Starting phenix.real_space_refine on Fri Aug 22 17:32:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.map" model { file = "/net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dso_8910/08_2025/6dso_8910.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 24 5.16 5 C 4212 2.51 5 N 1128 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "C" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "D" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "F" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "G" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "H" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Time building chain proxies: 1.82, per 1000 atoms: 0.28 Number of scatterers: 6588 At special positions: 0 Unit cell: (128.25, 81, 54, 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 24 16.00 O 1224 8.00 N 1128 7.00 C 4212 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: 0.51 Conformation dependent library (CDL) restraints added in 412.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 6.241A pdb=" N PHE A 2 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE C 5 " --> pdb=" O PHE A 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY C 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 6 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C 2 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE E 5 " --> pdb=" O PHE C 2 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 4 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY E 7 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 6 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE E 2 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE G 5 " --> pdb=" O PHE E 2 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER E 4 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLY G 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 6 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE G 2 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE I 5 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER G 4 " --> pdb=" O PHE I 5 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLY I 7 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE G 6 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE I 2 " --> pdb=" O PHE K 3 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE K 5 " --> pdb=" O PHE I 2 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER I 4 " --> pdb=" O PHE K 5 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY K 7 " --> pdb=" O SER I 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE I 6 " --> pdb=" O GLY K 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.332A pdb=" N TYR A 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR C 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR E 20 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 20 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR I 20 " --> pdb=" O THR K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.808A pdb=" N TRP A 28 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP C 28 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 28 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP G 28 " --> pdb=" O LYS I 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP I 28 " --> pdb=" O LYS K 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.555A pdb=" N LYS C 33 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS E 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 35 " --> pdb=" O HIS E 36 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG E 38 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 37 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS I 33 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N HIS K 36 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 35 " --> pdb=" O HIS K 36 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ARG K 38 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 37 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.145A pdb=" N VAL A 51 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 51 " --> pdb=" O TRP E 52 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL E 51 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL G 51 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL I 51 " --> pdb=" O TRP K 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.416A pdb=" N LYS A 56 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS G 56 " --> pdb=" O ILE I 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 8 removed outlier: 6.237A pdb=" N PHE B 2 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE D 5 " --> pdb=" O PHE B 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER B 4 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY D 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 6 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE D 2 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE F 5 " --> pdb=" O PHE D 2 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER D 4 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY F 7 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 6 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE F 2 " --> pdb=" O PHE H 3 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE H 5 " --> pdb=" O PHE F 2 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F 4 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY H 7 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 6 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 2 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE J 5 " --> pdb=" O PHE H 2 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER H 4 " --> pdb=" O PHE J 5 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY J 7 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE H 6 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE J 2 " --> pdb=" O PHE L 3 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE L 5 " --> pdb=" O PHE J 2 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER J 4 " --> pdb=" O PHE L 5 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY L 7 " --> pdb=" O SER J 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE J 6 " --> pdb=" O GLY L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.296A pdb=" N TYR B 20 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR