Starting phenix.real_space_refine on Mon Sep 23 12:14:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/09_2024/8ol2_16942.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/09_2024/8ol2_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_16942/09_2024/8ol2_16942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/09_2024/8ol2_16942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/09_2024/8ol2_16942.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol2_16942/09_2024/8ol2_16942.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= 0.001 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2260 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.62, per 1000 atoms: 0.72 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 - 3.00 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: 0.47 Conformation dependent library (CDL) restraints added in 371.8 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: 0.36 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: 0.52 Time building geometry restraints manager: 0.58 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: 0.00 - 0.54: 2630 0.54 - 1.08: 335 1.08 - 1.63: 69 1.63 - 2.17: 35 2.17 - 2.71: 11 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 3.120 nonbonded pdb=" NZ LYS B 28 " pdb=" OXT ALA C 42 " model vdw 2.275 3.120 nonbonded pdb=" NZ LYS F 28 " pdb=" OXT ALA G 42 " model vdw 2.276 3.120 nonbonded pdb=" NZ LYS C 28 " pdb=" OXT ALA F 42 " model vdw 2.276 3.120 nonbonded pdb=" NZ LYS H 28 " pdb=" OXT ALA I 42 " model vdw 2.276 3.120 ... (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 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' 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: 1.110 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.900 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- 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 : 0.253 Fit side-chains REVERT: G 22 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8385 (mm-30) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 1.0837 time to fit residues: 59.8677 Evaluate side-chains 53 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain J residue 12 VAL 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: 10.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2290 Z= 0.187 Angle : 0.439 3.915 3080 Z= 0.232 Chirality : 0.054 0.126 370 Planarity : 0.002 0.006 390 Dihedral : 6.440 33.089 319 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.91 % Allowed : 13.91 % Favored : 82.17 % 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: -2.28 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 14 PHE 0.005 0.001 PHE G 20 *********************** 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 58 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.248 Fit side-chains REVERT: G 22 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8302 (mm-30) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.9711 time to fit residues: 49.8851 Evaluate side-chains 52 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 2290 Z= 0.526 Angle : 0.623 4.829 3080 Z= 0.319 Chirality : 0.056 0.136 370 Planarity : 0.002 0.008 390 Dihedral : 8.820 48.443 316 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 8.70 % Allowed : 14.35 % Favored : 76.96 % 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: -2.72 (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 0.011 0.002 PHE H 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 86 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.252 Fit side-chains REVERT: A 22 GLU cc_start: 0.8794 (mm-30) cc_final: 0.7164 (mp0) REVERT: B 22 GLU cc_start: 0.8721 (mm-30) cc_final: 0.7147 (mp0) REVERT: C 22 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8446 (mm-30) REVERT: D 22 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8374 (mm-30) REVERT: F 22 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8295 (mm-30) REVERT: G 22 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8381 (mm-30) REVERT: G 28 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8775 (mtpt) REVERT: H 22 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8421 (mm-30) REVERT: I 35 MET cc_start: 0.7886 (ptm) cc_final: 0.7458 (ptt) outliers start: 20 outliers final: 15 residues processed: 71 average time/residue: 0.9465 time to fit residues: 68.8527 Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2290 Z= 0.318 Angle : 0.521 4.965 3080 Z= 0.267 Chirality : 0.054 0.125 370 Planarity : 0.002 0.007 390 Dihedral : 8.160 43.763 316 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 9.13 % Allowed : 12.61 % Favored : 78.26 % 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: -2.94 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 14 PHE 0.007 0.002 PHE I 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 78 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.274 