725 204 Min Nonbonded Distance : 2.664 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: -1.20 (0.55), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.42), 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 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 fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.162 Fit side-chains REVERT: D 28 LYS cc_start: 0.8419 (mttt) cc_final: 0.8111 (mttp) REVERT: A 28 LYS cc_start: 0.8810 (mttp) cc_final: 0.8579 (mttt) REVERT: B 28 LYS cc_start: 0.8439 (mttt) cc_final: 0.8095 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.9226 time to fit residues: 35.0977 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1852 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= 0.134 Angle : 0.415 5.266 2046 Z= 0.240 Chirality : 0.058 0.131 234 Planarity : 0.001 0.004 258 Dihedral : 4.283 12.947 204 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % 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: -1.14 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.002 0.001 PHE E 20 TYR 0.001 0.000 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.168 Fit side-chains REVERT: D 28 LYS cc_start: 0.8417 (mttt) cc_final: 0.8114 (mttp) REVERT: B 28 LYS cc_start: 0.8475 (mttt) cc_final: 0.8131 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.9937 time to fit residues: 36.3826 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.0050 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1875 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= 0.134 Angle : 0.408 4.811 2046 Z= 0.239 Chirality : 0.059 0.131 234 Planarity : 0.001 0.005 258 Dihedral : 4.306 13.110 204 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 1.33 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: -1.00 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.002 0.001 PHE E 20 TYR 0.001 0.000 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.174 Fit side-chains REVERT: D 28 LYS cc_start: 0.8430 (mttt) cc_final: 0.8095 (mttp) REVERT: B 28 LYS cc_start: 0.8483 (mttt) cc_final: 0.8146 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 2.0148 time to fit residues: 36.8342 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1732 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= 0.198 Angle : 0.442 4.915 2046 Z= 0.257 Chirality : 0.059 0.133 234 Planarity : 0.001 0.004 258 Dihedral : 4.480 13.251 204 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 0.66 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: -1.07 (0.57), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.004 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.155 Fit side-chains REVERT: D 28 LYS cc_start: 0.8444 (mttt) cc_final: 0.8087 (mttp) REVERT: B 28 LYS cc_start: 0.8516 (mttt) cc_final: 0.8178 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.8830 time to fit residues: 34.3743 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1527 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= 0.311 Angle : 0.490 4.545 2046 Z= 0.285 Chirality : 0.061 0.138 234 Planarity : 0.001 0.004 258 Dihedral : 4.769 13.829 204 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 0.66 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: -1.14 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.006 0.001 PHE C 20 TYR 0.002 0.001 TYR B 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 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.150 Fit side-chains REVERT: D 28 LYS cc_start: 0.8444 (mttt) cc_final: 0.8106 (mttp) REVERT: B 28 LYS cc_start: 0.8512 (mttt) cc_final: 0.8185 (mttp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 1.9128 time to fit residues: 34.9063 Evaluate side-chains 18 residues out of total 150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 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 = 0.3323 r_free = 0.3323 target = 0.095186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078494 restraints weight = 1961.213| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.28 r_work: 0.2962 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1637 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= 0.211 Angle : 0.448 4.278 2046 Z= 0.263 Chirality : 0.060 0.134 234 Planarity : 0.001 0.004 258 Dihedral : 4.662 13.701 204 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 0.66 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: -1.07 (0.56), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (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 C 20 TYR 0.002 0.001 TYR D 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.40 seconds wall clock time: 27 minutes 51.71 seconds (1671.71 seconds total)