D 20 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR F 20 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR H 20 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR J 20 " --> pdb=" O THR L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.805A pdb=" N TRP B 28 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP D 28 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 28 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 28 " --> pdb=" O LYS J 29 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP J 28 " --> pdb=" O LYS L 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 38 removed outlier: 6.566A pdb=" N LYS D 33 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS F 36 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 35 " --> pdb=" O HIS F 36 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG F 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA D 37 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS J 33 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N HIS L 36 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE J 35 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG L 38 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA J 37 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53 removed outlier: 6.134A pdb=" N VAL B 51 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 51 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL F 51 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL H 51 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL J 51 " --> pdb=" O TRP L 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.414A pdb=" N LYS B 56 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS H 56 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 68 82 hydrogen bonds defined for protein. 246 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: 1.11 Time building geometry restraints manager: 0.73 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: 2142 1.34 - 1.45: 1472 1.45 - 1.56: 3142 1.56 - 1.68: 0 1.68 - 1.79: 48 Bond restraints: 6804 Sorted by residual: bond pdb=" CG ARG E 46 " pdb=" CD ARG E 46 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CG ARG G 46 " pdb=" CD ARG G 46 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CG ARG A 46 " pdb=" CD ARG A 46 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CG ARG I 46 " pdb=" CD ARG I 46 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CG ARG K 46 " pdb=" CD ARG K 46 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.55e+00 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 7517 1.02 - 2.04: 1125 2.04 - 3.07: 298 3.07 - 4.09: 97 4.09 - 5.11: 71 Bond angle restraints: 9108 Sorted by residual: angle pdb=" C GLY B 27 " pdb=" N TRP B 28 " pdb=" CA TRP B 28 " ideal model delta sigma weight residual 121.75 116.64 5.11 1.73e+00 3.34e-01 8.73e+00 angle pdb=" C GLY J 27 " pdb=" N TRP J 28 " pdb=" CA TRP J 28 " ideal model delta sigma weight residual 121.75 116.67 5.08 1.73e+00 3.34e-01 8.63e+00 angle pdb=" C GLY F 27 " pdb=" N TRP F 28 " pdb=" CA TRP F 28 " ideal model delta sigma weight residual 121.75 116.67 5.08 1.73e+00 3.34e-01 8.62e+00 angle pdb=" C GLY H 27 " pdb=" N TRP H 28 " pdb=" CA TRP H 28 " ideal model delta sigma weight residual 121.75 116.67 5.08 1.73e+00 3.34e-01 8.61e+00 angle pdb=" C GLY C 27 " pdb=" N TRP C 28 " pdb=" CA TRP C 28 " ideal model delta sigma weight residual 121.75 116.68 5.07 1.73e+00 3.34e-01 8.59e+00 ... (remaining 9103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.30: 3138 7.30 - 14.61: 483 14.61 - 21.91: 63 21.91 - 29.21: 0 29.21 - 36.52: 24 Dihedral angle restraints: 3708 sinusoidal: 1464 harmonic: 2244 Sorted by residual: dihedral pdb=" CA THR J 21 " pdb=" C THR J 21 " pdb=" N ASP J 22 " pdb=" CA ASP J 22 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR D 21 " pdb=" C THR D 21 " pdb=" N ASP D 22 " pdb=" CA ASP D 22 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR B 21 " pdb=" C THR B 21 " pdb=" N ASP B 22 " pdb=" CA ASP B 22 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 3705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 240 0.027 - 0.054: 208 0.054 - 0.080: 134 0.080 - 0.107: 142 0.107 - 0.134: 20 Chirality restraints: 744 Sorted by residual: chirality pdb=" CA TRP A 28 " pdb=" N TRP A 28 " pdb=" C TRP A 28 " pdb=" CB TRP A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA TRP L 28 " pdb=" N TRP L 28 " pdb=" C TRP L 28 " pdb=" CB TRP L 28 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA TRP I 28 " pdb=" N TRP I 28 " pdb=" C TRP I 28 " pdb=" CB TRP I 28 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 741 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU J 66 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C GLU J 66 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU J 66 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE J 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 66 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C GLU B 66 " -0.022 2.00e-02 2.50e+03 pdb=" O GLU B 66 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE B 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 66 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C GLU D 66 " -0.022 2.00e-02 2.50e+03 pdb=" O GLU D 66 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE D 67 " 0.008 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 2815 2.93 - 3.42: 5523 3.42 - 3.91: 11466 3.91 - 4.41: 13343 4.41 - 4.90: 24345 Nonbonded interactions: 57492 Sorted by model distance: nonbonded pdb=" O GLY A 49 " pdb=" NH2 ARG C 46 " model vdw 2.431 3.120 nonbonded pdb=" O GLY B 49 " pdb=" NH2 ARG D 46 " model vdw 2.435 3.120 nonbonded pdb=" O GLY E 49 " pdb=" NH2 ARG G 46 " model vdw 2.436 3.120 nonbonded pdb=" O GLY I 49 " pdb=" NH2 ARG K 46 " model vdw 2.437 3.120 nonbonded pdb=" O GLY C 49 " pdb=" NH2 ARG E 46 " model vdw 2.437 3.120 ... (remaining 57487 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' selection = chain 'K' selection = chain 'L' } 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: 0.800 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:9.