Fit side-chains REVERT: A 22 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7155 (mp0) REVERT: B 22 GLU cc_start: 0.8752 (mm-30) cc_final: 0.7135 (mp0) REVERT: E 16 LYS cc_start: 0.8668 (mttp) cc_final: 0.8419 (mttt) REVERT: G 22 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8371 (mm-30) REVERT: G 28 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8697 (mttt) REVERT: H 22 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8379 (mm-30) REVERT: H 28 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8959 (mtpt) REVERT: I 35 MET cc_start: 0.8068 (ptm) cc_final: 0.7524 (ptt) outliers start: 21 outliers final: 18 residues processed: 62 average time/residue: 0.8671 time to fit residues: 55.3386 Evaluate side-chains 76 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8889 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2290 Z= 0.370 Angle : 0.540 4.004 3080 Z= 0.279 Chirality : 0.054 0.128 370 Planarity : 0.002 0.007 390 Dihedral : 7.744 36.628 316 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.97 % Favored : 90.34 % Rotamer: Outliers : 9.13 % Allowed : 14.35 % Favored : 76.52 % 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: -3.07 (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 0.002 0.001 HIS D 14 PHE 0.009 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 81 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.248 Fit side-chains REVERT: A 22 GLU cc_start: 0.8730 (mm-30) cc_final: 0.7108 (mt-10) REVERT: B 22 GLU cc_start: 0.8795 (mm-30) cc_final: 0.7194 (mp0) REVERT: C 22 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8483 (mm-30) REVERT: D 22 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8345 (mm-30) REVERT: G 22 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8455 (mm-30) REVERT: G 28 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8746 (mttt) REVERT: H 22 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8373 (mm-30) REVERT: I 35 MET cc_start: 0.8212 (ptm) cc_final: 0.7772 (ptt) outliers start: 21 outliers final: 19 residues processed: 66 average time/residue: 0.9078 time to fit residues: 61.5189 Evaluate side-chains 80 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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: 0.8863 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2290 Z= 0.221 Angle : 0.469 3.795 3080 Z= 0.244 Chirality : 0.054 0.123 370 Planarity : 0.002 0.007 390 Dihedral : 6.890 33.360 316 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 2.41 % Allowed : 2.07 % Favored : 95.52 % Rotamer: Outliers : 7.83 % Allowed : 13.91 % Favored : 78.26 % 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: -3.07 (0.41), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 14 PHE 0.005 0.001 PHE D 20 *********************** 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: 18 poor density : 59 time to evaluate : 0.247 Fit side-chains REVERT: A 22 GLU cc_start: 0.8727 (mm-30) cc_final: 0.7111 (mt-10) REVERT: A 35 MET cc_start: 0.7122 (ttp) cc_final: 0.6836 (ttp) REVERT: B 22 GLU cc_start: 0.8774 (mm-30) cc_final: 0.7164 (mt-10) REVERT: G 22 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8416 (mm-30) REVERT: G 28 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8722 (mttt) REVERT: H 22 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8359 (mm-30) REVERT: I 35 MET cc_start: 0.8098 (ptm) cc_final: 0.7591 (ptt) outliers start: 18 outliers final: 16 residues processed: 63 average time/residue: 0.7828 time to fit residues: 50.8472 Evaluate side-chains 75 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8836 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2290 Z= 0.150 Angle : 0.456 8.017 3080 Z= 0.231 Chirality : 0.053 0.122 370 Planarity : 0.001 0.006 390 Dihedral : 6.181 29.662 316 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 2.76 % Allowed : 2.76 % Favored : 94.48 % Rotamer: Outliers : 8.26 % Allowed : 15.65 % 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: -3.00 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 14 PHE 0.004 0.001 PHE D 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 72 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.252 Fit side-chains REVERT: B 22 GLU cc_start: 0.8749 (mm-30) cc_final: 0.7064 (mt-10) REVERT: E 23 ASP cc_start: 0.8272 (p0) cc_final: 0.7171 (m-30) REVERT: F 23 ASP cc_start: 0.8239 (p0) cc_final: 0.7125 (m-30) REVERT: G 22 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8114 (mm-30) REVERT: G 23 ASP cc_start: 0.8399 (p0) cc_final: 0.7263 (OUTLIER) REVERT: I 35 MET cc_start: 0.8040 (ptm) cc_final: 0.7572 (ptt) outliers start: 19 outliers final: 18 residues processed: 53 average time/residue: 0.6904 time to fit residues: 37.9627 Evaluate side-chains 69 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.3053 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= 