Starting phenix.real_space_refine on Tue Mar 11 18:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dso_8910/03_2025/6dso_8910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dso_8910/03_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_8910/03_2025/6dso_8910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dso_8910/03_2025/6dso_8910.map" model { file = "/net/cci-nas-00/data/ceres_data/6dso_8910/03_2025/6dso_8910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dso_8910/03_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-5624/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: 4.27, per 1000 atoms: 0.65 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: 1.50 Conformation dependent library (CDL) restraints added in 933.7 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: 1.04 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: 1.79 Time building geometry restraints manager: 1.78 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: 0.480 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.120 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- 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 : 0.673 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: 1.6008 time to fit residues: 325.0175 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 : 0.670 ------------------------------------------------------------------------------- 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: 0.3589 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8278 (mttt) cc_final: 0.7787 (mtpm) REVERT: B 24 LYS cc_start: 0.8274 (mttt) cc_final: 0.7511 (mtpp) REVERT: B 45 GLN cc_start: 0.8661 (mt0) cc_final: 0.7988 (mt0) REVERT: C 22 ASP cc_start: 0.8198 (t0) cc_final: 0.7717 (t0) REVERT: C 24 LYS cc_start: 0.7743 (mttt) cc_final: 0.7061 (mtpp) REVERT: C 25 GLU cc_start: 0.8573 (mp0) cc_final: 0.8234 (mp0) REVERT: C 38 ARG cc_start: 0.6646 (ttt180) cc_final: 0.6432 (ttm-80) REVERT: C 45 GLN cc_start: 0.8265 (mt0) cc_final: 0.7865 (mt0) REVERT: D 22 ASP cc_start: 0.8450 (t0) cc_final: 0.8090 (t0) REVERT: D 24 LYS cc_start: 0.7652 (mttt) cc_final: 0.7191 (mtpm) REVERT: D 45 GLN cc_start: 0.8416 (mt0) cc_final: 0.8037 (mt0) REVERT: D 56 LYS cc_start: 0.8220 (mttt) cc_final: 0.7989 (ttmt) REVERT: D 66 GLU cc_start: 0.8396 (pt0) cc_final: 0.8173 (pt0) REVERT: E 24 LYS cc_start: 0.7588 (mttt) cc_final: 0.7072 (mtpm) REVERT: F 24 LYS cc_start: 0.7506 (mttt) cc_final: 0.6963 (mtpp) REVERT: F 34 TYR cc_start: 0.8006 (m-80) cc_final: 0.7742 (m-80) REVERT: G 22 ASP cc_start: 0.8464 (t0) cc_final: 0.7842 (t0) REVERT: G 24 LYS cc_start: 0.7462 (mttt) cc_final: 0.7259 (mttp) REVERT: G 45 GLN cc_start: 0.8157 (mt0) cc_final: 0.7605 (mt0) REVERT: H 24 LYS cc_start: 0.7936 (mttt) cc_final: 0.6871 (mtpm) REVERT: H 25 GLU cc_start: 0.8252 (mp0) cc_final: 0.6975 (mp0) REVERT: H 45 GLN cc_start: 0.7934 (mt0) cc_final: 0.7714 (mt0) REVERT: I 56 LYS cc_start: 0.8282 (mttt) cc_final: 0.7862 (ttmm) REVERT: J 24 LYS cc_start: 0.7445 (mttt) cc_final: 0.6675 (mtpt) REVERT: J 25 GLU cc_start: 0.8655 (mp0) cc_final: 0.7848 (mp0) REVERT: K 16 MET cc_start: 0.8822 (mtt) cc_final: 0.8383 (mtp) REVERT: K 