Starting phenix.real_space_refine on Fri Aug 22 12:39:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol2_16942/08_2025/8ol2_16942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol2_16942/08_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_16942/08_2025/8ol2_16942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol2_16942/08_2025/8ol2_16942.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol2_16942/08_2025/8ol2_16942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol2_16942/08_2025/8ol2_16942.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.53, per 1000 atoms: 0.23 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: 0.19 Conformation dependent library (CDL) restraints added in 131.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.13 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: 0.30 Time building geometry restraints manager: 0.25 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: 0.01 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: 1.750 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.500 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.100 ------------------------------------------------------------------------------- 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= 0.191 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 PHE 0.006 0.002 PHE J 19 HIS 0.001 0.000 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2290) covalent geometry : angle 0.45494 ( 3080) hydrogen bonds : bond 0.10937 ( 32) hydrogen bonds : angle 8.71069 ( 96) *********************** 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 : 0.088 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: 0.5463 time to fit residues: 30.1300 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 : 0.091 ------------------------------------------------------------------------------- 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 27 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.107237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.079488 restraints weight = 2566.451| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.87 r_work: 0.2876 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.050 2290 Z= 0.436 Angle : 0.737 6.021 3080 Z= 0.379 Chirality : 0.060 0.144 370 Planarity : 0.003 0.010 390 Dihedral : 9.645 50.372 319 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 7.39 % Allowed : 10.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE J 19 HIS 0.005 0.002 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.01067 ( 2290) covalent geometry : angle 0.73732 ( 3080) hydrogen bonds : bond 0.03732 ( 32) hydrogen bonds : angle 6.37130 ( 96) *********************** 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 85 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.089 Fit side-chains REVERT: A 22 GLU cc_start: 0.8902 (mm-30) cc_final: 0.7005 (mp0) REVERT: B 22 GLU cc_start: 0.8779 (mm-30) cc_final: 0.7022 (mp0) REVERT: C 22 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8345 (mm-30) REVERT: D 22 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8238 (mm-30) REVERT: F 22 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8177 (mm-30) REVERT: G 22 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8235 (mm-30) REVERT: G 28 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8518 (mtpt) REVERT: H 22 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8282 (mm-30) REVERT: I 35 MET cc_start: 0.8108 (ptm) cc_final: 0.7526 (ptt) REVERT: J 22 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8223 (mm-30) outliers start: 17 outliers final: 13 residues processed: 72 average time/residue: 0.5057 time to fit residues: 37.2326 Evaluate side-chains 80 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 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 23 ASP Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087642 restraints weight = 2541.212| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.01 r_work: 0.3004 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2290 Z= 0.117 Angle : 0.464 3.514 3080 Z= 0.244 Chirality : 0.054 0.125 370 Planarity : 0.002 0.007 390 Dihedral : 8.310 46.229 319 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.26 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 20 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2290) covalent geometry : angle 0.46400 ( 3080) hydrogen bonds : bond 0.02183 ( 32) hydrogen bonds : angle 6.01065 ( 96) *********************** 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 80 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.086 Fit side-chains REVERT: A 22 GLU cc_start: 0.8802 (mm-30) cc_final: 0.6880 (mp0) REVERT: B 22 GLU cc_start: 0.8782 (mm-30) cc_final: 0.6916 (mp0) REVERT: I 35 MET cc_start: 0.7849 (ptm) cc_final: 0.7258 (ptt) outliers start: 19 outliers final: 17 residues processed: 63 average time/residue: 0.4352 time to fit residues: 28.1564 Evaluate side-chains 74 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 23 ASP 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 J residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.119168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092994 restraints weight = 2590.272| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.78 r_work: 0.3064 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2290 Z= 0.097 Angle : 0.421 3.210 3080 Z= 0.222 Chirality : 0.053 0.123 370 Planarity : 0.002 0.006 390 Dihedral : 7.741 46.718 319 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 8.26 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 PHE 0.005 0.001 PHE C 20 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2290) covalent geometry : angle 0.42103 ( 3080) hydrogen bonds : bond 0.01669 ( 32) hydrogen bonds : angle 5.59640 ( 96) *********************** 