Starting phenix.real_space_refine on Mon Feb 10 20:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol5_16949/02_2025/8ol5_16949.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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-5592/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: 1.67, per 1000 atoms: 0.74 Number of scatterers: 2260 At special positions: 0 Unit cell: (79.992, 54.136, 41.208, 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: 0.49 Conformation dependent library (CDL) restraints added in 255.9 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 10 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.368A pdb=" N HIS B 14 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS D 14 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS H 14 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.447A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 24 through 27 removed outlier: 8.611A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN F 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N SER D 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER F 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN H 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASN J 27 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N SER H 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.881A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA H 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY F 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ILE H 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET F 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LEU H 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU J 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY H 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N VAL J 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N MET H 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.418A pdb=" N HIS A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS E 14 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS G 14 " --> pdb=" O GLN I 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.526A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 27 removed outlier: 8.630A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER C 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN E 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN G 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N SER E 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN I 27 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N SER G 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.200A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA E 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY C 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE E 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET C 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LEU E 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL I 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.441A pdb=" N VAL E 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 102 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: 0.57 Time building geometry restraints manager: 0.59 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 - 1.46: 285 1.46 - 1.57: 1245 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2290 Sorted by residual: bond pdb=" CA GLY D 37 " pdb=" C GLY D 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 4.00e-01 bond pdb=" CA GLY A 37 " pdb=" C GLY A 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.99e-01 bond pdb=" CA GLY G 37 " pdb=" C GLY G 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.75e-01 bond pdb=" CA GLY H 37 " pdb=" C GLY H 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.69e-01 bond pdb=" CA GLY E 37 " pdb=" C GLY E 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.58e-01 ... (remaining 2285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.56: 2679 0.56 - 1.12: 312 1.12 - 1.69: 61 1.69 - 2.25: 18 2.25 - 2.81: 10 Bond angle restraints: 3080 Sorted by residual: angle pdb=" C GLN H 15 " pdb=" N LYS H 16 " pdb=" CA LYS H 16 " ideal model delta sigma weight residual 122.34 124.17 -1.83 1.39e+00 5.18e-01 1.73e+00 angle pdb=" C GLN E 15 " pdb=" N LYS E 16 " pdb=" CA LYS E 16 " ideal model delta sigma weight residual 122.34 124.17 -1.83 1.39e+00 5.18e-01 1.73e+00 angle pdb=" C GLN I 15 " pdb=" N LYS I 16 " pdb=" CA LYS I 16 " ideal model delta sigma weight residual 122.34 124.14 -1.80 1.39e+00 5.18e-01 1.68e+00 angle pdb=" C GLN J 15 " pdb=" N LYS J 16 " pdb=" CA LYS J 16 " ideal model delta sigma weight residual 122.34 124.13 -1.79 1.39e+00 5.18e-01 1.65e+00 angle pdb=" C GLN C 15 " pdb=" N LYS C 16 " pdb=" CA LYS C 16 " ideal model delta sigma weight residual 122.34 124.12 -1.78 1.39e+00 5.18e-01 1.63e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.65: 1140 8.65 - 17.30: 70 17.30 - 25.95: 50 25.95 - 34.60: 20 34.60 - 43.25: 10 Dihedral angle restraints: 1290 sinusoidal: 470 harmonic: 820 Sorted by residual: dihedral pdb=" CA MET J 35 " pdb=" CB MET J 35 " pdb=" CG MET J 35 " pdb=" SD MET J 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.25 -43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" CA MET D 35 " pdb=" CB MET D 35 " pdb=" CG MET D 35 " pdb=" SD MET D 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.25 -43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" CA