24 LYS cc_start: 0.7622 (mttt) cc_final: 0.6875 (mtpt) REVERT: K 46 ARG cc_start: 0.8306 (tpt90) cc_final: 0.5679 (mtt-85) REVERT: L 11 GLN cc_start: 0.9233 (mt0) cc_final: 0.8844 (mt0) REVERT: L 16 MET cc_start: 0.8739 (mtt) cc_final: 0.8478 (mtp) REVERT: L 24 LYS cc_start: 0.8011 (mttt) cc_final: 0.7116 (mtpp) REVERT: L 46 ARG cc_start: 0.8199 (tpt90) cc_final: 0.5444 (mtt-85) REVERT: L 56 LYS cc_start: 0.8403 (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: 1.7195 time to fit residues: 302.3360 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 : 0.679 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.104691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091133 restraints weight = 10184.773| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.49 r_work: 0.3495 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 6804 Z= 0.431 Angle : 0.614 4.701 9108 Z= 0.356 Chirality : 0.044 0.117 744 Planarity : 0.003 0.029 1236 Dihedral : 4.884 16.200 900 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.30 % Allowed : 11.98 % Favored : 84.72 % 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: -4.23 (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 0.008 0.001 TRP F 17 HIS 0.004 0.002 HIS L 36 PHE 0.021 0.002 PHE J 5 TYR 0.012 0.002 TYR A 34 ARG 0.005 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: 19 poor density : 157 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 23 MET cc_start: 0.8975 (mtm) cc_final: 0.8745 (mtm) REVERT: A 24 LYS cc_start: 0.8360 (mttt) cc_final: 0.7853 (mtpm) REVERT: B 24 LYS cc_start: 0.8274 (mttt) cc_final: 0.7553 (mtpp) REVERT: B 25 GLU cc_start: 0.8911 (mp0) cc_final: 0.8649 (mp0) REVERT: B 29 LYS cc_start: 0.8823 (tttt) cc_final: 0.8364 (ttpt) REVERT: B 38 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7611 (ttm-80) REVERT: B 45 GLN cc_start: 0.8684 (mt0) cc_final: 0.8343 (mt0) REVERT: C 22 ASP cc_start: 0.8264 (t0) cc_final: 0.7799 (t0) REVERT: C 23 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: C 24 LYS cc_start: 0.7889 (mttt) cc_final: 0.7192 (mtpp) REVERT: C 25 GLU cc_start: 0.8614 (mp0) cc_final: 0.8225 (mp0) REVERT: C 45 GLN cc_start: 0.8312 (mt0) cc_final: 0.7951 (mt0) REVERT: D 22 ASP cc_start: 0.8354 (t0) cc_final: 0.8101 (t0) REVERT: D 24 LYS cc_start: 0.7640 (mttt) cc_final: 0.7177 (mtpm) REVERT: D 45 GLN cc_start: 0.8444 (mt0) cc_final: 0.8062 (mt0) REVERT: D 56 LYS cc_start: 0.8223 (mttt) cc_final: 0.7711 (ttmm) REVERT: D 66 GLU cc_start: 0.8659 (pt0) cc_final: 0.8301 (pt0) REVERT: E 24 LYS cc_start: 0.7699 (mttt) cc_final: 0.7185 (mtpm) REVERT: F 23 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: F 24 LYS cc_start: 0.7455 (mttt) cc_final: 0.6946 (mtpt) REVERT: F 34 TYR cc_start: 0.8097 (m-80) cc_final: 0.7803 (m-80) REVERT: F 38 ARG cc_start: 0.7323 (ttt180) cc_final: 0.7082 (ttt180) REVERT: F 59 ASP cc_start: 0.9000 (m-30) cc_final: 0.8637 (m-30) REVERT: G 22 ASP cc_start: 0.8503 (t0) cc_final: 0.7810 (t0) REVERT: G 24 LYS cc_start: 0.7642 (mttt) cc_final: 0.7196 (mtmt) REVERT: G 29 LYS cc_start: 0.7979 (tttt) cc_final: 0.7542 (tttm) REVERT: G 45 GLN cc_start: 0.8113 (mt0) cc_final: 0.7621 (mt0) REVERT: