Starting phenix.real_space_refine on Tue Feb 3 12:51:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co4_45770/02_2026/9co4_45770.map" } resolution = 2.8 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= 0.000 sd= 0.007 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 1630 2.51 5 N 420 2.21 5 O 450 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.24, per 1000 atoms: 0.10 Number of scatterers: 2510 At special positions: 0 Unit cell: (67.284, 67.284, 50.196, 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 450 8.00 N 420 7.00 C 1630 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: 0.22 Conformation dependent library (CDL) restraints added in 102.0 milliseconds 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.293A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE C 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE A 19 " --> pdb=" O PHE C 20 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE C 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE G 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N PHE E 19 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE I 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N PHE G 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.737A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 36 removed outlier: 6.440A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.300A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE B 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE H 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE F 19 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE J 20 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE H 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 24 through 25 removed outlier: 6.745A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.449A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 41 40 hydrogen bonds defined for protein. 120 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: 0.36 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 820 1.34 - 1.45: 293 1.45 - 1.56: 1417 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 2550 Sorted by residual: bond pdb=" CG1 ILE G 32 " pdb=" CD1 ILE G 32 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG1 ILE B 32 " pdb=" CD1 ILE B 32 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.85e+00 bond pdb=" CG1 ILE I 32 " pdb=" CD1 ILE I 32 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CG1 ILE F 32 " pdb=" CD1 ILE F 32 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.83e+00 bond pdb=" CG1 ILE J 32 " pdb=" CD1 ILE J 32 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.82e+00 ... (remaining 2545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 3117 1.06 - 2.12: 233 2.12 - 3.18: 60 3.18 - 4.24: 10 4.24 - 5.31: 10 Bond angle restraints: 3430 Sorted by residual: angle pdb=" C VAL E 12 " pdb=" N HIS E 13 " pdb=" CA HIS E 13 " ideal model delta sigma weight residual 121.85 117.83 4.02 1.77e+00 3.19e-01 5.16e+00 angle pdb=" C VAL F 12 " pdb=" N HIS F 13 " pdb=" CA HIS F 13 " ideal model delta sigma weight residual 121.85 117.84 4.01 1.77e+00 3.19e-01 5.14e+00 angle pdb=" C VAL H 12 " pdb=" N HIS H 13 " pdb=" CA HIS H 13 " ideal model delta sigma weight residual 121.85 117.86 3.99 1.77e+00 3.19e-01 5.08e+00 angle pdb=" C VAL B 12 " pdb=" N HIS B 13 " pdb=" CA HIS B 13 " ideal model delta sigma weight residual 121.85 117.87 3.98 1.77e+00 3.19e-01 5.06e+00 angle pdb=" C VAL J 12 " pdb=" N HIS J 13 " pdb=" CA HIS J 13 " ideal model delta sigma weight residual 121.85 117.88 3.97 1.77e+00 3.19e-01 5.04e+00 ... (remaining 3425 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.83: 1220 17.83 - 35.65: 130 35.65 - 53.47: 60 53.47 - 71.29: 0 71.29 - 89.11: 10 Dihedral angle restraints: 1420 sinusoidal: 520 harmonic: 900 Sorted by residual: dihedral pdb=" CB LYS H 28 " pdb=" CG LYS H 28 " pdb=" CD LYS H 28 " pdb=" CE LYS H 28 " ideal model delta sinusoidal sigma weight residual 180.00 138.80 41.20 3 1.50e+01 4.44e-03 7.36e+00 dihedral pdb=" CB LYS I 28 " pdb=" CG LYS I 28 " pdb=" CD LYS I 28 " pdb=" CE LYS I 28 " ideal model delta sinusoidal sigma weight residual 180.00 138.80 41.20 3 1.50e+01 4.44e-03 7.36e+00 dihedral pdb=" CB LYS A 28 " pdb=" CG LYS A 