Starting phenix.real_space_refine on Tue Aug 4 15:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.map" model { file = "/net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wa0_65795/08_2026/9wa0_65795.cif" } resolution = 3.09 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= 0.005 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 6 5.16 5 C 2904 2.51 5 N 750 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4506 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "E" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "A" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "F" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 751 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Time building chain proxies: 1.16, per 1000 atoms: 0.26 Number of scatterers: 4506 At special positions: 0 Unit cell: (81.84, 163.68, 38.13, 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 6 16.00 O 846 8.00 N 750 7.00 C 2904 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: 0.25 Conformation dependent library (CDL) restraints added in 97.9 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 23 sheets defined 0.0% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.538A pdb=" N MET B 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL D 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.328A pdb=" N ALA B 19 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 29 removed outlier: 6.442A pdb=" N ALA B 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL D 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN B 27 " --> pdb=" O VAL D 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.170A pdb=" N VAL B 32 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 55 through 62 removed outlier: 6.993A pdb=" N GLU A 61 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 55 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU D 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY B 57 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N THR D 60 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N THR B 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU D 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLU B 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.391A pdb=" N VAL B 65 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.287A pdb=" N GLU B 72 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.624A pdb=" N LYS B 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 92 through 98 removed outlier: 6.724A pdb=" N VAL B 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR D 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE B 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN D 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 107 removed outlier: 6.441A pdb=" N ARG B 104 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 106 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 105 " --> pdb=" O THR D 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.192A pdb=" N VAL B 121 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.478A pdb=" N MET E 13 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL F 16 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS E 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 27 removed outlier: 6.904A pdb=" N ILE E 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.765A pdb=" N HIS E 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.328A pdb=" N LEU E 58 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.283A pdb=" N VAL E 65 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 71 through 73 removed outlier: 6.245A pdb=" N GLU E 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 76 through 80 removed outlier: 9.497A pdb=" N LYS E 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N TRP C 79 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR E 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.438A pdb=" N ALA E 91 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL F 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.452A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 104 through 107 removed outlier: 6.502A pdb=" N TYR E 105 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.799A pdb=" N TYR E 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.621A pdb=" N THR E 118 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL F 121 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA E 120 " --> pdb=" O VAL F 121 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 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: 0.59 Time building geometry restraints manager: 0.34 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: 1423 1.34 - 1.45: 649 1.45 - 1.57: 2530 1.57 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 4614 Sorted by residual: bond pdb=" CG MET A 13 " pdb=" SD MET A 13 " ideal model delta sigma weight residual 1.803 1.753 0.050 2.50e-02 1.60e+03 4.00e+00 bond pdb=" CG MET D 13 " pdb=" SD MET D 13 " ideal model delta sigma weight residual 1.803 1.753 0.050 2.50e-02 1.60e+03 3.96e+00 bond pdb=" CG MET B 13 " pdb=" SD MET B 13 " ideal model delta sigma weight residual 1.803 1.753 0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CB THR B 