Starting phenix.real_space_refine on Wed Mar 5 15:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_16942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_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/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_16942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_16942.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_16942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol2_16942/03_2025/8ol2_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-5624/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: 1.42, per 1000 atoms: 0.63 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: 0.52 Conformation dependent library (CDL) restraints added in 303.4 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: 0.40 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: 0.51 Time building geometry restraints manager: 0.63 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.230 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: 1.1741 time to fit residues: 64.8036 Evaluate side-chains 53 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096729 restraints weight = 2502.718| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.99 r_work: 0.3055 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.355 Fit side-chains REVERT: A 35 MET cc_start: 0.7406 (ptp) cc_final: 0.7092 (ttp) REVERT: G 22 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8062 (mm-30) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 1.0678 time to fit residues: 54.8740 Evaluate side-chains 52 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 21 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.0980 overall best weight: 2.1842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091405 restraints weight = 2485.345| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.94 r_work: 0.2965 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2290 Z= 0.335 Angle : 0.529 3.884 3080 Z= 0.273 Chirality : 0.054 0.131 370 Planarity : 0.002 0.007 390 Dihedral : 8.058 47.079 316 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 7.39 % Allowed : 15.22 % Favored : 77.39 % 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: -2.58 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 14 PHE 0.008 0.002 PHE J 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 75 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.254 Fit side-chains REVERT: A 35 MET cc_start: 0.7917 (ptp) cc_final: 0.7420 (ttp) REVERT: B 22 GLU cc_start: 0.8732 (mm-30) cc_final: 0.6851 (mp0) REVERT: D 22 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8253 (mm-30) REVERT: G 22 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8187 (mm-30) REVERT: G 28 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8585 (mttt) REVERT: H 22 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8261 (mm-30) outliers start: 17 outliers final: 13 residues processed: 60 average time/residue: 0.9303 time to fit residues: 57.4143 Evaluate side-chains 71 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain H residue 12 VAL 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 23 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089462 restraints weight = 2533.809| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.87 r_work: 0.2933 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2290 Z= 0.460 Angle : 0.589 4.708 3080 Z= 0.303 Chirality : 0.056 0.131 370 Planarity : 0.002 0.007 390 Dihedral : 8.539 42.134 316 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 9.57 % Allowed : 13.04 % Favored : 77.39 % 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: -2.90 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (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 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 86 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.267 Fit side-chains REVERT: A 22 GLU cc_start: 0.8841 (mm-30) cc_final: 0.6933 (mp0) REVERT: A 35 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7833 (ptt) REVERT: B 22 GLU cc_start: 0.8837 (mm-30) cc_final: 0.6973 (mp0) REVERT: C 22 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8393 (mm-30) REVERT: D 22 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8222 (mm-30) REVERT: G 22 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8263 (mm-30) REVERT: G 28 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8538 (mttt) REVERT: H 22 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8268 (mm-30) REVERT: I 35 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7476 (ptt) outliers start: 22 outliers final: 17 residues processed: 68 average time/residue: 1.1173 time to fit residues: 77.8832 Evaluate side-chains 84 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 35 MET 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 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 28 LYS Chi-restraints excluded: chain I residue 35 MET 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 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093531 restraints weight = 2541.096| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.95 r_work: 0.3007 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2777 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= 0.211 Angle : 0.463 3.323 3080 Z= 0.243 Chirality : 0.054 0.122 370 Planarity : 0.002 0.007 390 Dihedral : 7.580 38.481 316 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.83 % Allowed : 15.22 % 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: -2.94 (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 0.001 0.000 HIS A 14 PHE 0.005 0.001 PHE H 20 *********************** 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 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.316 Fit side-chains REVERT: A 22 GLU cc_start: 0.8814 (mm-30) cc_final: 0.6875 (mt-10) REVERT: B 22 GLU cc_start: 0.8806 (mm-30) cc_final: 0.6850 (mp0) REVERT: G 22 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8183 (mm-30) REVERT: H 22 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8166 (mm-30) REVERT: I 35 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7144 (ptt) outliers start: 18 outliers final: 17 residues processed: 60 average time/residue: 0.8619 time to fit residues: 53.2580 Evaluate side-chains 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 26 SER 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 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 I residue 35 MET 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 20 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.090414 restraints weight = 2654.846| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.80 r_work: 0.3044 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2290 Z= 0.156 Angle : 0.444 5.374 3080 Z= 0.229 Chirality : 0.053 0.122 370 Planarity : 0.001 0.007 390 Dihedral : 6.909 35.374 316 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.14 % Favored : 95.17 % 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: -2.93 (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 0.001 0.000 HIS D 14 PHE 0.005 0.001 PHE H 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 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.255 Fit side-chains REVERT: B 22 GLU cc_start: 0.8893 (mm-30) cc_final: 0.6965 (mt-10) REVERT: G 22 