28 " pdb=" CD LYS A 28 " pdb=" CE LYS A 28 " ideal model delta sinusoidal sigma weight residual 180.00 138.80 41.20 3 1.50e+01 4.44e-03 7.36e+00 ... (remaining 1417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 93 0.027 - 0.055: 122 0.055 - 0.082: 65 0.082 - 0.110: 71 0.110 - 0.137: 39 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 387 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 14 " 0.008 2.00e-02 2.50e+03 7.19e-03 7.76e-01 pdb=" CG HIS D 14 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS D 14 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 14 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 14 " 0.008 2.00e-02 2.50e+03 7.10e-03 7.56e-01 pdb=" CG HIS C 14 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS C 14 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 14 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 14 " 0.008 2.00e-02 2.50e+03 7.07e-03 7.51e-01 pdb=" CG HIS G 14 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS G 14 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS G 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS G 14 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 14 " 0.003 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 1807 3.11 - 3.55: 2589 3.55 - 4.00: 3747 4.00 - 4.45: 4620 4.45 - 4.90: 8033 Nonbonded interactions: 20796 Sorted by model distance: nonbonded pdb=" N GLU J 22 " pdb=" O GLU J 22 " model vdw 2.657 2.496 nonbonded pdb=" N GLU B 22 " pdb=" O GLU B 22 " model vdw 2.657 2.496 nonbonded pdb=" N GLU G 22 " pdb=" O GLU G 22 " model vdw 2.657 2.496 nonbonded pdb=" N GLU I 22 " pdb=" O GLU I 22 " model vdw 2.657 2.496 nonbonded pdb=" N GLU D 22 " pdb=" O GLU D 22 " model vdw 2.657 2.496 ... (remaining 20791 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: 0.560 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.540 Find NCS groups from input model: 0.030 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:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.009 0.053 2550 Z= 0.375 Angle : 0.703 5.306 3430 Z= 0.365 Chirality : 0.067 0.137 390 Planarity : 0.002 0.007 440 Dihedral : 19.167 89.106 860 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 28.00 % Favored : 72.00 % 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 are not related in a simple way. whole: -0.62 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR J 10 PHE 0.007 0.001 PHE A 20 HIS 0.006 0.003 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00899 ( 2550) covalent geometry : angle 0.70316 ( 3430) hydrogen bonds : bond 0.18991 ( 40) hydrogen bonds : angle 7.83397 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.055 Fit side-chains REVERT: B 23 ASP cc_start: 0.7481 (m-30) cc_final: 0.7146 (m-30) REVERT: D 11 GLU cc_start: 0.7020 (tt0) cc_final: 0.6609 (tm-30) REVERT: D 23 ASP cc_start: 0.7460 (m-30) cc_final: 0.7139 (m-30) REVERT: E 11 GLU cc_start: 0.7263 (tt0) cc_final: 0.6709 (tm-30) REVERT: J 11 GLU cc_start: 0.7025 (tt0) cc_final: 0.6656 (tt0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4502 time to fit residues: 29.3097 Evaluate side-chains 44 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS F 27 ASN H 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092462 restraints weight = 2463.622| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.66 r_work: 0.3214 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2550 Z= 0.102 Angle : 0.494 5.902 3430 Z= 0.275 Chirality : 0.062 0.137 390 Planarity : 0.002 0.006 440 Dihedral : 5.631 24.404 350 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.20 % Allowed : 21.60 % Favored : 77.20 % 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 are not related in a simple way. whole: -0.85 (0.44), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR E 10 PHE 0.004 0.001 PHE A 19 HIS 0.004 0.002 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2550) covalent geometry : angle 0.49374 ( 3430) hydrogen bonds : bond 0.03556 ( 40) hydrogen bonds : angle 6.53177 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.092 Fit side-chains REVERT: B 11 GLU cc_start: 0.6592 (tt0) cc_final: 0.6335 (tt0) REVERT: D 11 GLU cc_start: 0.6694 (tt0) cc_final: 0.6175 (tm-30) REVERT: E 11 GLU cc_start: 0.7322 (tt0) cc_final: 