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.048 6804 Z= 0.384 Angle : 0.942 5.111 9108 Z= 0.582 Chirality : 0.057 0.134 744 Planarity : 0.005 0.031 1236 Dihedral : 7.347 36.516 2316 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.13), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.10), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 46 TYR 0.015 0.003 TYR C 20 PHE 0.021 0.005 PHE E 10 TRP 0.012 0.003 TRP K 17 HIS 0.002 0.001 HIS D 36 Details of bonding type rmsd covalent geometry : bond 0.00869 ( 6804) covalent geometry : angle 0.94176 ( 9108) hydrogen bonds : bond 0.09118 ( 82) hydrogen bonds : angle 6.53772 ( 246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8582 (mtt) cc_final: 0.8354 (mtt) REVERT: A 24 LYS cc_start: 0.8096 (mttt) cc_final: 0.7202 (mtpm) REVERT: A 25 GLU cc_start: 0.8640 (mp0) cc_final: 0.6750 (pp20) REVERT: B 24 LYS cc_start: 0.8190 (mttt) cc_final: 0.7584 (mtpp) REVERT: B 29 LYS cc_start: 0.8737 (tttt) cc_final: 0.8412 (ttpt) REVERT: C 6 ILE cc_start: 0.8704 (mp) cc_final: 0.8496 (mt) REVERT: C 22 ASP cc_start: 0.8276 (t0) cc_final: 0.7841 (t0) REVERT: C 24 LYS cc_start: 0.7983 (mttt) cc_final: 0.7363 (mtpm) REVERT: C 38 ARG cc_start: 0.6707 (ttt180) cc_final: 0.6443 (ttm-80) REVERT: D 11 GLN cc_start: 0.8661 (mt0) cc_final: 0.8454 (mt0) REVERT: D 22 ASP cc_start: 0.8353 (t0) cc_final: 0.7987 (t0) REVERT: D 24 LYS cc_start: 0.7877 (mttt) cc_final: 0.7524 (mtpm) REVERT: D 56 LYS cc_start: 0.8087 (mttt) cc_final: 0.7656 (ttmm) REVERT: D 66 GLU cc_start: 0.8102 (pt0) cc_final: 0.7846 (pt0) REVERT: E 24 LYS cc_start: 0.7691 (mttt) cc_final: 0.7262 (mtpm) REVERT: E 56 LYS cc_start: 0.8178 (mttt) cc_final: 0.7905 (mttt) REVERT: F 24 LYS cc_start: 0.7764 (mttt) cc_final: 0.7325 (mtpt) REVERT: G 22 ASP cc_start: 0.8369 (t0) cc_final: 0.7833 (t0) REVERT: G 56 LYS cc_start: 0.7971 (mttt) cc_final: 0.7754 (mttt) REVERT: H 11 GLN cc_start: 0.8651 (mt0) cc_final: 0.8378 (mt0) REVERT: H 22 ASP cc_start: 0.8496 (t0) cc_final: 0.8186 (t0) REVERT: H 25 GLU cc_start: 0.8343 (mp0) cc_final: 0.7483 (mp0) REVERT: I 11 GLN cc_start: 0.8883 (mt0) cc_final: 0.8683 (mt0) REVERT: I 16 MET cc_start: 0.8293 (mtt) cc_final: 0.8028 (mtm) REVERT: I 38 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6915 (ttt90) REVERT: I 56 LYS cc_start: 0.8153 (mttt) cc_final: 0.7609 (ttmm) REVERT: J 25 GLU cc_start: 0.8571 (mp0) cc_final: 0.7875 (mp0) REVERT: K 16 MET cc_start: 0.8547 (mtt) cc_final: 0.8061 (mtp) REVERT: K 24 LYS cc_start: 0.7785 (mttt) cc_final: 0.7183 (mtpt) REVERT: K 46 ARG cc_start: 0.8022 (tpt90) cc_final: 0.5333 (mtt-85) REVERT: L 16 MET cc_start: 0.8503 (mtt) cc_final: 0.8255 (mtp) REVERT: L 22 ASP cc_start: 0.8722 (t0) cc_final: 0.8134 (t0) REVERT: L 24 LYS cc_start: 0.7961 (mttt) cc_final: 0.7281 (mtpp) REVERT: L 46 ARG cc_start: 0.8101 (tpt90) cc_final: 0.5619 (mtt-85) REVERT: L 56 LYS cc_start: 0.8214 (mttt) cc_final: 0.7998 (mttt) REVERT: L 62 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8163 (mt-10) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.7566 time to fit residues: 153.3161 Evaluate side-chains 140 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN E 11 GLN F 11 GLN F 45 GLN G 11 GLN K 11 GLN L 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097313 restraints weight = 9969.174| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.53 r_work: 0.3592 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6804 Z= 0.118 Angle : 0.513 5.669 9108 Z= 0.295 Chirality : 0.042 0.117 744 Planarity : 0.004 0.037 1236 Dihedral : 4.701 17.765 900 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.08 % Allowed : 11.98 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.38 (0.14), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.11), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 46 TYR 0.009 0.001 TYR H 20 PHE 0.013 0.001 PHE B 5 TRP 0.011 0.001 TRP H 17 HIS 0.002 0.001 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6804) covalent geometry : angle 0.51342 ( 9108) hydrogen bonds : bond 0.02910 ( 82) hydrogen bonds : angle 5.97712 ( 246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8283 (mttt) cc_final: 0.7785 (mtpm) REVERT: B 24 LYS cc_start: 0.8264 (mttt) cc_final: 0.7501 (mtpp) REVERT: B 45 GLN cc_start: 0.8665 (mt0) cc_final: 0.7983 (mt0) REVERT: C 22 ASP cc_start: 0.8187 (t0) cc_final: 0.7701 (t0) REVERT: C 24 LYS cc_start: 0.7719 (mttt) cc_final: 0.7042 (mtpp) REVERT: C 25 GLU cc_start: 0.8561 (mp0) cc_final: 0.8229 (mp0) REVERT: C 38 ARG cc_start: 0.6638 (ttt180) cc_final: 0.6421 (ttm-80) REVERT: C 45 GLN cc_start: 0.8262 (mt0) cc_final: 0.7857 (mt0) REVERT: D 16 MET cc_start: 0.8412 (mtm) cc_final: 0.8195 (mtp) REVERT: D 22 ASP cc_start: 0.8438 (t0) cc_final: 0.8080 (t0) REVERT: D 24 LYS cc_start: 0.7633 (mttt) cc_final: 0.7174 (mtpm) REVERT: D 45 GLN cc_start: 0.8421 (mt0) cc_final: 0.8016 (mt0) REVERT: D 56 LYS cc_start: 0.8240 (mttt) cc_final: 0.7985 (ttmt) REVERT: D 66 GLU cc_start: 0.8384 (pt0) cc_final: 0.8152 (pt0) REVERT: E 24 LYS cc_start: 0.7567 (mttt) cc_final: 0.7053 (mtpm) REVERT: F 24 LYS cc_start: 0.7477 (mttt) cc_final: 0.6933 (mtpp) REVERT: G 22 ASP cc_start: 0.8450 (t0) cc_final: 0.7812 (t0) REVERT: G 24 LYS cc_start: 0.7448 (mttt) cc_final: 0.7247 (mttp) REVERT: G 45 GLN cc_start: 0.8159 (mt0) cc_final: 0.7601 (mt0) REVERT: H 24 LYS cc_start: 0.7913 (mttt) cc_final: 0.6851 (mtpm) REVERT: H 25 GLU cc_start: 0.8240 (mp0) cc_final: 0.6964 (mp0) REVERT: H 45 GLN cc_start: 0.7929 (mt0) cc_final: 0.7710 (mt0) REVERT: I 56 LYS cc_start: 0.8275 (mttt) cc_final: 0.7857 (ttmm) REVERT: J 24 LYS cc_start: 0.7417 (mttt) cc_final: 0.6646 (mtpt) REVERT: J 25 GLU cc_start: 0.8640 (mp0) cc_final: 0.7827 (mp0) REVERT: K 16 MET cc_start: 0.8822 (mtt) cc_final: 0.8385 (mtp) REVERT: K 24 LYS cc_start: 0.7600 (mttt) cc_final: 0.6859 (mtpt) REVERT: K 46 ARG cc_start: 0.8306 (tpt90) cc_final: 0.5688 (mtt-85) REVERT: L 11 GLN cc_start: 0.9221 (mt0) cc_final: 0.8913 (mt0) REVERT: L 16 MET cc_start: 0.8735 (mtt) cc_final: 0.8479 (mtp) REVERT: L 24 LYS cc_start: 0.7988 (mttt) cc_final: 0.7094 (mtpp) REVERT: L 46 ARG cc_start: 0.8191 (tpt90) cc_final: 0.5436 (mtt-85) REVERT: L 56 LYS cc_start: 0.8402 (mttt) cc_final: 0.8192 (mttt) REVERT: L 62 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8436 (mt-10) outliers start: 12 outliers final: 1 residues processed: 171 average time/residue: 0.8214 time to fit residues: 