119 " pdb=" CG2 THR B 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 bond pdb=" CB THR D 119 " pdb=" CG2 THR D 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.82e+00 ... (remaining 4609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 6123 2.03 - 4.05: 132 4.05 - 6.08: 18 6.08 - 8.10: 0 8.10 - 10.13: 3 Bond angle restraints: 6276 Sorted by residual: angle pdb=" CB MET B 13 " pdb=" CG MET B 13 " pdb=" SD MET B 13 " ideal model delta sigma weight residual 112.70 122.83 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET A 13 " pdb=" CG MET A 13 " pdb=" SD MET A 13 " ideal model delta sigma weight residual 112.70 122.81 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET D 13 " pdb=" CG MET D 13 " pdb=" SD MET D 13 " ideal model delta sigma weight residual 112.70 122.81 -10.11 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ILE E 84 " pdb=" CA ILE E 84 " pdb=" C ILE E 84 " ideal model delta sigma weight residual 112.96 109.83 3.13 1.00e+00 1.00e+00 9.77e+00 angle pdb=" N ILE C 84 " pdb=" CA ILE C 84 " pdb=" C ILE C 84 " ideal model delta sigma weight residual 112.96 109.85 3.11 1.00e+00 1.00e+00 9.68e+00 ... (remaining 6271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 2367 15.39 - 30.78: 250 30.78 - 46.18: 68 46.18 - 61.57: 30 61.57 - 76.96: 3 Dihedral angle restraints: 2718 sinusoidal: 1032 harmonic: 1686 Sorted by residual: dihedral pdb=" CA PHE B 87 " pdb=" C PHE B 87 " pdb=" N HIS B 88 " pdb=" CA HIS B 88 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE A 87 " pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE D 87 " pdb=" C PHE D 87 " pdb=" N HIS D 88 " pdb=" CA HIS D 88 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 2715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 390 0.031 - 0.062: 199 0.062 - 0.094: 69 0.094 - 0.125: 70 0.125 - 0.156: 4 Chirality restraints: 732 Sorted by residual: chirality pdb=" CB THR B 119 " pdb=" CA THR B 119 " pdb=" OG1 THR B 119 " pdb=" CG2 THR B 119 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 119 " pdb=" CA THR A 119 " pdb=" OG1 THR A 119 " pdb=" CG2 THR A 119 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CB THR D 119 " pdb=" CA THR D 119 " pdb=" OG1 THR D 119 " pdb=" CG2 THR D 119 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 729 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 100 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C SER B 100 " 0.031 2.00e-02 2.50e+03 pdb=" O SER B 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY B 101 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C SER A 100 " 0.030 2.00e-02 2.50e+03 pdb=" O SER A 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 101 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C SER D 100 " 0.030 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY D 101 " -0.010 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 862 2.80 - 3.32: 3682 3.32 - 3.85: 7732 3.85 - 4.37: 8532 4.37 - 4.90: 16285 Nonbonded interactions: 37093 Sorted by model distance: nonbonded pdb=" OE1 GLU E 72 " pdb=" NZ LYS C 70 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS E 70 " pdb=" OE1 GLU F 72 " model vdw 2.284 3.120 nonbonded pdb=" OD2 ASP E 74 " pdb=" OH TYR F 105 " model vdw 2.337 3.040 nonbonded pdb=" OH TYR E 105 " pdb=" OD2 ASP C 74 " model vdw 2.347 3.040 nonbonded pdb=" OD1 ASP B 99 " pdb=" NH2 ARG B 103 " model vdw 2.448 3.120 ... (remaining 37088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4614 Z= 0.175 Angle : 0.729 10.129 6276 Z= 0.403 Chirality : 0.051 0.156 732 Planarity : 0.004 0.042 780 Dihedral : 15.476 76.962 1626 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % 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: -2.94 (0.32), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 34 TYR 0.023 0.002 TYR F 114 PHE 0.015 0.002 PHE A 64 TRP 0.003 0.001 TRP D 79 HIS 0.006 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 4614) covalent geometry : angle 0.72928 / 0.40 ( 6276) hydrogen bonds : bond 0.16715 / 10.22 ( 51) hydrogen bonds : angle 9.93363 / 6.63 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 104 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8129 (ttm-80) REVERT: E 18 ASP cc_start: 0.7439 (m-30) cc_final: 0.6942 (t70) REVERT: A 72 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6808 (mt-10) REVERT: A 104 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8183 (ttm170) REVERT: C 18 ASP cc_start: 0.7677 (m-30) cc_final: 0.7159 (t70) REVERT: C 75 THR cc_start: 0.8757 (m) cc_final: 0.8235 (p) REVERT: D 13 MET cc_start: 0.6135 (ttm) cc_final: 0.5651 (ptt) REVERT: F 18 ASP cc_start: 0.7438 (m-30) cc_final: 0.6876 (t70) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1031 time to fit residues: 8.5471 Evaluate side-chains 62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 56 HIS B 90 HIS A 56 HIS A 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125117 restraints weight = 5468.958| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.76 r_work: 0.3546 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4614 Z= 0.229 Angle : 0.617 4.959 6276 Z= 0.337 Chirality : 0.050 0.126 732 Planarity : 0.004 0.024 780 Dihedral : 5.676 17.250 618 