Starting phenix.real_space_refine on Thu Dec 7 16:12:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/12_2023/8ol2_16942.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/12_2023/8ol2_16942.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/8ol2_16942/12_2023/8ol2_16942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/12_2023/8ol2_16942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/12_2023/8ol2_16942.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/12_2023/8ol2_16942.pdb" } 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= 0.001 sd= 0.006 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 10 5.16 5 C 1470 2.51 5 N 390 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2260 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "H" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Time building chain proxies: 1.49, per 1000 atoms: 0.66 Number of scatterers: 2260 At special positions: 0 Unit cell: (83.224, 54.944, 40.4, 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 10 16.00 O 390 8.00 N 390 7.00 C 1470 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 - 3.50 Amino acid : False - 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: 0.80 Conformation dependent library (CDL) restraints added in 417.7 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.439A pdb=" N HIS A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS C 14 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS E 14 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS G 14 " --> pdb=" O GLN I 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.563A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 18 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.842A pdb=" N LEU C 34 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET A 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.389A pdb=" N HIS B 14 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS D 14 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS F 14 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS H 14 " --> pdb=" O GLN J 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.484A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL F 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.911A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 41 32 hydrogen bonds defined for protein. 96 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: 0.84 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: 1.23 - 1.34: 740 1.34 - 1.45: 276 1.45 - 1.57: 1254 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2290 Sorted by residual: bond pdb=" C GLY C 37 " pdb=" N GLY C 38 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.31e-01 bond pdb=" C GLY F 37 " pdb=" N GLY F 38 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.84e-01 bond pdb=" C GLY H 37 " pdb=" N GLY H 38 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.72e-01 bond pdb=" C GLY D 37 " pdb=" N GLY D 38 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.56e-01 bond pdb=" C GLY B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.41e-01 ... (remaining 2285 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.44: 10 105.44 - 111.90: 1265 111.90 - 118.37: 588 118.37 - 124.83: 1197 124.83 - 131.30: 20 Bond angle restraints: 3080 Sorted by residual: angle pdb=" CG MET J 35 " pdb=" SD MET J 35 " pdb=" CE MET J 35 " ideal model delta sigma weight residual 100.90 98.97 1.93 2.20e+00 2.07e-01 7.70e-01 angle pdb=" N GLN J 15 " pdb=" CA GLN J 15 " pdb=" C GLN J 15 " ideal model delta sigma weight residual 108.32 109.76 -1.44 1.64e+00 3.72e-01 7.68e-01 angle pdb=" N LYS G 28 " pdb=" CA LYS G 28 " pdb=" C LYS G 28 " ideal model delta sigma weight residual 112.94 111.71 1.23 1.41e+00 5.03e-01 7.66e-01 angle pdb=" N GLN D 15 " pdb=" CA GLN D 15 " pdb=" C GLN D 15 " ideal model delta sigma weight residual 108.32 109.75 -1.43 1.64e+00 3.72e-01 7.64e-01 angle pdb=" N GLN F 15 " pdb=" CA GLN F 15 " pdb=" C GLN F 15 " ideal model delta sigma weight residual 108.32 109.75 -1.43 1.64e+00 3.72e-01 7.62e-01 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.89: 1040 6.89 - 13.78: 160 13.78 - 20.66: 60 20.66 - 27.55: 10 27.55 - 34.44: 20 Dihedral angle restraints: 1290 sinusoidal: 470 harmonic: 820 Sorted by residual: dihedral pdb=" N MET E 35 " pdb=" CA MET E 35 " pdb=" CB MET E 35 " pdb=" CG MET E 35 " ideal model delta sinusoidal sigma weight residual 60.00 85.72 -25.72 3 1.50e+01 4.44e-03 3.69e+00 dihedral pdb=" N MET A 35 " pdb=" CA MET A 35 " pdb=" CB MET A 35 " pdb=" CG MET A 35 " ideal model delta sinusoidal sigma weight residual 60.00 85.70 -25.70 3 1.50e+01 4.44e-03 3.68e+00 dihedral pdb=" N MET F 35 " pdb=" CA MET F 35 " pdb=" CB MET F 35 " pdb=" CG MET F 35 " ideal model delta sinusoidal sigma weight residual 60.00 85.69 -25.69 3 1.50e+01 4.44e-03 3.68e+00 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.025: 169 0.025 - 0.049: 107 0.049 - 0.073: 24 0.073 - 0.097: 13 0.097 - 0.120: 57 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE I 31 " pdb=" N ILE I 31 " pdb=" C ILE I 31 " pdb=" CB ILE I 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE E 31 " pdb=" N ILE E 31 " pdb=" C ILE E 31 " pdb=" CB ILE