145.1665 Evaluate side-chains 145 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.104001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090509 restraints weight = 10138.979| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.47 r_work: 0.3485 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 6804 Z= 0.330 Angle : 0.642 4.156 9108 Z= 0.373 Chirality : 0.045 0.118 744 Planarity : 0.003 0.030 1236 Dihedral : 4.979 16.818 900 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.30 % Allowed : 12.33 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.14), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.11), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 46 TYR 0.012 0.002 TYR B 34 PHE 0.023 0.002 PHE J 5 TRP 0.010 0.001 TRP F 17 HIS 0.004 0.002 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 6804) covalent geometry : angle 0.64231 ( 9108) hydrogen bonds : bond 0.04566 ( 82) hydrogen bonds : angle 5.91169 ( 246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 23 MET cc_start: 0.8972 (mtm) cc_final: 0.8742 (mtm) REVERT: A 24 LYS cc_start: 0.8409 (mttt) cc_final: 0.7923 (mtpm) REVERT: B 24 LYS cc_start: 0.8325 (mttt) cc_final: 0.7623 (mtpp) REVERT: B 25 GLU cc_start: 0.8882 (mp0) cc_final: 0.8611 (mp0) REVERT: B 29 LYS cc_start: 0.8904 (tttt) cc_final: 0.8446 (ttpt) REVERT: B 38 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7653 (ttm-80) REVERT: B 45 GLN cc_start: 0.8694 (mt0) cc_final: 0.8382 (mt0) REVERT: C 22 ASP cc_start: 0.8324 (t0) cc_final: 0.7858 (t0) REVERT: C 23 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8178 (mtm) REVERT: C 24 LYS cc_start: 0.7981 (mttt) cc_final: 0.7290 (mtpp) REVERT: C 25 GLU cc_start: 0.8646 (mp0) cc_final: 0.8267 (mp0) REVERT: C 45 GLN cc_start: 0.8400 (mt0) cc_final: 0.8076 (mt0) REVERT: D 45 GLN cc_start: 0.8480 (mt0) cc_final: 0.8121 (mt0) REVERT: D 56 LYS cc_start: 0.8296 (mttt) cc_final: 0.7793 (ttmm) REVERT: D 66 GLU cc_start: 0.8652 (pt0) cc_final: 0.8340 (pt0) REVERT: E 24 LYS cc_start: 0.7894 (mttt) cc_final: 0.7342 (mtpm) REVERT: F 23 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: F 24 LYS cc_start: 0.7550 (mttt) cc_final: 0.7046 (mtpt) REVERT: F 34 TYR cc_start: 0.8177 (m-80) cc_final: 0.7894 (m-80) REVERT: F 38 ARG cc_start: 0.7363 (ttt180) cc_final: 0.7157 (ttt180) REVERT: F 59 ASP cc_start: 0.9015 (m-30) cc_final: 0.8677 (m-30) REVERT: F 62 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8408 (mt-10) REVERT: G 22 ASP cc_start: 0.8535 (t0) cc_final: 0.7881 (t0) REVERT: G 23 MET cc_start: 0.8613 (mtt) cc_final: 0.8344 (mtt) REVERT: G 24 LYS cc_start: 0.7715 (mttt) cc_final: 0.7277 (mtmt) REVERT: G 29 LYS cc_start: 0.8026 (tttt) cc_final: 0.7592 (tttm) REVERT: G 45 GLN cc_start: 0.8058 (mt0) cc_final: 0.7583 (mt0) REVERT: H 22 ASP cc_start: 0.8531 (t0) cc_final: 0.8108 (t0) REVERT: H 24 LYS cc_start: 0.8044 (mttt) cc_final: 0.6958 (mtpm) REVERT: H 25 GLU cc_start: 0.8303 (mp0) cc_final: 0.7122 (mp0) REVERT: H 45 GLN cc_start: 0.8101 (mt0) cc_final: 0.7829 (mt0) REVERT: I 24 LYS cc_start: 0.7930 (mttt) cc_final: 0.7393 (mtpm) REVERT: I 25 GLU cc_start: 0.8752 (mp0) cc_final: 0.8466 (mp0) REVERT: J 24 LYS cc_start: 0.7632 (mttt) cc_final: 0.6858 (mtpt) REVERT: J 25 GLU cc_start: 0.8630 (mp0) cc_final: 0.7869 (mp0) REVERT: K 24 LYS cc_start: 0.7995 (mttt) cc_final: 0.7165 (mtpt) REVERT: K 38 ARG cc_start: 0.7664 (ttt180) cc_final: 0.7274 (tpp-160) REVERT: K 46 ARG cc_start: 0.8611 (tpt90) cc_final: 0.5683 (mpt-90) REVERT: L 16 MET cc_start: 0.8908 (mtt) cc_final: 0.8543 (mtp) REVERT: L 22 ASP cc_start: 0.8962 (t0) cc_final: 0.8371 (t0) REVERT: L 24 LYS cc_start: 0.8040 (mttt) cc_final: 0.7153 (mtpm) REVERT: L 29 LYS cc_start: 0.8169 (tttt) cc_final: 0.7934 (tttp) REVERT: L 45 GLN cc_start: 0.8549 (mt0) cc_final: 0.8309 (mt0) REVERT: L 55 GLU cc_start: 0.8141 (tt0) cc_final: 0.6253 (pm20) REVERT: L 56 LYS cc_start: 0.8429 (mttt) cc_final: 0.8030 (mttt) REVERT: L 62 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8535 (mt-10) outliers start: 19 outliers final: 3 residues processed: 162 average time/residue: 0.8517 time to fit residues: 142.2013 Evaluate side-chains 155 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain J residue 23 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 40 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.104478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.090923 restraints weight = 10183.402| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.51 r_work: 0.3499 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6804 Z= 0.236 Angle : 0.572 4.479 9108 Z= 0.331 Chirality : 0.044 0.119 744 Planarity : 0.003 0.034 1236 Dihedral : 4.672 15.718 900 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.60 % Allowed : 13.72 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.11), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.009 0.001 TYR B 34 PHE 0.015 0.002 PHE F 5 TRP 0.007 0.001 TRP A 17 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6804) covalent geometry : angle 0.57211 ( 9108) hydrogen bonds : bond 0.04055 ( 82) hydrogen bonds : angle 5.84530 ( 246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8396 (mttt) cc_final: 0.7938 (mtpm) REVERT: A 40 ASN cc_start: 0.8631 (m110) cc_final: 0.8371 (m110) REVERT: B 24 LYS cc_start: 0.8416 (mttt) cc_final: 0.7757 (mtpp) REVERT: B 29 LYS cc_start: 0.8790 (tttt) cc_final: 0.8321 (ttpt) REVERT: B 38 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7628 (ttm-80) REVERT: B 45 GLN cc_start: 0.8700 (mt0) cc_final: 0.8409 (mt0) REVERT: C 22 ASP cc_start: 0.8298 (t0) cc_final: 0.7856 (t0) REVERT: C 23 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: C 24 LYS cc_start: 0.7994 (mttt) cc_final: 0.7277 (mtpp) REVERT: C 25 GLU cc_start: 0.8664 (mp0) cc_final: 0.8209 (mp0) REVERT: C 45 GLN cc_start: 0.8338 (mt0) cc_final: 0.7964 (mt0) REVERT: D 24 LYS cc_start: 0.7642 (mttt) cc_final: 0.7199 (mtpm) REVERT: D 45 GLN cc_start: 0.8458 (mt0) cc_final: 0.8067 (mt0) REVERT: D 56 LYS cc_start: 0.8317 (mttt) cc_final: 0.7791 (ttmm) REVERT: D 66 GLU cc_start: 0.8616 (pt0) cc_final: 0.8283 (pt0) REVERT: E 24 LYS cc_start: 0.7759 (mttt) cc_final: 0.7243 (mtpm) REVERT: F 23 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: F 24 LYS cc_start: 0.7605 (mttt) cc_final: 