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 73 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.087 Fit side-chains REVERT: B 22 GLU cc_start: 0.8895 (mm-30) cc_final: 0.7008 (mp0) REVERT: I 35 MET cc_start: 0.7923 (ptm) cc_final: 0.7402 (ptt) REVERT: J 28 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8456 (mtpt) outliers start: 19 outliers final: 14 residues processed: 57 average time/residue: 0.3895 time to fit residues: 22.8726 Evaluate side-chains 69 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 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 H residue 12 VAL Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain I residue 12 VAL 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 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.119640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093301 restraints weight = 2600.683| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.81 r_work: 0.3068 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 : 0.002 0.012 2290 Z= 0.092 Angle : 0.410 3.300 3080 Z= 0.217 Chirality : 0.053 0.122 370 Planarity : 0.001 0.005 390 Dihedral : 7.174 44.856 319 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 8.70 % Allowed : 13.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE D 20 HIS 0.001 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 2290) covalent geometry : angle 0.40998 ( 3080) hydrogen bonds : bond 0.01440 ( 32) hydrogen bonds : angle 5.30081 ( 96) *********************** 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 73 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.095 Fit side-chains REVERT: B 22 GLU cc_start: 0.8876 (mm-30) cc_final: 0.6992 (mp0) REVERT: I 35 MET cc_start: 0.8029 (ptm) cc_final: 0.7535 (ptt) outliers start: 20 outliers final: 18 residues processed: 55 average time/residue: 0.3890 time to fit residues: 22.0280 Evaluate side-chains 72 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 23 ASP 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 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 8 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 overall best weight: 1.2054 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.116814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090954 restraints weight = 2593.194| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.77 r_work: 0.3035 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2836 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= 0.118 Angle : 0.435 3.489 3080 Z= 0.228 Chirality : 0.053 0.122 370 Planarity : 0.002 0.005 390 Dihedral : 7.065 40.697 319 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE J 19 HIS 0.001 0.000 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 2290) covalent geometry : angle 0.43517 ( 3080) hydrogen bonds : bond 0.01735 ( 32) hydrogen bonds : angle 5.17861 ( 96) *********************** 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 to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.087 Fit side-chains REVERT: E 28 LYS cc_start: 0.8927 (mttm) cc_final: 0.8655 (mttt) REVERT: I 35 MET cc_start: 0.8161 (ptm) cc_final: 0.7677 (ptt) outliers start: 20 outliers final: 19 residues processed: 58 average time/residue: 0.3723 time to fit residues: 22.2174 Evaluate side-chains 75 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 23 ASP 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 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 8 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.116192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.089741 restraints weight = 2591.355| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.86 r_work: 0.2941 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3026 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= 0.251 Angle : 0.548 4.260 3080 Z= 0.282 Chirality : 0.055 0.129 370 Planarity : 0.002 0.007 390 Dihedral : 7.431 32.795 319 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 3.10 % Allowed : 6.21 % Favored : 90.69 % Rotamer: Outliers : 9.57 % Allowed : 12.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE J 19 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 2290) covalent geometry : angle 0.54770 ( 3080) hydrogen bonds : bond 0.02345 ( 32) hydrogen bonds : angle 5.20514 ( 96) *********************** 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 90 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.089 Fit side-chains REVERT: A 22 GLU cc_start: 0.8782 (mm-30) cc_final: 0.6866 (mp0) REVERT: B 22 GLU cc_start: 0.8871 (mm-30) cc_final: 0.6951 (mp0) REVERT: C 16 LYS cc_start: 0.8344 (mttt) cc_final: 0.8128 (mttp) REVERT: D 22 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8257 (mm-30) REVERT: G 22 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8317 (mm-30) REVERT: H 22 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8239 (mm-30) REVERT: I 35 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7912 (ptt) outliers start: 22 outliers final: 21 residues processed: 71 average time/residue: 0.4240 time to fit residues: 30.8284 Evaluate side-chains 89 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.117959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091658 restraints weight = 2510.740| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.86 r_work: 0.2977 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3031 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= 0.173 Angle : 0.510 4.582 3080 Z= 0.262 Chirality : 0.054 0.123 370 Planarity : 0.002 0.007 390 Dihedral : 7.057 33.084 319 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 3.45 % Allowed : 3.79 % Favored : 92.76 % Rotamer: Outliers : 10.43 % Allowed : 11.