E 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 367 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 39 " -0.003 2.00e-02 2.50e+03 6.54e-03 4.28e-01 pdb=" C VAL B 39 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL B 39 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL B 40 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 39 " -0.003 2.00e-02 2.50e+03 6.51e-03 4.24e-01 pdb=" C VAL H 39 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL H 39 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL H 40 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 39 " 0.003 2.00e-02 2.50e+03 6.46e-03 4.17e-01 pdb=" C VAL A 39 " -0.011 2.00e-02 2.50e+03 pdb=" O VAL A 39 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL A 40 " 0.004 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 523 2.80 - 3.33: 1817 3.33 - 3.85: 3718 3.85 - 4.38: 3979 4.38 - 4.90: 8234 Nonbonded interactions: 18271 Sorted by model distance: nonbonded pdb=" NZ LYS D 28 " pdb=" OXT ALA E 42 " model vdw 2.275 2.520 nonbonded pdb=" NZ LYS B 28 " pdb=" OXT ALA C 42 " model vdw 2.275 2.520 nonbonded pdb=" NZ LYS F 28 " pdb=" OXT ALA G 42 " model vdw 2.276 2.520 nonbonded pdb=" NZ LYS C 28 " pdb=" OXT ALA F 42 " model vdw 2.276 2.520 nonbonded pdb=" NZ LYS H 28 " pdb=" OXT ALA I 42 " model vdw 2.276 2.520 ... (remaining 18266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.440 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: 0.010 Extract box with map and model: 5.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2290 Z= 0.288 Angle : 0.455 2.708 3080 Z= 0.239 Chirality : 0.053 0.120 370 Planarity : 0.002 0.007 390 Dihedral : 9.079 34.436 770 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.35 % Allowed : 8.70 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 13 PHE 0.006 0.002 PHE J 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.229 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 1.0801 time to fit residues: 59.6682 Evaluate side-chains 53 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.218 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0229 time to fit residues: 0.6455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8814 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2290 Z= 0.262 Angle : 0.458 4.201 3080 Z= 0.236 Chirality : 0.054 0.130 370 Planarity : 0.002 0.007 390 Dihedral : 5.314 23.936 310 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.78 % Allowed : 16.52 % Favored : 78.70 % 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: -2.35 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.007 0.002 PHE J 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.266 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.8994 time to fit residues: 49.1061 Evaluate side-chains 60 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 9 average time/residue: 0.0392 time to fit residues: 0.8386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 2290 Z= 0.440 Angle : 0.556 4.452 3080 Z= 0.283 Chirality : 0.055 0.129 370 Planarity : 0.002 0.007 390 Dihedral : 6.227 23.590 310 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 8.70 % Allowed : 16.52 % Favored : 74.78 % 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: -2.72 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.010 0.002 PHE G 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.260 Fit side-chains outliers start: 20 outliers final: 15 residues processed: 65 average time/residue: 0.8351 time to fit residues: 55.9174 Evaluate side-chains 73 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 3 residues processed: 13 average time/residue: 0.0366 time to fit residues: 1.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2290 Z= 0.286 Angle : 0.505 5.561 3080 Z= 0.253 Chirality : 0.053 0.123 370 Planarity : 0.002 0.006 390 Dihedral : 6.046 31.923 310 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 10.00 % Allowed : 13.91 % Favored : 76.09 % 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: -2.87 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 14 PHE 0.007 0.002 PHE G 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 0.251 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 62 average time/residue: 0.8121 time to fit residues: 51.8977 Evaluate side-chains 71 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 2 residues processed: 14 average time/residue: 0.0426 time to fit residues: 1.1244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.8880 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2290 Z= 0.338 Angle : 0.522 5.404 3080 Z= 0.263 Chirality : 0.054 0.124 370 Planarity : 0.002 0.007 390 Dihedral : 7.088 49.843 310 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.31 % Favored : 90.34 % Rotamer: Outliers : 9.13 % Allowed : 16.09 % Favored : 74.78 % 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: -3.02 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 14 PHE 0.008 0.002 PHE I 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.246 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 63 average time/residue: 0.7625 time to fit residues: 49.5303 Evaluate side-chains 75 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.196 