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8319 (mm-30) REVERT: G 28 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8840 (mttt) REVERT: I 35 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7179 (ptt) outliers start: 21 outliers final: 17 residues processed: 59 average time/residue: 0.8504 time to fit residues: 51.6374 Evaluate side-chains 74 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 I residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 35 MET 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 14 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092789 restraints weight = 2617.492| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.95 r_work: 0.2998 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2290 Z= 0.225 Angle : 0.471 4.705 3080 Z= 0.243 Chirality : 0.053 0.125 370 Planarity : 0.002 0.007 390 Dihedral : 6.665 33.024 316 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 3.10 % Allowed : 3.10 % Favored : 93.79 % 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: -2.92 (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 0.001 0.000 HIS D 14 PHE 0.005 0.001 PHE B 19 *********************** 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 79 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.267 Fit side-chains REVERT: B 22 GLU cc_start: 0.8828 (mm-30) cc_final: 0.6877 (mt-10) REVERT: G 22 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8286 (mm-30) REVERT: G 28 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (mttt) REVERT: H 22 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8185 (mm-30) REVERT: I 35 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7223 (ptt) outliers start: 21 outliers final: 20 residues processed: 59 average time/residue: 0.8289 time to fit residues: 50.4123 Evaluate side-chains 80 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 23 ASP 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 I residue 35 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090061 restraints weight = 2726.234| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.78 r_work: 0.3042 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2290 Z= 0.171 Angle : 0.446 4.114 3080 Z= 0.231 Chirality : 0.053 0.122 370 Planarity : 0.001 0.006 390 Dihedral : 6.306 30.834 316 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 3.45 % Allowed : 2.07 % Favored : 94.48 % Rotamer: Outliers : 8.70 % Allowed : 12.17 % Favored : 79.13 % 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 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (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 H 20 *********************** 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 79 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.276 Fit side-chains REVERT: B 22 GLU cc_start: 0.8834 (mm-30) cc_final: 0.6909 (mt-10) REVERT: G 22 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8333 (mm-30) REVERT: G 28 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: H 22 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8237 (mm-30) REVERT: I 16 LYS cc_start: 0.8679 (mttt) cc_final: 0.8360 (mttp) REVERT: I 35 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7161 (ptt) outliers start: 20 outliers final: 17 residues processed: 60 average time/residue: 0.8842 time to fit residues: 54.6236 Evaluate side-chains 76 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 35 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.0040 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.7198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085387 restraints weight = 2594.164| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.96 r_work: 0.2986 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2951 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= 0.253 Angle : 0.478 4.610 3080 Z= 0.246 Chirality : 0.054 0.126 370 Planarity : 0.002 0.007 390 Dihedral : 6.315 29.969 316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 3.45 % Allowed : 5.52 % Favored : 91.03 % 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: -2.89 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (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 79 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.275 Fit side-chains REVERT: B 22 GLU cc_start: 0.8817 (mm-30) cc_final: 0.6851 (mt-10) REVERT: G 22 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8254 (mm-30) REVERT: G 28 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8730 (mttt) REVERT: H 22 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8165 (mm-30) REVERT: I 35 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7260 (ptt) outliers start: 21 outliers final: 18 residues processed: 60 average time/residue: 0.8715 time to fit residues: 53.8159 Evaluate side-chains 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 G residue 28 LYS 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 I residue 28 LYS Chi-restraints excluded: chain I residue 35 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.115699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089851 restraints weight = 2613.634| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.87 r_work: 0.2946 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2290 Z= 0.400 Angle : 0.578 6.198 3080 Z= 0.291 Chirality : 0.055 0.131 370 Planarity : 0.002 0.008 390 Dihedral : 6.660 30.099 316 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 3.45 % Allowed : 3.45 % Favored : 93.10 % Rotamer: Outliers : 8.26 % Allowed : 13.48 % 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: -2.99 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.009 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 85 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.261 Fit side-chains REVERT: A 22 GLU cc_start: 0.8763 (mm-30) cc_final: 0.6822 (mt-10) REVERT: B 22 GLU cc_start: 0.8804 (mm-30) cc_final: 0.6877 (mt-10) REVERT: D 22 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8232 (mm-30) REVERT: G 22 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8320 (mm-30) REVERT: G 28 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8494 (mttt) REVERT: H 22 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8179 (mm-30) REVERT: I 35 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7487 (ptt) outliers start: 19 outliers final: 17 residues processed: 69 average time/residue: 1.0312 time to fit residues: 72.8408 Evaluate side-chains 84 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 G residue 28 LYS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain I residue 35 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.114299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088801 restraints weight = 2588.903| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.84 r_work: 0.2927 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2290 Z= 0.426 Angle : 0.606 6.663 3080 Z= 0.305 Chirality : 0.055 0.129 370 Planarity : 0.002 0.007 390 Dihedral : 6.781 35.019 316 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 3.45 % Allowed : 7.59 % Favored : 88.97 % 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: -3.06 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 14 PHE 0.009 0.002 PHE I 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.91 seconds wall clock time: 38 minutes 2.03 seconds (2282.03 seconds total)