0.7133 (mtpm) REVERT: F 34 TYR cc_start: 0.8143 (m-80) cc_final: 0.7932 (m-80) REVERT: F 38 ARG cc_start: 0.7351 (ttt180) cc_final: 0.6966 (ttt180) REVERT: F 59 ASP cc_start: 0.8982 (m-30) cc_final: 0.8653 (m-30) REVERT: G 24 LYS cc_start: 0.7676 (mttt) cc_final: 0.7247 (mtpm) REVERT: G 29 LYS cc_start: 0.7989 (tttt) cc_final: 0.7576 (tttm) REVERT: G 45 GLN cc_start: 0.7954 (mt0) cc_final: 0.7354 (mt0) REVERT: H 24 LYS cc_start: 0.8173 (mttt) cc_final: 0.7167 (mtpm) REVERT: H 25 GLU cc_start: 0.8191 (mp0) cc_final: 0.7039 (mp0) REVERT: H 45 GLN cc_start: 0.8086 (mt0) cc_final: 0.7808 (mt0) REVERT: I 24 LYS cc_start: 0.7925 (mttt) cc_final: 0.7033 (mtpm) REVERT: I 25 GLU cc_start: 0.8799 (mp0) cc_final: 0.7674 (mp0) REVERT: J 24 LYS cc_start: 0.7584 (mttt) cc_final: 0.6974 (mtpt) REVERT: K 24 LYS cc_start: 0.7925 (mttt) cc_final: 0.7114 (mtpt) REVERT: K 38 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7442 (tpp-160) REVERT: K 55 GLU cc_start: 0.8151 (tt0) cc_final: 0.5866 (pm20) REVERT: L 16 MET cc_start: 0.8965 (mtt) cc_final: 0.8592 (mtp) REVERT: L 22 ASP cc_start: 0.8944 (t0) cc_final: 0.8349 (t0) REVERT: L 23 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: L 24 LYS cc_start: 0.8015 (mttt) cc_final: 0.7125 (mtpm) REVERT: L 29 LYS cc_start: 0.8117 (tttt) cc_final: 0.7818 (tttp) REVERT: L 45 GLN cc_start: 0.8477 (mt0) cc_final: 0.8251 (mt0) REVERT: L 55 GLU cc_start: 0.8173 (tt0) cc_final: 0.6352 (pm20) REVERT: L 56 LYS cc_start: 0.8352 (mttt) cc_final: 0.7990 (mttt) outliers start: 15 outliers final: 3 residues processed: 156 average time/residue: 0.8352 time to fit residues: 134.3629 Evaluate side-chains 154 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.090653 restraints weight = 10263.399| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.56 r_work: 0.3491 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6804 Z= 0.237 Angle : 0.570 5.037 9108 Z= 0.330 Chirality : 0.043 0.119 744 Planarity : 0.003 0.036 1236 Dihedral : 4.586 15.069 900 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.43 % Allowed : 15.45 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.012 0.001 TYR A 34 PHE 0.015 0.002 PHE F 5 TRP 0.007 0.001 TRP C 17 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 6804) covalent geometry : angle 0.57046 ( 9108) hydrogen bonds : bond 0.04020 ( 82) hydrogen bonds : angle 5.81882 ( 246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 24 LYS cc_start: 0.8432 (mttt) cc_final: 0.8054 (mtpm) REVERT: B 24 LYS cc_start: 0.8383 (mttt) cc_final: 0.7709 (mtpp) REVERT: B 25 GLU cc_start: 0.8880 (mp0) cc_final: 0.8679 (mp0) REVERT: B 29 LYS cc_start: 0.8851 (tttt) cc_final: 0.8418 (ttpt) REVERT: B 38 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7670 (ttm-80) REVERT: B 45 GLN cc_start: 0.8601 (mt0) cc_final: 0.8313 (mt0) REVERT: C 22 ASP cc_start: 0.8327 (t0) cc_final: 0.7900 (t0) REVERT: C 23 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8247 (mtm) REVERT: C 24 LYS cc_start: 0.7995 (mttt) cc_final: 0.7283 (mtpp) REVERT: C 25 GLU cc_start: 0.8648 (mp0) cc_final: 0.8214 (mp0) REVERT: C 45 GLN cc_start: 0.8341 (mt0) cc_final: 0.7983 (mt0) REVERT: D 24 LYS cc_start: 0.7657 (mttt) cc_final: 0.7213 (mtpm) REVERT: D 45 GLN cc_start: 0.8464 (mt0) cc_final: 0.8076 (mt0) REVERT: D 56 LYS cc_start: 0.8278 (mttt) cc_final: 0.7750 (ttmm) REVERT: D 66 GLU cc_start: 0.8679 (pt0) cc_final: 0.8323 (pt0) REVERT: E 24 LYS cc_start: 0.7577 (mttt) cc_final: 0.7048 (mtpm) REVERT: F 23 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8092 (mtm) REVERT: F 24 LYS cc_start: 0.7491 (mttt) cc_final: 0.7020 (mtpm) REVERT: F 33 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7709 (mptt) REVERT: F 34 TYR cc_start: 0.8124 (m-80) cc_final: 0.7912 (m-80) REVERT: F 38 ARG cc_start: 0.7343 (ttt180) cc_final: 0.6972 (ttt180) REVERT: F 59 ASP cc_start: 0.8962 (m-30) cc_final: 0.8617 (m-30) REVERT: G 23 MET cc_start: 0.8594 (mtt) cc_final: 0.8330 (mtt) REVERT: G 24 LYS cc_start: 0.7585 (mttt) cc_final: 0.7142 (mtpm) REVERT: G 29 LYS cc_start: 0.7943 (tttt) cc_final: 0.7529 (tttm) REVERT: G 45 GLN cc_start: 0.7959 (mt0) cc_final: 0.7360 (mt0) REVERT: H 22 ASP cc_start: 0.8488 (t0) cc_final: 0.8098 (t0) REVERT: H 24 LYS cc_start: 0.8159 (mttt) cc_final: 0.7114 (mtpm) REVERT: H 25 GLU cc_start: 0.8205 (mp0) cc_final: 0.6992 (mp0) REVERT: H 45 GLN cc_start: 0.8075 (mt0) cc_final: 0.7797 (mt0) REVERT: I 24 LYS cc_start: 0.7881 (mttt) cc_final: 0.6992 (mtpm) REVERT: I 25 GLU cc_start: 0.8766 (mp0) cc_final: 0.7643 (mp0) REVERT: J 24 LYS cc_start: 0.7575 (mttt) cc_final: 0.7041 (mtpt) REVERT: J 25 GLU cc_start: 0.8673 (mp0) cc_final: 0.8290 (mp0) REVERT: K 16 MET cc_start: 0.8843 (mtt) cc_final: 0.8437 (mtp) REVERT: K 24 LYS cc_start: 0.7890 (mttt) cc_final: 0.7100 (mtpm) REVERT: K 38 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7362 (tpp-160) REVERT: K 55 GLU cc_start: 0.8159 (tt0) cc_final: 0.5928 (pm20) REVERT: L 16 MET cc_start: 0.8943 (mtt) cc_final: 0.8559 (mtp) REVERT: L 22 ASP cc_start: 0.8979 (t0) cc_final: 0.8362 (t0) REVERT: L 23 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8470 (mtm) REVERT: L 24 LYS cc_start: 0.7956 (mttt) cc_final: 0.7100 (mtpm) REVERT: L 29 LYS cc_start: 0.8082 (tttt) cc_final: 0.7790 (tttp) REVERT: L 45 GLN cc_start: 0.8460 (mt0) cc_final: 0.8210 (mt0) REVERT: L 55 GLU cc_start: 0.8186 (tt0) cc_final: 0.6345 (pm20) REVERT: L 56 LYS cc_start: 0.8340 (mttt) cc_final: 0.7988 (mttt) outliers start: 14 outliers final: 4 residues processed: 153 average time/residue: 0.9438 time to fit residues: 148.8016 Evaluate side-chains 154 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.104083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090673 restraints weight = 10246.965| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.51 r_work: 0.3495 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6804 Z= 0.215 Angle : 0.556 4.775 9108 Z= 0.321 Chirality : 0.043 0.121 744 Planarity : 0.003 0.032 1236 Dihedral : 4.522 14.545 900 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.43 % Allowed : 16.32 % Favored : 81.25 % 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 aren not related in a simple way. whole: -4.21 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.008 0.001 TYR B 34 PHE 0.014 