0.7024 (tt0) REVERT: F 34 LEU cc_start: 0.8599 (tp) cc_final: 0.8371 (tt) REVERT: I 28 LYS cc_start: 0.8159 (mttp) cc_final: 0.7771 (mttt) outliers start: 3 outliers final: 3 residues processed: 55 average time/residue: 0.2958 time to fit residues: 16.7310 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER 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 2 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS I 14 HIS I 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.115325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086543 restraints weight = 2613.556| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.51 r_work: 0.3137 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 2550 Z= 0.282 Angle : 0.770 8.760 3430 Z= 0.383 Chirality : 0.068 0.146 390 Planarity : 0.003 0.008 440 Dihedral : 6.930 35.834 350 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.20 % Allowed : 22.40 % Favored : 74.40 % 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 are not related in a simple way. whole: -1.04 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 10 PHE 0.009 0.002 PHE B 20 HIS 0.006 0.003 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 2550) covalent geometry : angle 0.77012 ( 3430) hydrogen bonds : bond 0.05745 ( 40) hydrogen bonds : angle 6.52228 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.053 Fit side-chains REVERT: D 11 GLU cc_start: 0.7222 (tt0) cc_final: 0.6430 (tm-30) REVERT: F 13 HIS cc_start: 0.8096 (p90) cc_final: 0.7317 (p90) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.3118 time to fit residues: 14.7184 Evaluate side-chains 48 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.126841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095894 restraints weight = 2450.610| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.61 r_work: 0.3242 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2550 Z= 0.083 Angle : 0.570 7.082 3430 Z= 0.285 Chirality : 0.061 0.130 390 Planarity : 0.001 0.006 440 Dihedral : 5.819 28.373 350 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.80 % Allowed : 22.00 % Favored : 75.20 % 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 are not related in a simple way. whole: -1.15 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR I 10 PHE 0.003 0.001 PHE F 19 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 2550) covalent geometry : angle 0.56993 ( 3430) hydrogen bonds : bond 0.03792 ( 40) hydrogen bonds : angle 6.18043 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.091 Fit side-chains REVERT: D 11 GLU cc_start: 0.7165 (tt0) cc_final: 0.6405 (tm-30) REVERT: F 13 HIS cc_start: 0.7986 (p90) cc_final: 0.7253 (p90) REVERT: F 15 GLN cc_start: 0.8474 (tt0) cc_final: 0.8164 (tt0) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.3621 time to fit residues: 19.7010 Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.121299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092515 restraints weight = 2535.322| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.48 r_work: 0.3187 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2550 Z= 0.163 Angle : 0.626 7.985 3430 Z= 0.315 Chirality : 0.063 0.135 390 Planarity : 0.002 0.007 440 Dihedral : 6.185 32.101 350 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.60 % Allowed : 23.60 % Favored : 72.80 % 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 are not related in a simple way. whole: -1.23 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR I 10 PHE 0.005 0.001 PHE B 20 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2550) covalent geometry : angle 0.62585 ( 3430) hydrogen bonds : bond 0.04444 ( 40) hydrogen bonds : angle 6.18476 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.095 Fit side-chains REVERT: D 11 GLU cc_start: 0.7167 (tt0) cc_final: 0.6460 (tp30) REVERT: D 16 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7816 (ttmt) REVERT: E 11 GLU cc_start: 0.7500 (tt0) cc_final: 0.7009 (tt0) REVERT: F 13 HIS cc_start: 0.8114 (p90) cc_final: 0.7352 (p90) REVERT: F 15 GLN cc_start: 0.8477 (tt0) cc_final: 0.8160 (tt0) REVERT: G 13 HIS cc_start: 0.7926 (p90) cc_final: 0.7476 (p90) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.4683 time to fit residues: 25.3734 Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090298 restraints weight = 2518.279| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.50 r_work: 0.3171 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2550 Z= 0.198 Angle : 0.655 8.330 3430 Z= 0.330 Chirality : 0.064 0.136 390 Planarity : 0.002 0.007 440 Dihedral : 6.442 32.767 350 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.20 % Allowed : 24.00 % Favored : 72.80 % 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 are not related in a simple way. whole: -1.27 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 10 PHE 0.006 0.001 PHE G 20 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 2550) covalent geometry : angle 0.65546 ( 3430) hydrogen bonds : bond 0.04623 ( 40) hydrogen bonds : angle 6.17653 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.055 Fit side-chains REVERT: D 11 GLU cc_start: 0.7251 (tt0) cc_final: 0.6492 (tp30) REVERT: D 16 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7819 (ttmt) REVERT: F 13 HIS cc_start: 0.8091 (p90) cc_final: 0.7393 (p90) REVERT: F 15 GLN cc_start: 0.8478 (tt0) cc_final: 0.8165 (tt0) REVERT: G 10 TYR cc_start: 0.7279 (m-80) cc_final: 0.6685 (m-80) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.4389 time to fit residues: 22.4996 Evaluate side-chains 54 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087291 restraints weight = 2505.717| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.54 r_work: 0.3159 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 2550 Z= 0.226 Angle : 0.689 8.605 3430 Z= 0.346 Chirality : 0.065 0.140 390 Planarity : 0.002 0.007 440 Dihedral : 6.624 34.485 350 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.80 % Allowed : 26.40 % Favored : 70.80 % 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 are not related in a simple way. whole: -1.33 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 10 PHE 0.007 0.001 PHE B 20 HIS 0.006 0.003 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 2550) covalent geometry : angle 0.68885 ( 3430) hydrogen bonds : bond 0.04821 ( 40) hydrogen bonds : angle 6.17424 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.097 Fit side-chains REVERT: D 11 GLU cc_start: 0.7195 (tt0) cc_final: 0.6468 (tp30) REVERT: D 16 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7818 (ttmt) REVERT: E 11 GLU cc_start: 0.7474 (tt0) cc_final: 0.6881 (tp30) REVERT: F 13 HIS cc_start: 0.8168 (p90) cc_final: 0.7467 (p90) REVERT: F 15 GLN cc_start: 0.8469 (tt0) cc_final: 0.8152 (tt0) REVERT: G 13 HIS cc_start: 0.7912 (p90) cc_final: 0.7357 (p90) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.3910 time to fit residues: 20.8898 Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER 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 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS B 13 HIS I 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.122978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092664 restraints weight = 2493.293| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.56 r_work: 0.3254 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2550 Z= 0.104 Angle : 0.576 8.064 3430 Z= 0.290 Chirality : 0.061 0.128 390 Planarity : 0.001 0.007 440 Dihedral : 5.922 30.190 350 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.20 % Allowed : 25.60 % Favored : 71.20 % 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 are not related in a simple way. whole: -1.31 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 10 PHE 0.004 0.001 PHE F 19 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2550) covalent geometry : angle 0.57636 ( 3430) hydrogen bonds : bond 0.03765 ( 40) hydrogen bonds : angle 5.97458 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.059 Fit side-chains REVERT: D 11 GLU cc_start: 0.7213 (tt0) cc_final: 0.6413 (tp30) REVERT: D 16 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7814 (ttmt) REVERT: E 11 GLU cc_start: 0.7459 (tt0) cc_final: 0.6865 (tp30) REVERT: F 13 HIS cc_start: 0.8110 (p90) cc_final: 0.7267 (p90) REVERT: F 15 GLN cc_start: 0.8450 (tt0) cc_final: 0.8132 (tt0) REVERT: G 10 TYR cc_start: 0.6945 (m-80) cc_final: 0.6605 (m-80) REVERT: G 13 HIS cc_start: 0.7929 (p90) cc_final: 0.7643 (p90) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.3930 