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.32 % Allowed : 15.84 % Favored : 79.84 % 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: -2.74 (0.33), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 34 TYR 0.016 0.002 TYR B 114 PHE 0.015 0.003 PHE C 87 TRP 0.005 0.002 TRP E 79 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 ( 4614) covalent geometry : angle 0.61716 / 0.34 ( 6276) hydrogen bonds : bond 0.03433 / 1.97 ( 51) hydrogen bonds : angle 6.10855 / 4.09 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: A 72 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 80 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (ttmt) REVERT: C 84 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6056 (mt) REVERT: D 72 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7144 (mt-10) REVERT: D 80 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (ttmt) outliers start: 21 outliers final: 10 residues processed: 80 average time/residue: 0.0698 time to fit residues: 7.1218 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 HIS D 56 HIS F 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.147232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128784 restraints weight = 5428.996| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.69 r_work: 0.3572 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4614 Z= 0.150 Angle : 0.510 3.717 6276 Z= 0.280 Chirality : 0.048 0.124 732 Planarity : 0.003 0.024 780 Dihedral : 5.117 17.011 618 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.12 % Allowed : 17.90 % Favored : 77.98 % 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: -2.71 (0.33), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.015 0.002 TYR E 114 PHE 0.011 0.002 PHE C 87 TRP 0.003 0.001 TRP D 79 HIS 0.003 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 4614) covalent geometry : angle 0.51032 / 0.28 ( 6276) hydrogen bonds : bond 0.02566 / 1.47 ( 51) hydrogen bonds : angle 5.48599 / 3.65 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.161 Fit side-chains REVERT: A 55 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8298 (tt) REVERT: A 80 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8356 (ttmt) REVERT: D 55 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7905 (tt) REVERT: D 66 GLU cc_start: 0.8160 (tt0) cc_final: 0.7449 (tm-30) REVERT: D 72 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7190 (mt-10) REVERT: D 80 LYS cc_start: 0.8725 (tptm) cc_final: 0.8459 (ttmt) REVERT: F 104 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7325 (mtt-85) outliers start: 20 outliers final: 12 residues processed: 76 average time/residue: 0.0860 time to fit residues: 8.0403 Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 HIS F 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124327 restraints weight = 5563.969| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.75 r_work: 0.3530 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4614 Z= 0.195 Angle : 0.560 3.838 6276 Z= 0.307 Chirality : 0.049 0.129 732 Planarity : 0.003 0.023 780 Dihedral : 5.380 18.266 618 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.97 % Allowed : 18.11 % Favored : 75.93 % 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: -2.78 (0.32), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.018 0.002 TYR F 78 PHE 0.013 0.003 PHE C 87 TRP 0.005 0.001 TRP B 79 HIS 0.004 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 4614) covalent geometry : angle 0.56044 / 0.31 ( 6276) hydrogen bonds : bond 0.02626 / 1.50 ( 51) hydrogen bonds : angle 5.28423 / 3.52 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.107 Fit side-chains REVERT: B 89 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: A 55 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8117 (tt) REVERT: D 55 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7976 (tt) REVERT: D 66 GLU cc_start: 0.8184 (tt0) cc_final: 0.7474 (tm-30) REVERT: D 72 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7332 (mt-10) REVERT: D 80 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8429 (ttmt) REVERT: D 89 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7160 (mt-10) outliers start: 29 outliers final: 18 residues processed: 81 average time/residue: 0.0601 time to fit residues: 6.1138 Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS F 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129054 restraints weight = 5543.414| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.60 r_work: 0.3563 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4614 Z= 0.144 Angle : 0.499 3.770 6276 Z= 0.275 Chirality : 0.047 0.125 732 Planarity : 0.003 0.020 780 Dihedral : 5.028 17.836 618 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.53 % Allowed : 19.34 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.32), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.014 0.001 TYR E 114 PHE 0.011 0.002 PHE C 87 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 4614) covalent geometry : angle 0.49940 / 0.27 ( 6276) hydrogen bonds : bond 0.02227 / 1.27 ( 51) hydrogen bonds : angle 5.03688 / 3.33 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.095 Fit side-chains REVERT: B 55 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8006 (tt) REVERT: B 66 GLU cc_start: 0.8216 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 89 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: D 12 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6195 (tp) REVERT: D 55 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8009 (tt) REVERT: D 66 GLU cc_start: 0.8175 (tt0) cc_final: 0.7499 (tm-30) REVERT: D 72 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7303 (mt-10) REVERT: D 80 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8493 (ttmt) REVERT: D 89 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: F 104 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7341 (mtt-85) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 0.0644 time to fit residues: 6.3679 Evaluate side-chains 90 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 60 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 0.0040 overall best weight: 4.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.143724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124680 restraints weight = 5591.814| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.75 r_work: 0.3528 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4614 Z= 0.189 Angle : 0.550 3.877 6276 Z= 0.302 Chirality : 0.048 0.131 732 Planarity : 0.003 0.020 780 Dihedral : 5.296 18.418 618 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 6.38 % Allowed : 18.52 % Favored : 75.10 % 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: -2.68 (0.32), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.018 0.002 TYR F 78 PHE 0.013 0.003 PHE C 87 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 4614) covalent geometry : angle 0.54995 / 0.30 ( 6276) hydrogen bonds : bond 0.02509 / 1.43 ( 51) hydrogen bonds : angle 5.01689 / 3.33 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.219 Fit side-chains REVERT: B 55 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 89 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: A 55 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 89 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7269 (mt-10) REVERT: D 12 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6165 (tp) REVERT: D 55 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8042 (tt) REVERT: D 80 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8453 (ttmt) REVERT: D 89 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7267 (mt-10) outliers start: 31 outliers final: 19 residues processed: 85 average time/residue: 0.0796 time to fit residues: 8.5794 Evaluate side-chains 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123524 restraints weight = 5525.100| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.74 r_work: 0.3525 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4614 Z= 0.209 Angle : 0.567 3.922 6276 Z= 0.311 Chirality : 0.049 0.132 732 Planarity : 0.003 0.020 780 Dihedral : 5.385 18.723 618 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 7.20 % Allowed : 17.90 % Favored : 74.90 % 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: -2.70 (0.31), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.018 0.002 TYR F 78 PHE 0.014 0.003 PHE C 87 TRP 0.005 0.001 TRP B 79 HIS 0.004 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 4614) covalent geometry : angle 0.56740 / 0.31 ( 6276) hydrogen bonds : bond 0.02552 / 1.46 ( 51) hydrogen bonds : angle 5.00090 / 3.32 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.175 Fit side-chains REVERT: B 89 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: A 55 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 89 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: D 12 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6325 (tp) REVERT: D 55 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8070 (tt) REVERT: D 72 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 80 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8446 (ttmt) REVERT: D 89 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7235 (mt-10) outliers start: 35 outliers final: 26 residues processed: 88 average time/residue: 0.0766 time to fit residues: 8.5851 Evaluate side-chains 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 37 optimal weight: 0.0470 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127860 restraints weight = 5538.364| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.79 r_work: 0.3587 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4614 Z= 0.112 Angle : 0.469 3.684 6276 Z= 0.259 Chirality : 0.047 0.128 732 Planarity : 0.003 0.021 780 Dihedral : 4.839 17.604 618 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.35 % Allowed : 19.96 % Favored : 74.69 % 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: -2.54 (0.33), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.013 0.001 TYR E 114 PHE 0.009 0.002 PHE C 87 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 4614) covalent geometry : angle 0.46903 / 0.26 ( 6276) hydrogen bonds : bond 0.02008 / 1.14 ( 51) hydrogen bonds : angle 4.83415 / 3.18 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.168 Fit side-chains REVERT: B 12 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6258 (tp) REVERT: B 55 