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.0430 time to fit residues: 1.1230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.8880 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2290 Z= 0.329 Angle : 0.522 4.562 3080 Z= 0.263 Chirality : 0.054 0.123 370 Planarity : 0.002 0.007 390 Dihedral : 6.859 47.022 310 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 2.41 % Allowed : 3.79 % Favored : 93.79 % Rotamer: Outliers : 7.39 % Allowed : 16.96 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.04 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 14 PHE 0.008 0.002 PHE I 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.217 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 62 average time/residue: 0.6965 time to fit residues: 44.5067 Evaluate side-chains 73 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.217 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 13 average time/residue: 0.0310 time to fit residues: 0.8771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.8850 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2290 Z= 0.188 Angle : 0.452 4.566 3080 Z= 0.230 Chirality : 0.053 0.122 370 Planarity : 0.002 0.006 390 Dihedral : 5.966 38.742 310 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 2.76 % Allowed : 2.76 % Favored : 94.48 % Rotamer: Outliers : 5.65 % Allowed : 18.70 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.95 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 14 PHE 0.004 0.001 PHE I 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.258 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.7057 time to fit residues: 42.3537 Evaluate side-chains 66 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.247 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.0393 time to fit residues: 0.8960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8871 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2290 Z= 0.281 Angle : 0.505 4.564 3080 Z= 0.254 Chirality : 0.054 0.123 370 Planarity : 0.002 0.006 390 Dihedral : 6.091 33.897 310 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 3.45 % Allowed : 5.52 % Favored : 91.03 % Rotamer: Outliers : 4.78 % Allowed : 19.57 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.93 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 14 PHE 0.007 0.001 PHE I 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.268 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.8517 time to fit residues: 56.0898 Evaluate side-chains 67 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 5 average time/residue: 0.0542 time to fit residues: 0.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.8890 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2290 Z= 0.444 Angle : 0.589 4.955 3080 Z= 0.295 Chirality : 0.055 0.129 370 Planarity : 0.002 0.007 390 Dihedral : 6.141 27.891 310 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 3.45 % Allowed : 5.52 % Favored : 91.03 % Rotamer: Outliers : 4.78 % Allowed : 22.61 % Favored : 72.61 % 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: -3.06 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 14 PHE 0.010 0.002 PHE J 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.259 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.9285 time to fit residues: 65.6921 Evaluate side-chains 76 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 3 residues processed: 8 average time/residue: 0.0493 time to fit residues: 0.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8877 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2290 Z= 0.336 Angle : 0.557 5.304 3080 Z= 0.278 Chirality : 0.054 0.124 370 Planarity : 0.002 0.006 390 Dihedral : 5.715 25.056 310 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 3.45 % Allowed : 3.79 % Favored : 92.76 % Rotamer: Outliers : 2.17 % Allowed : 24.78 % Favored : 73.04 % 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: -3.12 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 14 PHE 0.008 0.002 PHE I 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.259 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.8579 time to fit residues: 57.3645 Evaluate side-chains 66 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 0.1668 time to fit residues: 0.6985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0470 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.111089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086847 restraints weight = 2676.242| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.72 r_work: 0.3003 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2290 Z= 0.238 Angle : 0.512 5.205 3080 Z= 0.256 Chirality : 0.054 0.122 370 Planarity : 0.002 0.006 390 Dihedral : 5.310 23.716 310 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 3.45 % Allowed : 3.45 % Favored : 93.10 % Rotamer: Outliers : 3.04 % Allowed : 23.48 % Favored : 73.48 % 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: -3.08 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 14 PHE 0.005 0.001 PHE J 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1392.25 seconds wall clock time: 25 minutes 19.22 seconds (1519.22 seconds total)