MET I 35 " pdb=" CB MET I 35 " pdb=" CG MET I 35 " pdb=" SD MET I 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.24 -43.24 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.024: 156 0.024 - 0.047: 85 0.047 - 0.070: 39 0.070 - 0.093: 8 0.093 - 0.116: 82 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 chirality pdb=" CA ILE H 31 " pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CB ILE H 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 367 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 16 " 0.004 2.00e-02 2.50e+03 7.62e-03 5.81e-01 pdb=" C LYS G 16 " -0.013 2.00e-02 2.50e+03 pdb=" O LYS G 16 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU G 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 16 " -0.004 2.00e-02 2.50e+03 7.58e-03 5.74e-01 pdb=" C LYS F 16 " 0.013 2.00e-02 2.50e+03 pdb=" O LYS F 16 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU F 17 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 16 " 0.004 2.00e-02 2.50e+03 7.54e-03 5.68e-01 pdb=" C LYS E 16 " -0.013 2.00e-02 2.50e+03 pdb=" O LYS E 16 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU E 17 " 0.004 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 824 2.89 - 3.40: 1710 3.40 - 3.90: 4030 3.90 - 4.40: 3993 4.40 - 4.90: 7617 Nonbonded interactions: 18174 Sorted by model distance: nonbonded pdb=" NZ LYS B 28 " pdb=" OXT ALA C 42 " model vdw 2.393 3.120 nonbonded pdb=" NZ LYS F 28 " pdb=" OXT ALA G 42 " model vdw 2.393 3.120 nonbonded pdb=" OXT ALA E 42 " pdb=" NZ LYS D 28 " model vdw 2.394 3.120 nonbonded pdb=" N ASP E 23 " pdb=" OD1 ASP E 23 " model vdw 2.400 3.120 nonbonded pdb=" N ASP J 23 " pdb=" OD1 ASP J 23 " model vdw 2.400 3.120 ... (remaining 18169 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.470 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.003 0.014 2290 Z= 0.236 Angle : 0.438 2.812 3080 Z= 0.261 Chirality : 0.057 0.116 370 Planarity : 0.002 0.008 390 Dihedral : 9.968 43.251 770 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -0.75 (0.48), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.007 0.002 PHE E 20 *********************** 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 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.234 Fit side-chains REVERT: H 22 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8404 (tp30) REVERT: E 22 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7838 (tt0) REVERT: A 22 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7823 (pm20) REVERT: C 22 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8218 (mm-30) REVERT: D 23 ASP cc_start: 0.7667 (p0) cc_final: 0.7131 (m-30) REVERT: G 22 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8392 (mm-30) REVERT: I 15 GLN cc_start: 0.8478 (tt0) cc_final: 0.8204 (tp40) REVERT: J 22 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8257 (mm-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1289 time to fit residues: 16.2965 Evaluate side-chains 81 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 chunk 8 optimal weight: 0.2980 overall best weight: 2.0342 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.099342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086047 restraints weight = 4676.339| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.02 r_work: 0.2981 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2290 Z= 0.227 Angle : 0.402 2.755 3080 Z= 0.223 Chirality : 0.056 0.130 370 Planarity : 0.002 0.009 390 Dihedral : 4.586 17.992 310 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 21.30 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.48), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 14 PHE 0.007 0.001 PHE E 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 89 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.271 Fit side-chains REVERT: H 23 ASP cc_start: 0.8392 (m-30) cc_final: 0.8146 (m-30) REVERT: E 22 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7960 (tt0) REVERT: A 22 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8034 (pm20) REVERT: C 22 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8121 (mm-30) REVERT: C 23 ASP cc_start: 0.8235 (p0) cc_final: 0.7470 (p0) REVERT: D 23 ASP cc_start: 0.8224 (p0) cc_final: 0.7988 (m-30) REVERT: D 35 MET cc_start: 0.8877 (tpt) cc_final: 0.8577 (tpt) REVERT: F 23 ASP cc_start: 0.8074 (p0) cc_final: 0.7870 (m-30) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0780 time to fit residues: 8.4847 Evaluate side-chains 85 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain I residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.098751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085025 restraints weight = 4727.413| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.21 r_work: 0.2926 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2705 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= 0.310 Angle : 0.433 3.209 3080 Z= 0.237 Chirality : 0.055 0.137 370 Planarity : 0.002 0.008 390 Dihedral : 5.169 27.796 310 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.61 % Allowed : 21.30 % 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: -1.06 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 14 PHE 0.006 0.001 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.262 Fit side-chains REVERT: H 23 ASP cc_start: 0.8664 (m-30) cc_final: 0.8361 (m-30) REVERT: E 22 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7954 (tt0) REVERT: A 22 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8052 (pt0) REVERT: A 23 ASP cc_start: 0.8476 (m-30) cc_final: 0.8215 (m-30) REVERT: C 22 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8149 (tp30) REVERT: C 23 ASP cc_start: 0.8157 (p0) cc_final: 0.7687 (p0) REVERT: D 22 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8430 (mm-30) REVERT: F 23 ASP cc_start: 0.8164 (p0) cc_final: 0.7612 (p0) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 0.0786 time to fit residues: 8.3300 Evaluate side-chains 84 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain I residue 32 ILE 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 23 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 8 optimal weight: 0.0040 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.101093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087278 restraints weight = 4659.984| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.24 r_work: 0.2984 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2290 Z= 0.143 Angle : 0.364 2.811 3080 Z= 0.205 Chirality : 0.055 0.131 370 Planarity : 0.001 0.009 390 Dihedral : 4.758 23.699 310 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.48 % Allowed : 19.57 % 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: -1.05 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.004 0.001 PHE H 20 *********************** 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 88 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.248 Fit side-chains REVERT: H 23 ASP cc_start: 0.8410 (m-30) cc_final: 0.8112 (m-30) REVERT: E 22 GLU cc_start: 0.8568 (mm-30) cc_final: 0.7904 (tt0) REVERT: A 22 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8025 (pt0) REVERT: C 22 GLU cc_start: 0.8730 (mm-30) cc_final: 0.7969 (mm-30) REVERT: C 23 ASP cc_start: 0.8190 (p0) cc_final: 0.7609 (p0) REVERT: D 22 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8287 (mm-30) REVERT: F 22 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8419 (mm-30) REVERT: F 23 ASP cc_start: 0.8304 (p0) cc_final: 0.7660 (p0) outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 0.0770 time to fit residues: 8.2166 Evaluate side-chains 83 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081162 restraints weight = 4855.984| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.21 r_work: 0.2855 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.046 2290 Z= 0.729 Angle : 0.630 5.061 3080 Z= 0.332 Chirality : 0.055 0.123 370 Planarity : 0.003 0.007 390 Dihedral : 6.556 38.327 310 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 9.13 % Allowed : 14.78 % 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: -1.49 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 14 PHE 0.007 0.002 PHE D 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 87 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.275 Fit side-chains REVERT: H 23 ASP cc_start: 0.8457 (m-30) cc_final: 0.8131 (m-30) REVERT: H 35 MET cc_start: 0.8963 (tpt) cc_final: 0.8683 (tpt) REVERT: E 22 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7973 (tt0) REVERT: A 22 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8023 (pt0) REVERT: C 22 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7956 (tp30) REVERT: C 23 ASP cc_start: 0.8039 (p0) cc_final: 0.7673 (p0) REVERT: D 22 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8398 (mm-30) REVERT: D 23 ASP cc_start: 0.8549 (m-30) cc_final: 0.8346 (m-30) REVERT: F 13 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7847 (m-70) REVERT: F 22 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8501 (mm-30) REVERT: J 23 ASP cc_start: 0.8603 (m-30) cc_final: 0.8395 (m-30) outliers start: 21 outliers final: 18 residues processed: 80 average time/residue: 0.0933 time to fit residues: 9.5130 Evaluate side-chains 83 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 13 HIS Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.099248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085443 restraints weight = 4731.110| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.24 r_work: 0.2936 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2290 Z= 0.236 Angle : 0.410 3.016 3080 Z= 0.228 Chirality : 0.055 0.123 370 Planarity : 0.002 0.007 390 Dihedral : 5.622 31.864 310 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.78 % Allowed : 17.83 % 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: -1.32 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.004 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 87 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.256 Fit side-chains REVERT: H 23 ASP cc_start: 0.8360 (m-30) cc_final: 0.8092 (m-30) REVERT: H 35 MET cc_start: 0.8800 (tpt) cc_final: 0.8411 (tpt) REVERT: A 22 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8047 (pt0) REVERT: D 22 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8366 (mm-30) REVERT: F 22 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8484 (mm-30) REVERT: F 23 ASP cc_start: 0.8351 (p0) cc_final: 0.8028 (p0) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.0805 time to fit residues: 8.7103 Evaluate side-chains 81 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.3224 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.098822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.084982 restraints weight = 4790.896| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.19 