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7965 (tt) REVERT: B 89 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: E 84 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6102 (mt) REVERT: A 55 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8083 (tt) REVERT: A 89 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: D 55 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7942 (tt) REVERT: D 72 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 80 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8487 (ttmt) REVERT: D 89 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7218 (mt-10) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.0914 time to fit residues: 9.5217 Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 5 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125431 restraints weight = 5550.524| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.73 r_work: 0.3551 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4614 Z= 0.166 Angle : 0.523 3.829 6276 Z= 0.287 Chirality : 0.048 0.129 732 Planarity : 0.003 0.020 780 Dihedral : 5.131 18.312 618 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 6.38 % Allowed : 19.96 % Favored : 73.66 % 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: -2.58 (0.32), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 21 TYR 0.014 0.002 TYR E 114 PHE 0.012 0.002 PHE C 87 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 4614) covalent geometry : angle 0.52313 / 0.29 ( 6276) hydrogen bonds : bond 0.02261 / 1.31 ( 51) hydrogen bonds : angle 4.82551 / 3.19 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.100 Fit side-chains REVERT: B 12 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6252 (tp) REVERT: B 89 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: E 84 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6160 (mt) REVERT: A 55 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 89 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7276 (mt-10) REVERT: D 12 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6292 (tp) REVERT: D 55 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8074 (tt) REVERT: D 72 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7311 (mt-10) REVERT: D 80 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8480 (ttmt) REVERT: D 89 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7231 (mt-10) outliers start: 31 outliers final: 22 residues processed: 86 average time/residue: 0.0718 time to fit residues: 7.6182 Evaluate side-chains 101 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122770 restraints weight = 5573.920| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.76 r_work: 0.3514 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4614 Z= 0.221 Angle : 0.583 3.934 6276 Z= 0.318 Chirality : 0.049 0.133 732 Planarity : 0.003 0.021 780 Dihedral : 5.442 18.903 618 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 6.79 % Allowed : 19.96 % Favored : 73.25 % 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: -2.66 (0.31), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 21 TYR 0.018 0.002 TYR F 78 PHE 0.014 0.003 PHE C 87 TRP 0.005 0.002 TRP B 79 HIS 0.004 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 ( 4614) covalent geometry : angle 0.58305 / 0.32 ( 6276) hydrogen bonds : bond 0.02561 / 1.50 ( 51) hydrogen bonds : angle 4.93069 / 3.27 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.101 Fit side-chains REVERT: B 12 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6158 (tp) REVERT: B 89 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: A 12 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6809 (tt) REVERT: A 55 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 89 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: D 12 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6300 (tp) REVERT: D 55 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8073 (tt) REVERT: D 80 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8441 (ttmt) REVERT: D 89 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7281 (mt-10) outliers start: 33 outliers final: 24 residues processed: 88 average time/residue: 0.0537 time to fit residues: 5.9452 Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 0.0000 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127921 restraints weight = 5609.056| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.77 r_work: 0.3583 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4614 Z= 0.114 Angle : 0.470 3.681 6276 Z= 0.259 Chirality : 0.046 0.125 732 Planarity : 0.003 0.020 780 Dihedral : 4.846 17.426 618 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 6.38 % Allowed : 19.75 % Favored : 73.87 % 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: -2.52 (0.33), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 21 TYR 0.012 0.001 TYR E 114 PHE 0.010 0.002 PHE C 87 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.11 ( 4614) covalent geometry : angle 0.47016 / 0.26 ( 6276) hydrogen bonds : bond 0.01982 / 1.13 ( 51) hydrogen bonds : angle 4.79238 / 3.16 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.82 seconds wall clock time: 20 minutes 19.30 seconds (1219.30 seconds total)