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.42), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 19 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2290) covalent geometry : angle 0.50992 ( 3080) hydrogen bonds : bond 0.02136 ( 32) hydrogen bonds : angle 5.20247 ( 96) *********************** 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 89 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.083 Fit side-chains REVERT: A 22 GLU cc_start: 0.8759 (mm-30) cc_final: 0.6804 (mp0) REVERT: B 22 GLU cc_start: 0.8806 (mm-30) cc_final: 0.6872 (mp0) REVERT: D 22 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8218 (mm-30) REVERT: G 22 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8222 (mm-30) REVERT: H 22 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8177 (mm-30) REVERT: I 35 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7764 (ptt) outliers start: 24 outliers final: 21 residues processed: 68 average time/residue: 0.3753 time to fit residues: 26.1708 Evaluate side-chains 89 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 23 ASP 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 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 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 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 9 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090802 restraints weight = 2594.732| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.85 r_work: 0.2960 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2290 Z= 0.194 Angle : 0.520 4.447 3080 Z= 0.267 Chirality : 0.054 0.123 370 Planarity : 0.002 0.007 390 Dihedral : 6.907 29.235 319 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 3.45 % Allowed : 6.55 % Favored : 90.00 % Rotamer: Outliers : 11.30 % Allowed : 12.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE J 19 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 2290) covalent geometry : angle 0.51951 ( 3080) hydrogen bonds : bond 0.02230 ( 32) hydrogen bonds : angle 5.16736 ( 96) *********************** 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 92 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.051 Fit side-chains REVERT: A 22 GLU cc_start: 0.8777 (mm-30) cc_final: 0.6840 (mt-10) REVERT: B 22 GLU cc_start: 0.8796 (mm-30) cc_final: 0.6905 (mt-10) REVERT: D 22 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8293 (mm-30) REVERT: G 22 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8269 (mm-30) REVERT: H 22 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8249 (mm-30) REVERT: I 35 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7876 (ptt) outliers start: 26 outliers final: 24 residues processed: 69 average time/residue: 0.3916 time to fit residues: 27.6175 Evaluate side-chains 91 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.049 ------------------------------------------------------------------------------- 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 23 ASP 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 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 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 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 15 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.112468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.086735 restraints weight = 2611.252| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.81 r_work: 0.2884 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 2290 Z= 0.384 Angle : 0.684 5.789 3080 Z= 0.346 Chirality : 0.057 0.129 370 Planarity : 0.002 0.008 390 Dihedral : 7.368 26.606 319 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 3.45 % Allowed : 12.41 % Favored : 84.14 % Rotamer: Outliers : 10.87 % Allowed : 12.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE G 19 HIS 0.004 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 2290) covalent geometry : angle 0.68435 ( 3080) hydrogen bonds : bond 0.02572 ( 32) hydrogen bonds : angle 5.22560 ( 96) ********************** 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 93 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.084 Fit side-chains REVERT: A 22 GLU cc_start: 0.8795 (mm-30) cc_final: 0.6965 (mt-10) REVERT: B 22 GLU cc_start: 0.8826 (mm-30) cc_final: 0.6964 (mt-10) REVERT: D 22 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8415 (mm-30) REVERT: G 22 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8328 (mm-30) REVERT: H 22 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8268 (mm-30) REVERT: I 35 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8039 (ptt) outliers start: 25 outliers final: 21 residues processed: 72 average time/residue: 0.3995 time to fit residues: 29.4870 Evaluate side-chains 90 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.085 ------------------------------------------------------------------------------- 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 23 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.113634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088155 restraints weight = 2639.650| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.77 r_work: 0.3134 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3246 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= 0.115 Angle : 0.485 4.703 3080 Z= 0.251 Chirality : 0.053 0.122 370 Planarity : 0.002 0.008 390 Dihedral : 6.410 24.156 319 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 3.45 % Allowed : 2.07 % Favored : 94.48 % Rotamer: Outliers : 8.70 % Allowed : 16.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.44), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE D 20 HIS 0.001 0.000 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 2290) covalent geometry : angle 0.48459 ( 3080) hydrogen bonds : bond 0.01896 ( 32) hydrogen bonds : angle 5.28460 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1043.89 seconds wall clock time: 19 minutes 8.78 seconds (1148.78 seconds total)