Starting phenix.real_space_refine on Tue Feb 11 18:47:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dso_8910/02_2025/6dso_8910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dso_8910/02_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_8910/02_2025/6dso_8910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dso_8910/02_2025/6dso_8910.map" model { file = "/net/cci-nas-00/data/ceres_data/6dso_8910/02_2025/6dso_8910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dso_8910/02_2025/6dso_8910.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.93, per 1000 atoms: 0.60 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: 1.35 Conformation dependent library (CDL) restraints added in 847.8 milliseconds 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: 1.12 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: 1.75 Time building geometry restraints manager: 1.63 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: 0.02 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: 0.390 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- 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= 0.561 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.003 TRP K 17 HIS 0.002 0.001 HIS D 36 PHE 0.021 0.005 PHE E 10 TYR 0.015 0.003 TYR C 20 ARG 0.005 0.001 ARG C 46 *********************** 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 : 0.699 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: 0.7777 (mtpm) 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: 0.8413 (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: 0.7843 (t0) REVERT: C 24 LYS cc_start: 0.7983 (mttt) cc_final: 0.7358 (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: 0.8455 (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: 0.7523 (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: 0.7263 (mtpm) REVERT: E 56 LYS cc_start: 0.8178 (mttt) cc_final: 0.7904 (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: 0.7831 (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: 0.7484 (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: 0.7610 (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: 0.8060 (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: 1.6587 time to fit residues: 336.2528 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 : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 K 40 ASN L 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.110951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.097011 restraints weight = 9897.201| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.52 r_work: 0.3588 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6804 Z= 0.181 Angle : 0.516 6.007 9108 Z= 0.296 Chirality : 0.042 0.118 744 Planarity : 0.004 0.039 1236 Dihedral : 4.738 17.760 900 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP H 17 HIS 0.002 0.001 HIS H 36 PHE 0.013 0.001 PHE B 5 TYR 0.009 0.001 TYR H 20 ARG 0.005 0.001 ARG F 46 *********************** 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 179 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8277 (mttt) cc_final: 0.7784 (mtpm) REVERT: B 24 LYS cc_start: 0.8269 (mttt) cc_final: 0.7505 (mtpp) REVERT: B 45 GLN cc_start: 0.8660 (mt0) cc_final: 0.7983 (mt0) REVERT: C 22 ASP cc_start: 0.8195 (t0) cc_final: 0.7714 (t0) REVERT: C 24 LYS cc_start: 0.7732 (mttt) cc_final: 0.7051 (mtpp) REVERT: C 25 GLU cc_start: 0.8569 (mp0) cc_final: 0.8229 (mp0) REVERT: C 38 ARG cc_start: 0.6645 (ttt180) cc_final: 0.6431 (ttm-80) REVERT: C 45 GLN cc_start: 0.8261 (mt0) cc_final: 0.7860 (mt0) REVERT: D 22 ASP cc_start: 0.8447 (t0) cc_final: 0.8086 (t0) REVERT: D 24 LYS cc_start: 0.7639 (mttt) cc_final: 0.7179 (mtpm) REVERT: D 45 GLN cc_start: 0.8413 (mt0) cc_final: 0.8032 (mt0) REVERT: D 56 LYS cc_start: 0.8218 (mttt) cc_final: 0.7987 (ttmt) REVERT: D 66 GLU cc_start: 0.8391 (pt0) cc_final: 0.8169 (pt0) REVERT: E 24 LYS cc_start: 0.7579 (mttt) cc_final: 0.7063 (mtpm) REVERT: F 24 LYS cc_start: 0.7493 (mttt) cc_final: 0.6951 (mtpp) REVERT: F 34 TYR cc_start: 0.8002 (m-80) cc_final: 0.7737 (m-80) REVERT: G 22 ASP cc_start: 0.8461 (t0) cc_final: 0.7839 (t0) REVERT: G 24 LYS cc_start: 0.7453 (mttt) cc_final: 0.7251 (mttp) REVERT: G 45 GLN cc_start: 0.8154 (mt0) cc_final: 0.7600 (mt0) REVERT: H 24 LYS cc_start: 0.7925 (mttt) cc_final: 0.6862 (mtpm) REVERT: H 25 GLU cc_start: 0.8248 (mp0) cc_final: 0.6971 (mp0) REVERT: H 45 GLN cc_start: 0.7931 (mt0) cc_final: 0.7711 (mt0) REVERT: I 56 LYS cc_start: 0.8279 (mttt) cc_final: 0.7863 (ttmm) REVERT: J 24 LYS cc_start: 0.7433 (mttt) cc_final: 0.6665 (mtpt) REVERT: J 25 GLU cc_start: 0.8651 (mp0) cc_final: 0.7841 (mp0) REVERT: K 16 MET cc_start: 0.8821 (mtt) cc_final: 0.8381 (mtp) REVERT: K 24 LYS cc_start: 0.7612 (mttt) cc_final: 0.6866 (mtpt) REVERT: K 46 ARG cc_start: 0.8303 (tpt90) cc_final: 0.5677 (mtt-85) REVERT: L 11 GLN cc_start: 0.9232 (mt0) cc_final: 0.8843 (mt0) REVERT: L 16 MET cc_start: 0.8738 (mtt) cc_final: 0.8478 (mtp) REVERT: L 24 LYS cc_start: 0.8001 (mttt) cc_final: 0.7106 (mtpp) REVERT: L 46 ARG cc_start: 0.8194 (tpt90) cc_final: 0.5441 (mtt-85) REVERT: L 56 LYS cc_start: 0.8404 (mttt) cc_final: 0.8197 (mttt) REVERT: L 62 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8442 (mt-10) outliers start: 12 outliers final: 1 residues processed: 170 average time/residue: 1.7656 time to fit residues: 310.2132 Evaluate side-chains 147 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.0020 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.105191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.091573 restraints weight = 10151.352| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.49 r_work: 0.3506 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2366 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= 0.383 Angle : 0.591 4.258 9108 Z= 0.342 Chirality : 0.044 0.116 744 Planarity : 0.003 0.029 1236 Dihedral : 4.795 16.223 900 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.12 % Allowed : 12.33 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP F 17 HIS 0.003 0.001 HIS L 36 PHE 0.018 0.002 PHE F 5 TYR 0.012 0.002 TYR A 34 ARG 0.004 0.001 ARG E 46 *********************** 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 176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 23 MET cc_start: 0.8967 (mtm) cc_final: 0.8748 (mtm) REVERT: A 24 LYS cc_start: 0.8358 (mttt) cc_final: 0.7850 (mtpm) REVERT: B 24 LYS cc_start: 0.8277 (mttt) cc_final: 0.7557 (mtpp) REVERT: B 25 GLU cc_start: 0.8877 (mp0) cc_final: 0.8606 (mp0) REVERT: B 29 LYS cc_start: 0.8750 (tttt) cc_final: 0.8271 (ttpt) REVERT: B 38 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7621 (ttm-80) REVERT: B 45 GLN cc_start: 0.8685 (mt0) cc_final: 0.8356 (mt0) REVERT: C 22 ASP cc_start: 0.8256 (t0) cc_final: 0.7779 (t0) REVERT: C 23 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8262 (mtm) REVERT: C 24 LYS cc_start: 0.7876 (mttt) cc_final: 0.7182 (mtpp) REVERT: C 25 GLU cc_start: 0.8625 (mp0) cc_final: 0.8240 (mp0) REVERT: C 45 GLN cc_start: 0.8315 (mt0) cc_final: 0.7944 (mt0) REVERT: D 24 LYS cc_start: 0.7659 (mttt) cc_final: 0.7174 (mtpm) REVERT: D 45 GLN cc_start: 0.8446 (mt0) cc_final: 0.8077 (mt0) REVERT: D 56 LYS cc_start: 0.8206 (mttt) cc_final: 0.7699 (ttmm) REVERT: D 66 GLU cc_start: 0.8671 (pt0) cc_final: 0.8282 (pt0) REVERT: E 24 LYS cc_start: 0.7653 (mttt) cc_final: 0.7135 (mtpm) REVERT: F 23 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8623 (mtt) REVERT: F 24 LYS cc_start: 0.7452 (mttt) cc_final: 0.6943 (mtpt) REVERT: F 34 TYR cc_start: 0.8085 (m-80) cc_final: 0.7798 (m-80) REVERT: F 38 ARG cc_start: 0.7314 (ttt180) cc_final: 0.7071 (ttt180) REVERT: F 59 ASP cc_start: 0.8991 (m-30) cc_final: 0.8639 (m-30) REVERT: G 22 ASP cc_start: 0.8488 (t0) cc_final: 0.7799 (t0) REVERT: G 24 LYS cc_start: 0.7482 (mttt) cc_final: 0.7026 (mtpm) REVERT: G 25 GLU cc_start: 0.8371 (mp0) cc_final: 0.8142 (mp0) REVERT: G 29 LYS cc_start: 0.7955 (tttt) cc_final: 0.7529 (tttm) REVERT: G 45 GLN cc_start: 0.8114 (mt0) cc_final: 0.7532 (mt0) REVERT: H 24 LYS cc_start: 0.7977 (mttt) cc_final: 0.6883 (mtpm) REVERT: H 25 GLU cc_start: 0.8252 (mp0) cc_final: 0.7005 (mp0) REVERT: H 45 GLN cc_start: 0.7984 (mt0) cc_final: 0.7685 (mt0) REVERT: I 23 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8717 (mtm) REVERT: I 24 LYS cc_start: 0.7843 (mttt) cc_final: 0.6982 (mtpm) REVERT: I 25 GLU cc_start: 0.8700 (mp0) cc_final: 0.7696 (mp0) REVERT: I 56 LYS cc_start: 0.8315 (mttt) cc_final: 0.7769 (ttmm) REVERT: J 24 LYS cc_start: 0.7566 (mttt) cc_final: 0.6678 (mtpt) REVERT: J 25 GLU cc_start: 0.8576 (mp0) cc_final: 0.7770 (mp0) REVERT: J 46 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8178 (tmt-80) REVERT: K 24 LYS cc_start: 0.7922 (mttt) cc_final: 0.7089 (mtpt) REVERT: K 38 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7062 (ttt-90) REVERT: K 46 ARG cc_start: 0.8534 (tpt90) cc_final: 0.5523 (mtt-85) REVERT: L 16 MET cc_start: 0.8869 (mtt) cc_final: 0.8498 (mtp) REVERT: L 22 ASP cc_start: 0.8915 (t0) cc_final: 0.8295 (t0) REVERT: L 24 LYS cc_start: 0.7967 (mttt) cc_final: 0.7038 (mtpm) REVERT: L 55 GLU cc_start: 0.8057 (tt0) cc_final: 0.6126 (pm20) REVERT: L 56 LYS cc_start: 0.8323 (mttt) cc_final: 0.7922 (mttt) REVERT: L 62 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8519 (mt-10) outliers start: 18 outliers final: 2 residues processed: 164 average time/residue: 1.8307 time to fit residues: 309.7162 Evaluate side-chains 157 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 I residue 23 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 46 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** J 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.106135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.092374 restraints weight = 10213.790| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.54 r_work: 0.3530 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6804 Z= 0.270 Angle : 0.531 4.362 9108 Z= 0.307 Chirality : 0.042 0.118 744 Planarity : 0.002 0.027 1236 Dihedral : 4.495 15.234 900 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.95 % Allowed : 13.72 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 28 HIS 0.002 0.001 HIS L 36 PHE 0.013 0.002 PHE F 5 TYR 0.007 0.001 TYR H 34 ARG 0.003 0.001 ARG E 46 *********************** 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 169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8361 (mttt) cc_final: 0.7864 (mtpm) REVERT: B 24 LYS cc_start: 0.8407 (mttt) cc_final: 0.7735 (mtpp) REVERT: B 25 GLU cc_start: 0.8932 (mp0) cc_final: 0.8675 (mp0) REVERT: B 38 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7560 (ttm-80) REVERT: B 45 GLN cc_start: 0.8653 (mt0) cc_final: 0.8328 (mt0) REVERT: B 62 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8629 (mm-30) REVERT: C 22 ASP cc_start: 0.8255 (t0) cc_final: 0.7806 (t0) REVERT: C 24 LYS cc_start: 0.7961 (mttt) cc_final: 0.7247 (mtpp) REVERT: C 25 GLU cc_start: 0.8670 (mp0) cc_final: 0.8244 (mp0) REVERT: C 45 GLN cc_start: 0.8323 (mt0) cc_final: 0.7888 (mt0) REVERT: D 24 LYS cc_start: 0.7646 (mttt) cc_final: 0.7194 (mtpm) REVERT: D 45 GLN cc_start: 0.8461 (mt0) cc_final: 0.8088 (mt0) REVERT: D 56 LYS cc_start: 0.8280 (mttt) cc_final: 0.7757 (ttmm) REVERT: D 66 GLU cc_start: 0.8592 (pt0) cc_final: 0.8314 (pt0) REVERT: E 24 LYS cc_start: 0.7540 (mttt) cc_final: 0.7012 (mtpm) REVERT: E 33 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7916 (mmtp) REVERT: F 23 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: F 24 LYS cc_start: 0.7572 (mttt) cc_final: 0.7085 (mtpm) REVERT: F 38 ARG cc_start: 0.7316 (ttt180) cc_final: 0.6901 (ttt90) REVERT: G 24 LYS cc_start: 0.7597 (mttt) cc_final: 0.7147 (mtpm) REVERT: G 29 LYS cc_start: 0.8006 (tttt) cc_final: 0.7597 (tttm) REVERT: G 45 GLN cc_start: 0.8095 (mt0) cc_final: 0.7520 (mt0) REVERT: H 22 ASP cc_start: 0.8461 (t0) cc_final: 0.8053 (t0) REVERT: H 24 LYS cc_start: 0.8180 (mttt) cc_final: 0.7106 (mtpm) REVERT: H 25 GLU cc_start: 0.8190 (mp0) cc_final: 0.6981 (mp0) REVERT: H 45 GLN cc_start: 0.7994 (mt0) cc_final: 0.7731 (mt0) REVERT: I 24 LYS cc_start: 0.7818 (mttt) cc_final: 0.7275 (mtpm) REVERT: I 25 GLU cc_start: 0.8763 (mp0) cc_final: 0.8408 (mp0) REVERT: I 56 LYS cc_start: 0.8317 (mttt) cc_final: 0.7878 (ttmm) REVERT: J 24 LYS cc_start: 0.7497 (mttt) cc_final: 0.6799 (mtpt) REVERT: J 25 GLU cc_start: 0.8745 (mp0) cc_final: 0.8494 (mp0) REVERT: K 16 MET cc_start: 0.8864 (mtt) cc_final: 0.8448 (mtp) REVERT: K 24 LYS cc_start: 0.7814 (mttt) cc_final: 0.6983 (mtpt) REVERT: K 38 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7263 (ttt-90) REVERT: K 55 GLU cc_start: 0.8137 (tt0) cc_final: 0.5926 (pm20) REVERT: L 16 MET cc_start: 0.8934 (mtt) cc_final: 0.8590 (mtp) REVERT: L 23 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8457 (mtm) REVERT: L 24 LYS cc_start: 0.7981 (mttt) cc_final: 0.7138 (mtpm) REVERT: L 55 GLU cc_start: 0.8158 (tt0) cc_final: 0.6352 (pm20) REVERT: L 56 LYS cc_start: 0.8351 (mttt) cc_final: 0.7974 (mttt) outliers start: 17 outliers final: 4 residues processed: 158 average time/residue: 1.8687 time to fit residues: 304.5663 Evaluate side-chains 153 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 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 11 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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** B 40 ASN D 40 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088498 restraints weight = 10406.904| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.53 