0.339 Angle : 0.552 7.471 3080 Z= 0.275 Chirality : 0.054 0.127 370 Planarity : 0.002 0.007 390 Dihedral : 6.411 26.021 316 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 3.45 % Allowed : 6.21 % Favored : 90.34 % Rotamer: Outliers : 9.57 % Allowed : 13.91 % Favored : 76.52 % 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 (0.42), 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 0.002 0.001 HIS D 14 PHE 0.008 0.002 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 82 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.237 Fit side-chains REVERT: A 22 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7080 (mt-10) REVERT: B 22 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7125 (mt-10) REVERT: G 22 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8443 (mm-30) REVERT: G 28 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8721 (mttt) REVERT: H 22 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8391 (mm-30) REVERT: I 35 MET cc_start: 0.8236 (ptm) cc_final: 0.7830 (ptt) outliers start: 22 outliers final: 22 residues processed: 65 average time/residue: 0.8274 time to fit residues: 55.2549 Evaluate side-chains 83 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.3084 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= 0.261 Angle : 0.520 7.120 3080 Z= 0.261 Chirality : 0.054 0.125 370 Planarity : 0.002 0.007 390 Dihedral : 6.203 25.378 316 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 3.45 % Allowed : 3.10 % Favored : 93.45 % Rotamer: Outliers : 9.13 % Allowed : 15.65 % Favored : 75.22 % 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: -3.11 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 14 PHE 0.006 0.001 PHE I 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 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 REVERT: A 22 GLU cc_start: 0.8727 (mm-30) cc_final: 0.7075 (mt-10) REVERT: B 22 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7133 (mt-10) REVERT: E 23 ASP cc_start: 0.8283 (p0) cc_final: 0.7176 (m-30) REVERT: F 23 ASP cc_start: 0.8263 (p0) cc_final: 0.7137 (m-30) REVERT: G 22 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8125 (mm-30) REVERT: G 23 ASP cc_start: 0.8459 (p0) cc_final: 0.7336 (OUTLIER) REVERT: G 28 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8740 (mttt) REVERT: H 22 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8090 (mm-30) REVERT: H 23 ASP cc_start: 0.8429 (p0) cc_final: 0.7293 (OUTLIER) REVERT: I 16 LYS cc_start: 0.8904 (mttt) cc_final: 0.8654 (mttp) REVERT: I 35 MET cc_start: 0.8186 (ptm) cc_final: 0.7784 (ptt) outliers start: 21 outliers final: 22 residues processed: 64 average time/residue: 0.7933 time to fit residues: 52.2911 Evaluate side-chains 82 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3250 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= 0.474 Angle : 0.627 7.057 3080 Z= 0.312 Chirality : 0.056 0.130 370 Planarity : 0.002 0.007 390 Dihedral : 6.551 22.754 316 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 3.45 % Allowed : 7.24 % Favored : 89.31 % Rotamer: Outliers : 9.57 % Allowed : 15.22 % Favored : 75.22 % 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: -3.14 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.010 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 87 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.247 Fit side-chains REVERT: A 22 GLU cc_start: 0.8763 (mm-30) cc_final: 0.7160 (mt-10) REVERT: B 22 GLU cc_start: 0.8794 (mm-30) cc_final: 0.7174 (mt-10) REVERT: D 22 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8505 (mm-30) REVERT: G 22 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8465 (mm-30) REVERT: G 28 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8728 (mttt) REVERT: H 22 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8391 (mm-30) REVERT: I 35 MET cc_start: 0.8347 (ptm) cc_final: 0.7949 (ptt) outliers start: 22 outliers final: 19 residues processed: 70 average time/residue: 0.8980 time to fit residues: 64.4899 Evaluate side-chains 86 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.116126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090766 restraints weight = 2564.228| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.81 r_work: 0.2977 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2290 Z= 0.230 Angle : 0.567 6.547 3080 Z= 0.283 Chirality : 0.055 0.128 370 Planarity : 0.002 0.006 390 Dihedral : 6.114 22.060 316 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 3.45 % Allowed : 2.41 % Favored : 94.14 % Rotamer: Outliers : 6.96 % Allowed : 18.70 % Favored : 74.35 % 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 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 14 PHE 0.007 0.001 PHE G 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.36 seconds wall clock time: 26 minutes 43.87 seconds (1603.87 seconds total)