0.002 PHE F 5 TRP 0.006 0.001 TRP E 28 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 6804) covalent geometry : angle 0.55577 ( 9108) hydrogen bonds : bond 0.03859 ( 82) hydrogen bonds : angle 5.76848 ( 246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 24 LYS cc_start: 0.8331 (mttt) cc_final: 0.7965 (mtpm) REVERT: B 24 LYS cc_start: 0.8365 (mttt) cc_final: 0.7682 (mtpp) REVERT: B 25 GLU cc_start: 0.8872 (mp0) cc_final: 0.8604 (mp0) REVERT: B 29 LYS cc_start: 0.8838 (tttt) cc_final: 0.8378 (ttpt) REVERT: B 38 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7630 (ttm-80) REVERT: B 45 GLN cc_start: 0.8562 (mt0) cc_final: 0.8288 (mt0) REVERT: C 22 ASP cc_start: 0.8310 (t0) cc_final: 0.7901 (t0) REVERT: C 23 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8127 (mtm) REVERT: C 24 LYS cc_start: 0.7986 (mttt) cc_final: 0.7261 (mtpp) REVERT: C 25 GLU cc_start: 0.8641 (mp0) cc_final: 0.8184 (mp0) REVERT: C 45 GLN cc_start: 0.8299 (mt0) cc_final: 0.7916 (mt0) REVERT: D 24 LYS cc_start: 0.7677 (mttt) cc_final: 0.7215 (mtpm) REVERT: D 45 GLN cc_start: 0.8415 (mt0) cc_final: 0.8009 (mt0) REVERT: D 56 LYS cc_start: 0.8257 (mttt) cc_final: 0.7722 (ttmm) REVERT: D 66 GLU cc_start: 0.8634 (pt0) cc_final: 0.8301 (pt0) REVERT: E 24 LYS cc_start: 0.7563 (mttt) cc_final: 0.7029 (mtpm) REVERT: F 23 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8123 (mtm) REVERT: F 24 LYS cc_start: 0.7449 (mttt) cc_final: 0.6971 (mtpm) REVERT: F 34 TYR cc_start: 0.8081 (m-80) cc_final: 0.7853 (m-80) REVERT: F 38 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7031 (ttt180) REVERT: F 59 ASP cc_start: 0.8978 (m-30) cc_final: 0.8645 (m-30) REVERT: G 23 MET cc_start: 0.8601 (mtt) cc_final: 0.8244 (mtt) REVERT: G 24 LYS cc_start: 0.7533 (mttt) cc_final: 0.7072 (mtpm) REVERT: G 29 LYS cc_start: 0.7915 (tttt) cc_final: 0.7510 (tttp) REVERT: G 45 GLN cc_start: 0.7904 (mt0) cc_final: 0.7282 (mt0) REVERT: H 22 ASP cc_start: 0.8444 (t0) cc_final: 0.8052 (t0) REVERT: H 24 LYS cc_start: 0.8143 (mttt) cc_final: 0.7108 (mtpm) REVERT: H 25 GLU cc_start: 0.8211 (mp0) cc_final: 0.6983 (mp0) REVERT: H 45 GLN cc_start: 0.7985 (mt0) cc_final: 0.7692 (mt0) REVERT: I 24 LYS cc_start: 0.7852 (mttt) cc_final: 0.6948 (mtpm) REVERT: I 25 GLU cc_start: 0.8759 (mp0) cc_final: 0.7598 (mp0) REVERT: J 24 LYS cc_start: 0.7538 (mttt) cc_final: 0.6940 (mtpt) REVERT: J 25 GLU cc_start: 0.8637 (mp0) cc_final: 0.8291 (mp0) REVERT: K 23 MET cc_start: 0.9252 (mtm) cc_final: 0.9013 (mpp) REVERT: K 24 LYS cc_start: 0.7725 (mttt) cc_final: 0.6917 (mtpm) REVERT: K 38 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7341 (tpp-160) REVERT: K 55 GLU cc_start: 0.8135 (tt0) cc_final: 0.5811 (pm20) REVERT: L 16 MET cc_start: 0.8916 (mtt) cc_final: 0.8539 (mtp) REVERT: L 22 ASP cc_start: 0.8925 (t0) cc_final: 0.8298 (t0) REVERT: L 23 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8467 (mtm) REVERT: L 24 LYS cc_start: 0.7972 (mttt) cc_final: 0.7087 (mtpm) REVERT: L 29 LYS cc_start: 0.8096 (tttt) cc_final: 0.7862 (tttp) REVERT: L 45 GLN cc_start: 0.8439 (mt0) cc_final: 0.8183 (mt0) REVERT: L 55 GLU cc_start: 0.8160 (tt0) cc_final: 0.6295 (pm20) REVERT: L 56 LYS cc_start: 0.8346 (mttt) cc_final: 0.7997 (mttt) outliers start: 14 outliers final: 5 residues processed: 152 average time/residue: 0.9529 time to fit residues: 149.2636 Evaluate side-chains 152 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.103448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.090055 restraints weight = 10232.599| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.55 r_work: 0.3476 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6804 Z= 0.266 Angle : 0.592 4.356 9108 Z= 0.342 Chirality : 0.044 0.123 744 Planarity : 0.003 0.032 1236 Dihedral : 4.655 15.030 900 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.91 % Allowed : 16.49 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 46 TYR 0.010 0.001 TYR B 34 PHE 0.016 0.002 PHE F 5 TRP 0.008 0.001 TRP C 17 HIS 0.004 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 6804) covalent geometry : angle 0.59208 ( 9108) hydrogen bonds : bond 0.04203 ( 82) hydrogen bonds : angle 5.79696 ( 246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 24 LYS cc_start: 0.8430 (mttt) cc_final: 0.8081 (mtpm) REVERT: B 24 LYS cc_start: 0.8350 (mttt) cc_final: 0.7652 (mtpp) REVERT: B 25 GLU cc_start: 0.8886 (mp0) cc_final: 0.8604 (mp0) REVERT: B 29 LYS cc_start: 0.8903 (tttt) cc_final: 0.8433 (ttpt) REVERT: B 38 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7676 (ttm-80) REVERT: B 45 GLN cc_start: 0.8583 (mt0) cc_final: 0.8301 (mt0) REVERT: C 22 ASP cc_start: 0.8353 (t0) cc_final: 0.7952 (t0) REVERT: C 23 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: C 24 LYS cc_start: 0.8076 (mttt) cc_final: 0.7357 (mtpp) REVERT: C 25 GLU cc_start: 0.8675 (mp0) cc_final: 0.8227 (mp0) REVERT: C 45 GLN cc_start: 0.8363 (mt0) cc_final: 0.8032 (mt0) REVERT: D 24 LYS cc_start: 0.7746 (mttt) cc_final: 0.7294 (mtpm) REVERT: D 45 GLN cc_start: 0.8489 (mt0) cc_final: 0.8117 (mt0) REVERT: D 56 LYS cc_start: 0.8333 (mttt) cc_final: 0.7813 (ttmm) REVERT: D 66 GLU cc_start: 0.8670 (pt0) cc_final: 0.8363 (pt0) REVERT: E 24 LYS cc_start: 0.7650 (mttt) cc_final: 0.7076 (mtpm) REVERT: F 23 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: F 24 LYS cc_start: 0.7525 (mttt) cc_final: 0.7061 (mtpm) REVERT: F 34 TYR cc_start: 0.8270 (m-80) cc_final: 0.8000 (m-80) REVERT: F 38 ARG cc_start: 0.7483 (ttt180) cc_final: 0.7099 (ttt90) REVERT: G 24 LYS cc_start: 0.7600 (mttt) cc_final: 0.7163 (mtpm) REVERT: G 29 LYS cc_start: 0.8004 (tttt) cc_final: 0.7594 (tttp) REVERT: G 45 GLN cc_start: 0.7982 (mt0) cc_final: 0.7476 (mt0) REVERT: H 22 ASP cc_start: 0.8511 (t0) cc_final: 0.8125 (t0) REVERT: H 24 LYS cc_start: 0.8194 (mttt) cc_final: 0.7159 (mtpm) REVERT: H 25 GLU cc_start: 0.8237 (mp0) cc_final: 0.7013 (mp0) REVERT: H 45 GLN cc_start: 0.8087 (mt0) cc_final: 0.7821 (mt0) REVERT: I 24 LYS cc_start: 0.7912 (mttt) cc_final: 0.7019 (mtpm) REVERT: I 25 GLU cc_start: 0.8810 (mp0) cc_final: 0.7672 (mp0) REVERT: J 24 LYS cc_start: 0.7623 (mttt) cc_final: 0.6891 (mtpt) REVERT: K 24 LYS cc_start: 0.7879 (mttt) cc_final: 0.7121 (mtpm) REVERT: K 38 ARG cc_start: 0.7721 (ttt180) cc_final: 0.7392 (tpp-160) REVERT: K 55 GLU cc_start: 0.8180 (tt0) cc_final: 0.5934 (pm20) REVERT: L 16 MET cc_start: 0.8953 (mtt) cc_final: 0.8576 (mtp) REVERT: L 22 ASP cc_start: 0.9037 (t0) cc_final: 0.8388 (t0) REVERT: L 23 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: L 24 LYS cc_start: 0.8052 (mttt) cc_final: 0.7217 (mtpm) REVERT: L 29 LYS cc_start: 0.8170 (tttt) cc_final: 0.7930 (tttp) REVERT: L 55 GLU cc_start: 0.8199 (tt0) cc_final: 0.6377 (pm20) REVERT: L 56 LYS cc_start: 0.8365 (mttt) cc_final: 0.8018 (mttt) outliers start: 11 outliers final: 5 residues processed: 148 average time/residue: 0.9268 time to fit residues: 141.3682 Evaluate side-chains 150 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.103449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090148 restraints weight = 10385.361| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.56 r_work: 0.3482 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6804 Z= 0.254 Angle : 0.587 5.144 9108 Z= 0.339 Chirality : 0.044 0.123 744 Planarity : 0.003 0.031 1236 Dihedral : 4.660 15.046 900 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.43 % Allowed : 16.84 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.36 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 46 TYR 0.010 0.001 TYR B 34 PHE 0.015 0.002 PHE E 67 TRP 0.007 0.001 TRP H 28 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 6804) covalent geometry : angle 0.58712 ( 9108) hydrogen bonds : bond 0.04164 ( 82) hydrogen bonds : angle 5.79243 ( 246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 23 MET cc_start: 0.9051 (mtm) cc_final: 0.8747 (mtm) REVERT: A 24 LYS cc_start: 0.8424 (mttt) cc_final: 0.7942 (mtpm) REVERT: B 24 LYS cc_start: 0.8411 (mttt) cc_final: 0.7727 (mtpp) REVERT: B 29 LYS cc_start: 0.8889 (tttt) cc_final: 0.8421 (ttpt) REVERT: B 38 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7648 (ttm-80) REVERT: C 22 ASP cc_start: 0.8334 (t0) cc_final: 0.7927 (t0) REVERT: C 23 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: C 24 LYS cc_start: 0.8040 (mttt) cc_final: 0.7321 (mtpp) REVERT: C 25 GLU cc_start: 0.8652 (mp0) cc_final: 0.8191 (mp0) REVERT: C 45 GLN cc_start: 0.8431 (mt0) cc_final: 0.8115 (mt0) REVERT: D 24 LYS cc_start: 0.7710 (mttt) cc_final: 0.7247 (mtpm) REVERT: D 45 GLN cc_start: 0.8449 (mt0) cc_final: 0.8057 (mt0) REVERT: D 56 LYS cc_start: 0.8282 (mttt) cc_final: 0.7756 (ttmm) REVERT: E 24 LYS cc_start: 0.7612 (mttt) cc_final: 0.7006 (mtpm) REVERT: F 23 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: F 24 LYS cc_start: 0.7486 (mttt) cc_final: 0.6997 (mtpm) REVERT: F 34 TYR cc_start: 0.8226 (m-80) cc_final: 0.8002 (m-80) REVERT: F 38 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7050 (ttt90) REVERT: G 24 LYS cc_start: 0.7649 (mttt) cc_final: 0.7191 (mtpm) REVERT: G 25 GLU cc_start: 0.8450 (mp0) cc_final: 0.8244 (mp0) REVERT: G 29 LYS cc_start: 0.7977 (tttt) cc_final: 0.7566 (tttp) REVERT: G 45 GLN cc_start: 0.7966 (mt0) cc_final: 0.7442 (mt0) REVERT: H 22 ASP cc_start: 0.8532 (t0) cc_final: 0.8145 (t0) REVERT: H 24 LYS cc_start: 0.8191 (mttt) cc_final: 0.7145 (mtpm) REVERT: H 25 GLU cc_start: 0.8202 (mp0) cc_final: 0.6993 (mp0) REVERT: H 45 GLN cc_start: 0.8066 (mt0) cc_final: 0.7791 (mt0) REVERT: I 24 LYS cc_start: 0.7879 (mttt) cc_final: 0.6988 (mtpm) REVERT: I 25 GLU cc_start: 0.8591 (mp0) cc_final: 0.7493 (mp0) REVERT: J 24 LYS cc_start: 0.7527 (mttt) cc_final: 0.6784 (mtpp) REVERT: J 25 GLU cc_start: 0.8601 (mp0) cc_final: 0.8290 (mp0) REVERT: K 23 MET cc_start: 0.9229 (mtm) cc_final: 0.8762 (mpp) REVERT: K 24 LYS cc_start: 0.7896 (mttt) cc_final: 0.7104 (mtpm) REVERT: K 38 ARG cc_start: 0.7711 (ttt180) cc_final: 0.7379 (tpp-160) REVERT: K 55 GLU cc_start: 0.8153 (tt0) cc_final: 0.5912 (pm20) REVERT: L 16 MET cc_start: 0.8938 (mtt) cc_final: 0.8562 (mtp) REVERT: L 22 ASP cc_start: 0.9008 (t0) cc_final: 0.8355 (t0) REVERT: L 23 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8504 (mtm) REVERT: L 24 LYS cc_start: 0.7943 (mttt) cc_final: 0.7080 (mtpm) REVERT: L 29 LYS cc_start: 0.8129 (tttt) cc_final: 0.7864 (tttp) REVERT: L 55 GLU cc_start: 0.8206 (tt0) cc_final: 0.6385 (pm20) REVERT: L 56 LYS cc_start: 0.8346 (mttt) cc_final: 0.8005 (mttt) outliers start: 14 outliers final: 6 residues processed: 148 average time/residue: 0.9077 time to fit residues: 138.5239 Evaluate side-chains 151 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN B 45 GLN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.105418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.091838 restraints weight = 10249.650| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.59 r_work: 0.3517 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6804 Z= 0.164 Angle : 0.531 4.589 9108 Z= 0.307 Chirality : 0.043 0.124 744 Planarity : 0.003 0.031 1236 Dihedral : 4.429 14.816 900 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.91 % Allowed : 17.71 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.31 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.012 0.001 TYR B 34 PHE 0.013 0.001 PHE E 67 TRP 0.007 0.001 TRP E 28 HIS 0.002 0.001 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6804) covalent geometry : angle 0.53069 ( 9108) hydrogen bonds : bond 0.03551 ( 82) hydrogen bonds : angle 5.62100 ( 246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 24 LYS cc_start: 0.8453 (mttt) cc_final: 0.7975 (mtpm) REVERT: B 23 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8601 (mtm) REVERT: B 24 LYS cc_start: 0.8362 (mttt) cc_final: 0.7688 (mtpp) REVERT: B 25 GLU cc_start: 0.8912 (mp0) cc_final: 0.8662 (mp0) REVERT: B 29 LYS cc_start: 0.8717 (tttt) cc_final: 0.8225 (ttpt) REVERT: B 38 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7652 (ttm-80) REVERT: C 22 ASP cc_start: 0.8287 (t0) cc_final: 0.7878 (t0) REVERT: C 24 LYS cc_start: 0.8033 (mttt) cc_final: 0.7318 (mtpp) REVERT: C 25 GLU cc_start: 0.8685 (mp0) cc_final: 0.8217 (mp0) REVERT: C 45 GLN cc_start: 0.8335 (mt0) cc_final: 0.8009 (mt0) REVERT: D 24 LYS cc_start: 0.7781 (mttt) cc_final: 0.7194 (mtpp) REVERT: D 45 GLN cc_start: 0.8486 (mt0) cc_final: 0.8053 (mt0) REVERT: D 56 LYS cc_start: 0.8309 (mttt) cc_final: 0.7794 (ttmm) REVERT: E 24 LYS cc_start: 0.7642 (mttt) cc_final: 0.7016 (mtpm) REVERT: F 23 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: F 24 LYS cc_start: 0.7459 (mttt) cc_final: 0.6985 (mtpm) REVERT: F 34 TYR cc_start: 0.8258 (m-80) cc_final: 0.8012 (m-80) REVERT: F 38 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7045 (ttt90) REVERT: G 24 LYS cc_start: 0.7808 (mttt) cc_final: 0.7285 (mtpm) REVERT: G 29 LYS cc_start: 0.7932 (tttt) cc_final: 0.7563 (tttp) REVERT: G 45 GLN cc_start: 0.7994 (mt0) cc_final: 0.7387 (mt0) REVERT: H 22 ASP cc_start: 0.8583 (t0) cc_final: 0.8225 (t0) REVERT: H 24 LYS cc_start: 0.8258 (mttt) cc_final: 0.7164 (mtpm) REVERT: H 25 GLU cc_start: 0.8217 (mp0) cc_final: 0.6985 (mp0) REVERT: H 45 GLN cc_start: 0.7989 (mt0) cc_final: 0.7736 (mt0) REVERT: I 24 LYS cc_start: 0.7937 (mttt) cc_final: 0.7113 (mtpm) REVERT: I 25 GLU cc_start: 0.8750 (mp0) cc_final: 0.7630 (mp0) REVERT: J 24 LYS cc_start: 0.7474 (mttt) cc_final: 0.6840 (mtpt) REVERT: K 23 MET cc_start: 0.9195 (mtm) cc_final: 0.8785 (mpp) REVERT: K 24 LYS cc_start: 0.7783 (mttt) cc_final: 0.6975 (mtpm) REVERT: K 38 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7356 (tpp-160) REVERT: K 55 GLU cc_start: 0.8131 (tt0) cc_final: 0.5829 (pm20) REVERT: L 16 MET cc_start: 0.8882 (mtt) cc_final: 0.8519 (mtp) REVERT: L 22 ASP cc_start: 0.8974 (t0) cc_final: 0.8321 (t0) REVERT: L 23 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: L 24 LYS cc_start: 0.7960 (mttt) cc_final: 0.7110 (mtpm) REVERT: L 29 LYS cc_start: 0.8127 (tttt) cc_final: 0.7884 (tttp) REVERT: L 55 GLU cc_start: 0.8211 (tt0) cc_final: 0.6416 (pm20) outliers start: 11 outliers final: 4 residues processed: 148 average time/residue: 0.8967 time to fit residues: 136.8072 Evaluate side-chains 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.103586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.090241 restraints weight = 10332.116| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.58 r_work: 0.3486 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6804 Z= 0.255 Angle : 0.600 5.909 9108 Z= 0.344 Chirality : 0.044 0.122 744 Planarity : 0.003 0.033 1236 Dihedral : 4.666 15.599 900 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.08 % Allowed : 18.58 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.38 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 46 TYR 0.012 0.001 TYR B 34 PHE 0.014 0.002 PHE F 5 TRP 0.008 0.001 TRP C 17 HIS 0.003 0.001 HIS L 36 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 6804) covalent geometry : angle 0.59970 ( 9108) hydrogen bonds : bond 0.04144 ( 82) hydrogen bonds : angle 5.68609 ( 246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 24 LYS cc_start: 0.8439 (mttt) cc_final: 0.8025 (mtpm) REVERT: B 23 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8562 (mtm) REVERT: B 24 LYS cc_start: 0.8375 (mttt) cc_final: 0.7711 (mtpp) REVERT: B 25 GLU cc_start: 0.8919 (mp0) cc_final: 0.8697 (mp0) REVERT: B 29 LYS cc_start: 0.8754 (tttt) cc_final: 0.8317 (ttpt) REVERT: B 38 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7692 (ttm-80) REVERT: C 22 ASP cc_start: 0.8275 (t0) cc_final: 0.7862 (t0) REVERT: C 24 LYS cc_start: 0.8112 (mttt) cc_final: 0.7017 (mtpp) REVERT: C 25 GLU cc_start: 0.8659 (mp0) cc_final: 0.7357 (mp0) REVERT: C 45 GLN cc_start: 0.8292 (mt0) cc_final: 0.7956 (mt0) REVERT: D 24 LYS cc_start: 0.7849 (mttt) cc_final: 0.7271 (mtpp) REVERT: D 45 GLN cc_start: 0.8483 (mt0) cc_final: 0.8077 (mt0) REVERT: D 56 LYS cc_start: 0.8309 (mttt) cc_final: 0.7796 (ttmm) REVERT: E 24 LYS cc_start: 0.7664 (mttt) cc_final: 0.7075 (mtpm) REVERT: F 23 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8189 (mtm) REVERT: F 24 LYS cc_start: 0.7521 (mttt) cc_final: 0.7010 (mtpm) REVERT: F 34 TYR cc_start: 0.8279 (m-80) cc_final: 0.8045 (m-80) REVERT: G 24 LYS cc_start: 0.7802 (mttt) cc_final: 0.7332 (mtpm) REVERT: G 29 LYS cc_start: 0.8005 (tttt) cc_final: 0.7600 (tttp) REVERT: G 45 GLN cc_start: 0.8002 (mt0) cc_final: 0.7400 (mt0) REVERT: H 22 ASP cc_start: 0.8627 (t0) cc_final: 0.8254 (t0) REVERT: H 24 LYS cc_start: 0.8222 (mttt) cc_final: 0.7177 (mtpm) REVERT: H 25 GLU cc_start: 0.8214 (mp0) cc_final: 0.7017 (mp0) REVERT: H 45 GLN cc_start: 0.8028 (mt0) cc_final: 0.7722 (mt0) REVERT: I 24 LYS cc_start: 0.7921 (mttt) cc_final: 0.7131 (mtpm) REVERT: I 25 GLU cc_start: 0.8775 (mp0) cc_final: 0.7700 (mp0) REVERT: I 33 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8145 (mttm) REVERT: J 24 LYS cc_start: 0.7506 (mttt) cc_final: 0.6930 (mtpt) REVERT: K 23 MET cc_start: 0.9246 (mtm) cc_final: 0.8880 (mpp) REVERT: K 24 LYS cc_start: 0.7767 (mttt) cc_final: 0.6977 (mtpm) REVERT: K 38 ARG cc_start: 0.7724 (ttt180) cc_final: 0.7396 (tpp-160) REVERT: K 55 GLU cc_start: 0.8160 (tt0) cc_final: 0.5921 (pm20) REVERT: L 16 MET cc_start: 0.8947 (mtt) cc_final: 0.8571 (mtp) REVERT: L 22 ASP cc_start: 0.9043 (t0) cc_final: 0.8405 (t0) REVERT: L 23 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8501 (mtm) REVERT: L 24 LYS cc_start: 0.7960 (mttt) cc_final: 0.7111 (mtpm) REVERT: L 29 LYS cc_start: 0.8169 (tttt) cc_final: 0.7935 (tttp) REVERT: L 55 GLU cc_start: 0.8217 (tt0) cc_final: 0.6403 (pm20) outliers start: 12 outliers final: 4 residues processed: 148 average time/residue: 0.8577 time to fit residues: 130.9140 Evaluate side-chains 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 45 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.107236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093620 restraints weight = 10104.602| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.60 r_work: 0.3558 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6804 Z= 0.121 Angle : 0.514 4.925 9108 Z= 0.296 Chirality : 0.042 0.125 744 Planarity : 0.002 0.033 1236 Dihedral : 4.328 16.287 900 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.56 % Allowed : 18.92 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.17), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 46 TYR 0.011 0.001 TYR B 34 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP I 17 HIS 0.002 0.001 HIS H 36 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6804) covalent geometry : angle 0.51407 ( 9108) hydrogen bonds : bond 0.03056 ( 82) hydrogen bonds : angle 5.49561 ( 246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.32 seconds wall clock time: 51 minutes 2.32 seconds (3062.32 seconds total)