r_work: 0.3450 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 6804 Z= 0.576 Angle : 0.678 4.798 9108 Z= 0.392 Chirality : 0.047 0.123 744 Planarity : 0.004 0.061 1236 Dihedral : 4.990 15.723 900 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.12 % Allowed : 14.93 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 17 HIS 0.005 0.002 HIS L 36 PHE 0.021 0.003 PHE E 3 TYR 0.017 0.002 TYR B 34 ARG 0.004 0.001 ARG A 46 *********************** 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 168 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (mp) REVERT: A 23 MET cc_start: 0.8934 (mtm) cc_final: 0.8712 (mtm) REVERT: A 24 LYS cc_start: 0.8451 (mttt) cc_final: 0.8070 (mtpm) REVERT: B 24 LYS cc_start: 0.8348 (mttt) cc_final: 0.7656 (mtpp) REVERT: B 29 LYS cc_start: 0.8898 (tttt) cc_final: 0.8421 (ttpt) REVERT: B 38 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7685 (ttm-80) REVERT: B 45 GLN cc_start: 0.8625 (mt0) cc_final: 0.8393 (mt0) REVERT: C 22 ASP cc_start: 0.8423 (t0) cc_final: 0.7932 (t0) REVERT: C 23 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8347 (mtm) REVERT: C 24 LYS cc_start: 0.8056 (mttt) cc_final: 0.7363 (mtpp) REVERT: C 25 GLU cc_start: 0.8661 (mp0) cc_final: 0.8249 (mp0) REVERT: C 45 GLN cc_start: 0.8276 (mt0) cc_final: 0.7914 (mt0) REVERT: D 24 LYS cc_start: 0.7644 (mttt) cc_final: 0.7196 (mtpm) REVERT: D 45 GLN cc_start: 0.8475 (mt0) cc_final: 0.8118 (mt0) REVERT: D 56 LYS cc_start: 0.8292 (mttt) cc_final: 0.7776 (ttmm) REVERT: D 66 GLU cc_start: 0.8748 (pt0) cc_final: 0.8426 (pt0) REVERT: E 24 LYS cc_start: 0.7813 (mttt) cc_final: 0.7315 (mtpm) REVERT: E 33 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8178 (mmtp) REVERT: F 23 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: F 24 LYS cc_start: 0.7610 (mttt) cc_final: 0.7150 (mtpm) REVERT: F 34 TYR cc_start: 0.8106 (m-80) cc_final: 0.7831 (m-80) REVERT: F 38 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7051 (ttt90) REVERT: G 24 LYS cc_start: 0.7676 (mttt) cc_final: 0.7203 (mtpm) REVERT: G 29 LYS cc_start: 0.7975 (tttt) cc_final: 0.7546 (tttm) REVERT: G 45 GLN cc_start: 0.8016 (mt0) cc_final: 0.7530 (mt0) REVERT: H 22 ASP cc_start: 0.8499 (t0) cc_final: 0.8115 (t0) REVERT: H 24 LYS cc_start: 0.8178 (mttt) cc_final: 0.7155 (mtpm) REVERT: H 25 GLU cc_start: 0.8379 (mp0) cc_final: 0.7078 (mp0) REVERT: H 45 GLN cc_start: 0.8082 (mt0) cc_final: 0.7805 (mt0) REVERT: I 24 LYS cc_start: 0.7928 (mttt) cc_final: 0.7061 (mtpm) REVERT: I 25 GLU cc_start: 0.8806 (mp0) cc_final: 0.7740 (mp0) REVERT: I 38 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7353 (ttt180) REVERT: J 24 LYS cc_start: 0.7625 (mttt) cc_final: 0.6934 (mtpt) REVERT: J 25 GLU cc_start: 0.8690 (mp0) cc_final: 0.8390 (mp0) REVERT: K 24 LYS cc_start: 0.7914 (mttt) cc_final: 0.7108 (mtpm) REVERT: K 38 ARG cc_start: 0.7714 (ttt180) cc_final: 0.7398 (tpp-160) REVERT: K 55 GLU cc_start: 0.8234 (tt0) cc_final: 0.6046 (pm20) REVERT: L 16 MET cc_start: 0.8921 (mtt) cc_final: 0.8556 (mtp) REVERT: L 22 ASP cc_start: 0.8984 (t0) cc_final: 0.8354 (t0) REVERT: L 23 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8504 (mtm) REVERT: L 24 LYS cc_start: 0.8030 (mttt) cc_final: 0.7183 (mtpm) REVERT: L 55 GLU cc_start: 0.8177 (tt0) cc_final: 0.6344 (pm20) REVERT: L 56 LYS cc_start: 0.8312 (mttt) cc_final: 0.7956 (mttt) REVERT: L 62 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8571 (mt-10) outliers start: 18 outliers final: 8 residues processed: 157 average time/residue: 1.9051 time to fit residues: 308.2692 Evaluate side-chains 159 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 E residue 33 LYS 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 5 PHE Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.106813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.093219 restraints weight = 9917.240| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.51 r_work: 0.3544 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6804 Z= 0.185 Angle : 0.506 5.159 9108 Z= 0.292 Chirality : 0.042 0.121 744 Planarity : 0.003 0.034 1236 Dihedral : 4.358 13.927 900 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.26 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 28 HIS 0.002 0.001 HIS I 36 PHE 0.010 0.001 PHE B 5 TYR 0.013 0.001 TYR D 34 ARG 0.003 0.000 ARG E 46 *********************** 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 158 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8396 (mttt) cc_final: 