time to fit residues: 21.7814 Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 0.0270 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS B 13 HIS E 14 HIS F 15 GLN I 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088424 restraints weight = 2640.490| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.61 r_work: 0.3190 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2550 Z= 0.186 Angle : 0.660 8.842 3430 Z= 0.329 Chirality : 0.063 0.136 390 Planarity : 0.002 0.007 440 Dihedral : 6.324 32.723 350 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.00 % Allowed : 29.20 % Favored : 68.80 % 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 are not related in a simple way. whole: -1.35 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 10 PHE 0.005 0.001 PHE G 20 HIS 0.005 0.002 HIS I 13 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 2550) covalent geometry : angle 0.65955 ( 3430) hydrogen bonds : bond 0.04520 ( 40) hydrogen bonds : angle 6.07927 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.054 Fit side-chains REVERT: D 11 GLU cc_start: 0.7087 (tt0) cc_final: 0.6354 (tp30) REVERT: D 16 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7796 (ttmt) REVERT: E 11 GLU cc_start: 0.7434 (tt0) cc_final: 0.6819 (tp30) REVERT: F 13 HIS cc_start: 0.8207 (p90) cc_final: 0.7332 (p90) REVERT: F 15 GLN cc_start: 0.8446 (tt0) cc_final: 0.8122 (tt0) REVERT: G 13 HIS cc_start: 0.7984 (p90) cc_final: 0.7687 (p90) REVERT: I 34 LEU cc_start: 0.8959 (tp) cc_final: 0.8650 (tm) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.3562 time to fit residues: 19.3836 Evaluate side-chains 57 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS B 13 HIS I 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.120256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090317 restraints weight = 2648.653| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.66 r_work: 0.3235 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2550 Z= 0.123 Angle : 0.604 8.661 3430 Z= 0.301 Chirality : 0.062 0.130 390 Planarity : 0.002 0.007 440 Dihedral : 6.021 31.082 350 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.20 % Allowed : 27.60 % Favored : 69.20 % 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 are not related in a simple way. whole: -1.33 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR G 10 PHE 0.004 0.001 PHE D 20 HIS 0.005 0.002 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 2550) covalent geometry : angle 0.60400 ( 3430) hydrogen bonds : bond 0.03918 ( 40) hydrogen bonds : angle 5.97924 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.096 Fit side-chains REVERT: B 41 ILE cc_start: 0.8363 (mp) cc_final: 0.7869 (mt) REVERT: D 11 GLU cc_start: 0.7025 (tt0) cc_final: 0.6323 (tm-30) REVERT: D 16 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7821 (ttmt) REVERT: E 11 GLU cc_start: 0.7445 (tt0) cc_final: 0.6839 (tp30) REVERT: F 13 HIS cc_start: 0.8140 (p90) cc_final: 0.7567 (p90) REVERT: F 15 GLN cc_start: 0.8405 (tt0) cc_final: 0.8134 (tt0) REVERT: G 13 HIS cc_start: 0.7903 (p90) cc_final: 0.7582 (p90) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.3936 time to fit residues: 22.2202 Evaluate side-chains 60 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS E 14 HIS I 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097478 restraints weight = 2632.696| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.68 r_work: 0.3334 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2550 Z= 0.083 Angle : 0.564 8.784 3430 Z= 0.277 Chirality : 0.060 0.125 390 Planarity : 0.001 0.007 440 Dihedral : 5.445 26.186 350 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 3.20 % Allowed : 27.60 % Favored : 69.20 % 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 are not related in a simple way. whole: -1.31 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR G 10 PHE 0.003 0.000 PHE F 19 HIS 0.005 0.002 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 2550) covalent geometry : angle 0.56401 ( 3430) hydrogen bonds : bond 0.03428 ( 40) hydrogen bonds : angle 5.85216 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 902.76 seconds wall clock time: 16 minutes 2.27 seconds (962.27 seconds total)