r_work: 0.2937 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2290 Z= 0.258 Angle : 0.433 3.951 3080 Z= 0.239 Chirality : 0.054 0.120 370 Planarity : 0.002 0.007 390 Dihedral : 5.528 29.441 310 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.35 % Allowed : 20.43 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.004 0.001 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.264 Fit side-chains REVERT: H 23 ASP cc_start: 0.8364 (m-30) cc_final: 0.8066 (m-30) REVERT: H 35 MET cc_start: 0.8802 (tpt) cc_final: 0.8502 (tpt) REVERT: A 22 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7954 (pt0) REVERT: C 23 ASP cc_start: 0.8194 (p0) cc_final: 0.7849 (p0) REVERT: D 22 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8361 (mm-30) outliers start: 10 outliers final: 9 residues processed: 81 average time/residue: 0.0857 time to fit residues: 8.9839 Evaluate side-chains 84 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.095965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081812 restraints weight = 4881.883| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.21 r_work: 0.2870 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 2290 Z= 0.567 Angle : 0.566 4.570 3080 Z= 0.304 Chirality : 0.053 0.116 370 Planarity : 0.002 0.006 390 Dihedral : 6.395 36.422 310 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.35 % Allowed : 19.57 % 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: -1.46 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 14 PHE 0.006 0.001 PHE B 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 76 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.252 Fit side-chains REVERT: H 23 ASP cc_start: 0.8356 (m-30) cc_final: 0.8043 (m-30) REVERT: H 35 MET cc_start: 0.8943 (tpt) cc_final: 0.8715 (tpt) REVERT: A 22 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7870 (pt0) REVERT: D 22 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8366 (mm-30) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.0786 time to fit residues: 7.5299 Evaluate side-chains 75 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS 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: 4.9990 chunk 22 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.100136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086329 restraints weight = 4677.147| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.19 r_work: 0.2963 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2290 Z= 0.197 Angle : 0.404 3.182 3080 Z= 0.228 Chirality : 0.054 0.123 370 Planarity : 0.001 0.007 390 Dihedral : 5.485 29.186 310 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.04 % Allowed : 21.30 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 13 PHE 0.004 0.001 PHE H 20 *********************** 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 84 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.278 Fit side-chains REVERT: H 23 ASP cc_start: 0.8355 (m-30) cc_final: 0.8081 (m-30) REVERT: A 22 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7903 (pt0) REVERT: C 23 ASP cc_start: 0.8208 (p0) cc_final: 0.7938 (p0) REVERT: D 22 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8263 (mm-30) REVERT: F 23 ASP cc_start: 0.8338 (p0) cc_final: 0.8074 (p0) outliers start: 7 outliers final: 7 residues processed: 81 average time/residue: 0.0760 time to fit residues: 8.0022 Evaluate side-chains 82 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.097784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083920 restraints weight = 4734.789| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.19 r_work: 0.2919 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2290 Z= 0.362 Angle : 0.492 4.235 3080 Z= 0.267 Chirality : 0.054 0.119 370 Planarity : 0.002 0.007 390 Dihedral : 5.898 31.915 310 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.04 % Allowed : 22.17 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.005 0.001 PHE H 20 ********************** 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 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.272 Fit side-chains REVERT: H 23 ASP cc_start: 0.8364 (m-30) cc_final: 0.8079 (m-30) REVERT: A 22 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7907 (pt0) REVERT: B 35 MET cc_start: 0.7974 (tpt) cc_final: 0.6863 (ttp) REVERT: C 23 ASP cc_start: 0.8194 (p0) cc_final: 0.7971 (p0) REVERT: D 22 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8366 (mm-30) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 0.0837 time to fit residues: 8.1534 Evaluate side-chains 78 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 13 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 2.7784 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.098526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084585 restraints weight = 4721.080| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.20 r_work: 0.2931 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3552 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= 0.302 Angle : 0.461 3.952 3080 Z= 0.253 Chirality : 0.054 0.120 370 Planarity : 0.002 0.007 390 Dihedral : 5.759 31.251 310 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.91 % Allowed : 21.30 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 14 PHE 0.004 0.001 PHE H 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.71 seconds wall clock time: 22 minutes 48.90 seconds (1368.90 seconds total)