0.8022 (mtpm) REVERT: B 24 LYS cc_start: 0.8343 (mttt) cc_final: 0.7628 (mtpp) REVERT: B 25 GLU cc_start: 0.8910 (mp0) cc_final: 0.8644 (mp0) REVERT: B 38 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7641 (ttm-80) REVERT: B 45 GLN cc_start: 0.8616 (mt0) cc_final: 0.8364 (mt0) REVERT: C 22 ASP cc_start: 0.8241 (t0) cc_final: 0.7796 (t0) REVERT: C 24 LYS cc_start: 0.7940 (mttt) cc_final: 0.7219 (mtpp) REVERT: C 25 GLU cc_start: 0.8663 (mp0) cc_final: 0.8157 (mp0) REVERT: C 45 GLN cc_start: 0.8243 (mt0) cc_final: 0.7801 (mt0) REVERT: D 16 MET cc_start: 0.8460 (mtm) cc_final: 0.8243 (mtp) REVERT: D 24 LYS cc_start: 0.7685 (mttt) cc_final: 0.7213 (mtpm) REVERT: D 45 GLN cc_start: 0.8345 (mt0) cc_final: 0.7912 (mt0) REVERT: D 56 LYS cc_start: 0.8235 (mttt) cc_final: 0.7703 (ttmm) REVERT: D 66 GLU cc_start: 0.8569 (pt0) cc_final: 0.8258 (pt0) REVERT: E 24 LYS cc_start: 0.7574 (mttt) cc_final: 0.7013 (mtpm) REVERT: F 23 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8080 (mtm) REVERT: F 24 LYS cc_start: 0.7497 (mttt) cc_final: 0.7033 (mtpm) REVERT: F 34 TYR cc_start: 0.8000 (m-80) cc_final: 0.7736 (m-80) REVERT: F 59 ASP cc_start: 0.8866 (m-30) cc_final: 0.8664 (m-30) REVERT: G 24 LYS cc_start: 0.7597 (mttt) cc_final: 0.7101 (mtpm) REVERT: G 29 LYS cc_start: 0.7940 (tttt) cc_final: 0.7540 (tttp) REVERT: G 45 GLN cc_start: 0.7913 (mt0) cc_final: 0.7299 (mt0) REVERT: H 22 ASP cc_start: 0.8462 (t0) cc_final: 0.8087 (t0) REVERT: H 24 LYS cc_start: 0.8206 (mttt) cc_final: 0.7123 (mtpm) REVERT: H 25 GLU cc_start: 0.8178 (mp0) cc_final: 0.6950 (mp0) REVERT: I 24 LYS cc_start: 0.7852 (mttt) cc_final: 0.7233 (mtpm) REVERT: I 25 GLU cc_start: 0.8771 (mp0) cc_final: 0.8395 (mp0) REVERT: J 24 LYS cc_start: 0.7459 (mttt) cc_final: 0.6743 (mtpt) REVERT: J 25 GLU cc_start: 0.8713 (mp0) cc_final: 0.8395 (mp0) REVERT: J 66 GLU cc_start: 0.8450 (pt0) cc_final: 0.8149 (pt0) REVERT: K 23 MET cc_start: 0.9275 (mtm) cc_final: 0.8863 (mpp) REVERT: K 24 LYS cc_start: 0.7719 (mttt) cc_final: 0.6870 (mtpt) REVERT: K 38 ARG cc_start: 0.7699 (ttt180) cc_final: 0.7284 (tpp-160) REVERT: K 55 GLU cc_start: 0.8076 (tt0) cc_final: 0.5785 (pm20) REVERT: L 16 MET cc_start: 0.8885 (mtt) cc_final: 0.8537 (mtp) REVERT: L 22 ASP cc_start: 0.8940 (t0) cc_final: 0.8291 (t0) REVERT: L 24 LYS cc_start: 0.7938 (mttt) cc_final: 0.7098 (mtpm) REVERT: L 55 GLU cc_start: 0.8153 (tt0) cc_final: 0.6291 (pm20) REVERT: L 56 LYS cc_start: 0.8355 (mttt) cc_final: 0.7999 (mttt) outliers start: 13 outliers final: 2 residues processed: 147 average time/residue: 1.9096 time to fit residues: 290.0558 Evaluate side-chains 142 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.102312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.089071 restraints weight = 10296.972| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.55 r_work: 0.3466 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 6804 Z= 0.494 Angle : 0.638 5.260 9108 Z= 0.368 Chirality : 0.046 0.121 744 Planarity : 0.003 0.033 1236 Dihedral : 4.793 15.310 900 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.43 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.15), 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 TRP 0.011 0.002 TRP F 17 HIS 0.004 0.002 HIS L 36 PHE 0.017 0.002 PHE E 3 TYR 0.014 0.002 TYR D 34 ARG 0.004 0.001 ARG L 18 *********************** 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 163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8688 (mp) REVERT: A 24 LYS cc_start: 0.8444 (mttt) cc_final: 0.8040 (mtpm) REVERT: B 23 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8557 (mtm) REVERT: B 24 LYS cc_start: 0.8343 (mttt) cc_final: 0.7659 (mtpp) REVERT: B 29 LYS cc_start: 0.8897 (tttt) cc_final: 0.8425 (ttpt) REVERT: B 38 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7672 (ttm-80) REVERT: B 45 GLN cc_start: 0.8588 (mt0) cc_final: 0.8332 (mt0) REVERT: C 22 ASP cc_start: 0.8380 (t0) cc_final: 0.7973 (t0) REVERT: C 23 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: C 24 LYS cc_start: 0.8059 (mttt) cc_final: 0.6922 (mtpp) REVERT: C 25 GLU cc_start: 0.8678 (mp0) cc_final: 0.7395 (mp0) REVERT: C 45 GLN cc_start: 0.8273 (mt0) cc_final: 0.7926 (mt0) REVERT: D 24 LYS cc_start: 0.7720 (mttt) cc_final: 0.7249 (mtpm) REVERT: D 45 GLN cc_start: 0.8471 (mt0) cc_final: 0.8085 (mt0) REVERT: D 56 LYS cc_start: 0.8323 (mttt) cc_final: 0.7804 (ttmm) REVERT: D 66 GLU cc_start: 0.8730 (pt0) cc_final: 0.8387 (pt0) REVERT: E 24 LYS cc_start: 0.7600 (mttt) cc_final: 0.7014 (mtpm) REVERT: E 29 LYS cc_start: 0.8330 (tttt) cc_final: 0.7974 (ttpp) REVERT: F 23 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8243 (mtm) REVERT: F 24 LYS cc_start: 0.7478 (mttt) cc_final: 0.7002 (mtpm) REVERT: F 34 TYR cc_start: 0.8125 (m-80) cc_final: 0.7810 (m-80) REVERT: G 24 LYS cc_start: 0.7623 (mttt) cc_final: 0.7205 (mtpm) REVERT: G 29 LYS cc_start: 0.8004 (tttt) cc_final: 0.7603 (tttm) REVERT: G 45 GLN cc_start: 0.7969 (mt0) cc_final: 0.7457 (mt0) REVERT: H 22 ASP cc_start: 0.8485 (t0) cc_final: 0.8090 (t0) REVERT: H 24 LYS cc_start: 0.8168 (mttt) cc_final: 0.7137 (mtpm) REVERT: H 25 GLU cc_start: 0.8246 (mp0) cc_final: 0.7034 (mp0) REVERT: H 45 GLN cc_start: 0.8083 (mt0) cc_final: 0.7807 (mt0) REVERT: I 24 LYS cc_start: 0.7829 (mttt) cc_final: 0.6980 (mtpm) REVERT: I 25 GLU cc_start: 0.8768 (mp0) cc_final: 0.7672 (mp0) REVERT: I 33 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8253 (mttm) REVERT: J 24 LYS cc_start: 0.7522 (mttt) cc_final: 0.6823 (mtpt) REVERT: J 25 GLU cc_start: 0.8725 (mp0) cc_final: 0.8432 (mp0) REVERT: K 24 LYS cc_start: 0.7895 (mttt) cc_final: 0.7158 (mtpm) REVERT: K 38 ARG cc_start: 0.7721 (ttt180) cc_final: 0.7384 (tpp-160) REVERT: K 55 GLU cc_start: 0.8149 (tt0) cc_final: 0.5885 (pm20) REVERT: L 16 MET cc_start: 0.8911 (mtt) cc_final: 0.8507 (mtp) REVERT: L 22 ASP cc_start: 0.8989 (t0) cc_final: 0.8319 (t0) REVERT: L 23 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8577 (mtm) REVERT: L 24 LYS cc_start: 0.8017 (mttt) cc_final: 0.7198 (mtpm) REVERT: L 55 GLU cc_start: 0.8203 (tt0) cc_final: 0.6359 (pm20) REVERT: L 56 LYS cc_start: 0.8337 (mttt) cc_final: 0.7983 (mttt) REVERT: L 62 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8570 (mt-10) outliers start: 14 outliers final: 5 residues processed: 153 average time/residue: 1.9128 time to fit residues: 301.7976 Evaluate side-chains 157 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 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 52 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** 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 = 0.3857 r_free = 0.3857 target = 0.107727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.093979 restraints weight = 9880.551| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.58 r_work: 0.3559 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6804 Z= 0.162 Angle : 0.491 4.301 9108 Z= 0.285 Chirality : 0.042 0.123 744 Planarity : 0.002 0.031 1236 Dihedral : 4.246 14.498 900 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.56 % Allowed : 18.23 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.16), 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 TRP 0.007 0.001 TRP E 28 HIS 0.002 0.001 HIS H 36 PHE 0.009 0.001 PHE B 5 TYR 0.013 0.001 TYR L 34 ARG 0.003 0.000 ARG L 18 *********************** 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 152 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8449 (mttt) cc_final: 0.8010 (mtpm) REVERT: B 24 LYS cc_start: 0.8308 (mttt) cc_final: 0.7648 (mtpp) REVERT: B 25 GLU cc_start: 0.8858 (mp0) cc_final: 0.8609 (mp0) REVERT: B 38 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7607 (ttm-80) REVERT: C 22 ASP cc_start: 0.8172 (t0) cc_final: 0.7811 (t0) REVERT: C 24 LYS cc_start: 0.8147 (mttt) cc_final: 0.7025 (mtpp) REVERT: C 25 GLU cc_start: 0.8657 (mp0) cc_final: 0.7314 (mp0) REVERT: C 45 GLN cc_start: 0.8268 (mt0) cc_final: 0.7834 (mt0) REVERT: D 24 LYS cc_start: 0.7736 (mttt) cc_final: 0.7162 (mtpp) REVERT: D 45 GLN cc_start: 0.8364 (mt0) cc_final: 0.7939 (mt0) REVERT: D 56 LYS cc_start: 0.8293 (mttt) cc_final: 0.7760 (ttmm) REVERT: E 24 LYS cc_start: 0.7572 (mttt) cc_final: 0.6976 (mtpm) REVERT: E 29 LYS cc_start: 0.8279 (tttt) cc_final: 0.7925 (ttpp) REVERT: F 23 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8135 (mtm) REVERT: F 24 LYS cc_start: 0.7399 (mttt) cc_final: 0.6877 (mtpm) REVERT: F 34 TYR cc_start: 0.8018 (m-80) cc_final: 0.7755 (m-80) REVERT: G 24 LYS cc_start: 0.7869 (mttt) cc_final: 0.7374 (mtpm) REVERT: G 29 LYS cc_start: 0.7901 (tttt) cc_final: 0.7539 (tttp) REVERT: G 45 GLN cc_start: 0.7908 (mt0) cc_final: 0.7325 (mt0) REVERT: H 22 ASP cc_start: 0.8534 (t0) cc_final: 0.8164 (t0) REVERT: H 24 LYS cc_start: 0.8232 (mttt) cc_final: 0.7137 (mtpm) REVERT: H 25 GLU cc_start: 0.8197 (mp0) cc_final: 0.6960 (mp0) REVERT: I 24 LYS cc_start: 0.7898 (mttt) cc_final: 0.7055 (mtpm) REVERT: I 25 GLU cc_start: 0.8747 (mp0) cc_final: 0.7578 (mp0) REVERT: I 56 LYS cc_start: 0.8353 (mttm) cc_final: 0.7856 (ttmm) REVERT: I 66 GLU cc_start: 0.8359 (pt0) cc_final: 0.8137 (pt0) REVERT: J 24 LYS cc_start: 0.7473 (mttt) cc_final: 0.6765 (mtpt) REVERT: J 25 GLU cc_start: 0.8717 (mp0) cc_final: 0.8384 (mp0) REVERT: J 66 GLU cc_start: 0.8432 (pt0) cc_final: 0.8139 (pt0) REVERT: K 23 MET cc_start: 0.9170 (mtm) cc_final: 0.8860 (mpp) REVERT: K 24 LYS cc_start: 0.7732 (mttt) cc_final: 0.6815 (mtpt) REVERT: K 38 ARG cc_start: 0.7765 (ttt180) cc_final: 0.7359 (tpp-160) REVERT: K 55 GLU cc_start: 0.8110 (tt0) cc_final: 0.5802 (pm20) REVERT: L 16 MET cc_start: 0.8809 (mtt) cc_final: 0.8464 (mtp) REVERT: L 22 ASP cc_start: 0.8854 (t0) cc_final: 0.8136 (t0) REVERT: L 24 LYS cc_start: 0.7945 (mttt) cc_final: 0.7149 (mtpm) REVERT: L 55 GLU cc_start: 0.8130 (tt0) cc_final: 0.6242 (pm20) outliers start: 9 outliers final: 1 residues processed: 145 average time/residue: 1.8970 time to fit residues: 283.9247 Evaluate side-chains 142 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain J residue 23 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.101030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.087781 restraints weight = 10607.245| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.58 r_work: 0.3439 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.051 6804 Z= 0.606 Angle : 0.695 6.638 9108 Z= 0.401 Chirality : 0.048 0.122 744 Planarity : 0.004 0.030 1236 Dihedral : 4.987 15.893 900 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.08 % Allowed : 17.88 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP F 17 HIS 0.005 0.002 HIS L 36 PHE 0.021 0.002 PHE E 3 TYR 0.015 0.002 TYR D 34 ARG 0.004 0.001 ARG J 61 *********************** 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 163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 24 LYS cc_start: 0.8398 (mttt) cc_final: 0.8011 (mtpm) REVERT: B 23 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: B 24 LYS cc_start: 0.8385 (mttt) cc_final: 0.7700 (mtpp) REVERT: B 29 LYS cc_start: 0.8919 (tttt) cc_final: 0.8447 (ttpt) REVERT: B 38 ARG cc_start: 0.7975 (ttt180) cc_final: 0.7668 (ttm-80) REVERT: C 22 ASP cc_start: 0.8422 (t0) cc_final: 0.8017 (t0) REVERT: C 24 LYS cc_start: 0.8131 (mttt) cc_final: 0.7069 (mtpp) REVERT: C 25 GLU cc_start: 0.8627 (mp0) cc_final: 0.7424 (mp0) REVERT: C 45 GLN cc_start: 0.8309 (mt0) cc_final: 0.7974 (mt0) REVERT: D 24 LYS cc_start: 0.7818 (mttt) cc_final: 0.7223 (mtpp) REVERT: D 45 GLN cc_start: 0.8504 (mt0) cc_final: 0.8102 (mt0) REVERT: E 24 LYS cc_start: 0.7835 (mttt) cc_final: 0.7333 (mtpt) REVERT: E 29 LYS cc_start: 0.8340 (tttt) cc_final: 0.8030 (ttpp) REVERT: F 23 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8297 (mtm) REVERT: F 24 LYS cc_start: 0.7493 (mttt) cc_final: 0.7025 (mtpm) REVERT: F 34 TYR cc_start: 0.8169 (m-80) cc_final: 0.7891 (m-80) REVERT: G 8 GLU cc_start: 0.8353 (tt0) cc_final: 0.7797 (tp30) REVERT: G 24 LYS cc_start: 0.7727 (mttt) cc_final: 0.7319 (mtpm) REVERT: G 29 LYS cc_start: 0.8014 (tttt) cc_final: 0.7610 (tttm) REVERT: G 45 GLN cc_start: 0.8028 (mt0) cc_final: 0.7542 (mt0) REVERT: H 22 ASP cc_start: 0.8551 (t0) cc_final: 0.8158 (t0) REVERT: H 24 LYS cc_start: 0.8215 (mttt) cc_final: 0.7197 (mtpm) REVERT: H 25 GLU cc_start: 0.8283 (mp0) cc_final: 0.7088 (mp0) REVERT: H 45 GLN cc_start: 0.8111 (mt0) cc_final: 0.7837 (mt0) REVERT: I 24 LYS cc_start: 0.7863 (mttt) cc_final: 0.7044 (mtpm) REVERT: I 25 GLU cc_start: 0.8826 (mp0) cc_final: 0.7747 (mp0) REVERT: I 33 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8170 (mttm) REVERT: I 38 ARG cc_start: 0.7391 (ttt180) cc_final: 0.7110 (ttt180) REVERT: J 24 LYS cc_start: 0.7614 (mttt) cc_final: 0.6765 (mtpp) REVERT: J 25 GLU cc_start: 0.8692 (mp0) cc_final: 0.8271 (mp0) REVERT: K 23 MET cc_start: 0.9260 (mtm) cc_final: 0.8814 (mpp) REVERT: K 24 LYS cc_start: 0.7949 (mttt) cc_final: 0.7198 (mtpm) REVERT: K 38 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7347 (tpp-160) REVERT: K 55 GLU cc_start: 0.8258 (tt0) cc_final: 0.5996 (pm20) REVERT: L 16 MET cc_start: 0.8940 (mtt) cc_final: 0.8539 (mtp) REVERT: L 22 ASP cc_start: 0.8943 (t0) cc_final: 0.8235 (t0) REVERT: L 23 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8575 (mtm) REVERT: L 24 LYS cc_start: 0.7972 (mttt) cc_final: 0.7202 (mtpm) REVERT: L 55 GLU cc_start: 0.8235 (tt0) cc_final: 0.6413 (pm20) REVERT: L 62 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8590 (mt-10) REVERT: L 66 GLU cc_start: 0.8587 (tt0) cc_final: 0.8300 (tt0) outliers start: 12 outliers final: 6 residues processed: 156 average time/residue: 1.8923 time to fit residues: 304.7156 Evaluate side-chains 158 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 23 MET Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 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 58 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 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 ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3834 r_free = 0.3834 target = 0.106574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.092697 restraints weight = 10178.216| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.62 r_work: 0.3534 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6804 Z= 0.192 Angle : 0.518 4.814 9108 Z= 0.299 Chirality : 0.042 0.122 744 Planarity : 0.002 0.031 1236 Dihedral : 4.434 16.363 900 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.87 % Allowed : 20.31 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 17 HIS 0.002 0.001 HIS H 36 PHE 0.011 0.001 PHE F 5 TYR 0.011 0.001 TYR D 34 ARG 0.003 0.000 ARG E 46 ********************** 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 146 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8469 (mttt) cc_final: 0.8031 (mtpm) REVERT: B 24 LYS cc_start: 0.8408 (mttt) cc_final: 0.7756 (mtpp) REVERT: B 38 ARG cc_start: 0.7906 (ttt180) cc_final: 0.7624 (ttm-80) REVERT: C 22 ASP cc_start: 0.8186 (t0) cc_final: 0.7808 (t0) REVERT: C 24 LYS cc_start: 0.8160 (mttt) cc_final: 0.7139 (mtpp) REVERT: C 25 GLU cc_start: 0.8616 (mp0) cc_final: 0.7334 (mp0) REVERT: C 45 GLN cc_start: 0.8275 (mt0) cc_final: 0.7936 (mt0) REVERT: D 24 LYS cc_start: 0.7813 (mttt) cc_final: 0.7277 (mtpp) REVERT: D 45 GLN cc_start: 0.8368 (mt0) cc_final: 0.7922 (mt0) REVERT: E 24 LYS cc_start: 0.7808 (mttt) cc_final: 0.7276 (mtpm) REVERT: E 29 LYS cc_start: 0.8311 (tttt) cc_final: 0.7989 (ttpp) REVERT: F 23 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: F 24 LYS cc_start: 0.7438 (mttt) cc_final: 0.6896 (mtpm) REVERT: F 34 TYR cc_start: 0.8146 (m-80) cc_final: 0.7856 (m-80) REVERT: G 24 LYS cc_start: 0.7921 (mttt) cc_final: 0.7373 (mtpm) REVERT: G 29 LYS cc_start: 0.7897 (tttt) cc_final: 0.7537 (tttp) REVERT: G 45 GLN cc_start: 0.7928 (mt0) cc_final: 0.7355 (mt0) REVERT: H 22 ASP cc_start: 0.8553 (t0) cc_final: 0.8174 (t0) REVERT: H 24 LYS cc_start: 0.8272 (mttt) cc_final: 0.7166 (mtpm) REVERT: H 25 GLU cc_start: 0.8224 (mp0) cc_final: 0.6954 (mp0) REVERT: H 45 GLN cc_start: 0.7925 (mt0) cc_final: 0.7659 (mt0) REVERT: I 16 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: I 24 LYS cc_start: 0.7867 (mttt) cc_final: 0.7071 (mtpm) REVERT: I 25 GLU cc_start: 0.8749 (mp0) cc_final: 0.7693 (mp0) REVERT: I 33 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7677 (mttm) REVERT: I 56 LYS cc_start: 0.8489 (mttt) cc_final: 0.7954 (ttmm) REVERT: J 24 LYS cc_start: 0.7505 (mttt) cc_final: 0.6795 (mtpt) REVERT: J 25 GLU cc_start: 0.8682 (mp0) cc_final: 0.8367 (mp0) REVERT: J 66 GLU cc_start: 0.8489 (pt0) cc_final: 0.8179 (pt0) REVERT: K 23 MET cc_start: 0.9154 (mtm) cc_final: 0.8919 (mpp) REVERT: K 24 LYS cc_start: 0.7741 (mttt) cc_final: 0.6824 (mtpt) REVERT: K 38 ARG cc_start: 0.7814 (ttt180) cc_final: 0.7443 (tpp-160) REVERT: K 55 GLU cc_start: 0.8118 (tt0) cc_final: 0.5822 (pm20) REVERT: L 16 MET cc_start: 0.8825 (mtt) cc_final: 0.8461 (mtp) REVERT: L 22 ASP cc_start: 0.8741 (t0) cc_final: 0.8002 (t0) REVERT: L 24 LYS cc_start: 0.7983 (mttt) cc_final: 0.7188 (mtpm) REVERT: L 55 GLU cc_start: 0.8189 (tt0) cc_final: 0.6391 (pm20) outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 1.8920 time to fit residues: 277.3216 Evaluate side-chains 141 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 23 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN F 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090954 restraints weight = 10329.357| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.64 r_work: 0.3506 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6804 Z= 0.280 Angle : 0.555 4.801 9108 Z= 0.320 Chirality : 0.043 0.124 744 Planarity : 0.003 0.034 1236 Dihedral : 4.511 16.011 900 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.39 % Allowed : 19.62 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 28 HIS 0.002 0.001 HIS H 36 PHE 0.013 0.001 PHE F 5 TYR 0.014 0.001 TYR L 34 ARG 0.003 0.000 ARG E 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5946.76 seconds wall clock time: 105 minutes 5.81 seconds (6305.81 seconds total)