H 22 ASP cc_start: 0.8486 (t0) cc_final: 0.8081 (t0) REVERT: H 24 LYS cc_start: 0.7981 (mttt) cc_final: 0.6894 (mtpm) REVERT: H 25 GLU cc_start: 0.8251 (mp0) cc_final: 0.7007 (mp0) REVERT: H 45 GLN cc_start: 0.7993 (mt0) cc_final: 0.7695 (mt0) REVERT: I 24 LYS cc_start: 0.7845 (mttt) cc_final: 0.7284 (mtpm) REVERT: I 25 GLU cc_start: 0.8706 (mp0) cc_final: 0.8472 (mp0) REVERT: J 24 LYS cc_start: 0.7576 (mttt) cc_final: 0.6696 (mtpt) REVERT: J 25 GLU cc_start: 0.8577 (mp0) cc_final: 0.7777 (mp0) REVERT: K 24 LYS cc_start: 0.7929 (mttt) cc_final: 0.7084 (mtpt) REVERT: K 38 ARG cc_start: 0.7523 (ttt180) cc_final: 0.7191 (ttt-90) REVERT: K 46 ARG cc_start: 0.8533 (tpt90) cc_final: 0.5707 (mtt-85) REVERT: L 16 MET cc_start: 0.8887 (mtt) cc_final: 0.8515 (mtp) REVERT: L 22 ASP cc_start: 0.8972 (t0) cc_final: 0.8380 (t0) REVERT: L 23 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: L 24 LYS cc_start: 0.7974 (mttt) cc_final: 0.7037 (mtpm) REVERT: L 29 LYS cc_start: 0.8079 (tttt) cc_final: 0.7834 (tttp) REVERT: L 55 GLU cc_start: 0.8088 (tt0) cc_final: 0.6178 (pm20) REVERT: L 56 LYS cc_start: 0.8326 (mttt) cc_final: 0.7923 (mttt) REVERT: L 62 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8517 (mt-10) outliers start: 19 outliers final: 2 residues processed: 164 average time/residue: 1.8554 time to fit residues: 313.9787 Evaluate side-chains 154 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 J residue 23 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 0.0000 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3840 r_free = 0.3840 target = 0.106845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092911 restraints weight = 10169.700| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.56 r_work: 0.3538 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6804 Z= 0.239 Angle : 0.520 4.213 9108 Z= 0.301 Chirality : 0.042 0.118 744 Planarity : 0.002 0.034 1236 Dihedral : 4.447 15.065 900 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.95 % Allowed : 13.54 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.11 (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 H 52 HIS 0.002 0.001 HIS L 36 PHE 0.012 0.001 PHE F 5 TYR 0.007 0.001 TYR B 20 ARG 0.003 0.000 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 168 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8359 (mttt) cc_final: 0.7868 (mtpm) REVERT: B 24 LYS cc_start: 0.8406 (mttt) cc_final: 0.7731 (mtpp) REVERT: B 25 GLU cc_start: 0.8935 (mp0) cc_final: 0.8675 (mp0) REVERT: B 38 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7551 (ttm-80) REVERT: B 45 GLN cc_start: 0.8657 (mt0) cc_final: 0.8340 (mt0) REVERT: B 62 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8617 (mm-30) REVERT: C 22 ASP cc_start: 0.8258 (t0) cc_final: 0.7809 (t0) REVERT: C 24 LYS cc_start: 0.7936 (mttt) cc_final: 0.7223 (mtpp) REVERT: C 25 GLU cc_start: 0.8670 (mp0) cc_final: 0.8230 (mp0) REVERT: C 45 GLN cc_start: 0.8317 (mt0) cc_final: 0.7918 (mt0) REVERT: D 24 LYS cc_start: 0.7632 (mttt) cc_final: 0.7194 (mtpm) REVERT: D 45 GLN cc_start: 0.8468 (mt0) cc_final: 0.8081 (mt0) REVERT: D 56 LYS cc_start: 0.8285 (mttt) cc_final: 0.7757 (ttmm) REVERT: D 66 GLU cc_start: 0.8570 (pt0) cc_final: 0.8272 (pt0) REVERT: E 24 LYS cc_start: 0.7583 (mttt) cc_final: 0.7116 (mtpm) REVERT: E 33 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7895 (mmtp) REVERT: F 23 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8009 (mtt) REVERT: F 24 LYS cc_start: 0.7560 (mttt) cc_final: 0.7075 (mtpm) REVERT: F 38 ARG cc_start: 0.7325 (ttt180) cc_final: 0.6892 (ttt90) REVERT: G 24 LYS cc_start: 0.7667 (mttt) cc_final: 0.7228 (mtpm) REVERT: G 29 LYS cc_start: 0.8048 (tttt) cc_final: 0.7638 (tttm) REVERT: G 45 GLN cc_start: 0.8084 (mt0) cc_final: 0.7504 (mt0) REVERT: H 24 LYS cc_start: 0.8168 (mttt) cc_final: 0.7020 (mtpm) REVERT: H 25 GLU cc_start: 0.8173 (mp0) cc_final: 0.6906 (mp0) REVERT: H 45 GLN cc_start: 0.7983 (mt0) cc_final: 0.7715 (mt0) REVERT: I 24 LYS cc_start: 0.7873 (mttt) cc_final: 0.7048 (mtpm) REVERT: I 25 GLU cc_start: 0.8755 (mp0) cc_final: 0.7627 (mp0) REVERT: I 56 LYS cc_start: 0.8440 (mttt) cc_final: 0.7873 (ttmm) REVERT: J 24 LYS cc_start: 0.7478 (mttt) cc_final: 0.6755 (mtpt) REVERT: J 25 GLU cc_start: 0.8729 (mp0) cc_final: 0.8476 (mp0) REVERT: K 16 MET cc_start: 0.8835 (mtt) cc_final: 0.8414 (mtp) REVERT: K 24 LYS cc_start: 0.7789 (mttt) cc_final: 0.6958 (mtpt) REVERT: K 38 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7173 (ttt-90) REVERT: K 55 GLU cc_start: 0.8133 (tt0) cc_final: 0.5928 (pm20) REVERT: L 16 MET cc_start: 0.8937 (mtt) cc_final: 0.8558 (mtp) REVERT: L 23 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8493 (mtm) REVERT: L 24 LYS cc_start: 0.7909 (mttt) cc_final: 0.7057 (mtpm) REVERT: L 55 GLU cc_start: 0.8139 (tt0) cc_final: 0.6343 (pm20) REVERT: L 56 LYS cc_start: 0.8361 (mttt) cc_final: 0.7986 (mttt) outliers start: 17 outliers final: 4 residues processed: 158 average time/residue: 1.8972 time to fit residues: 309.0631 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 : 0.682 ------------------------------------------------------------------------------- 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: 0.0270 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN B 40 ASN ** 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** 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 = 0.3774 r_free = 0.3774 target = 0.102773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089485 restraints weight = 10297.230| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.54 r_work: 0.3471 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 6804 Z= 0.486 Angle : 0.634 4.500 9108 Z= 0.366 Chirality : 0.045 0.121 744 Planarity : 0.004 0.057 1236 Dihedral : 4.820 15.542 900 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.78 % Allowed : 15.97 % 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: -4.19 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 17 HIS 0.004 0.002 HIS K 36 PHE 0.018 0.002 PHE F 5 TYR 0.013 0.002 TYR B 34 ARG 0.003 0.001 ARG E 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 165 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 24 LYS cc_start: 0.8433 (mttt) cc_final: 0.8044 (mtpm) REVERT: B 24 LYS cc_start: 0.8409 (mttt) cc_final: 0.7721 (mtpp) REVERT: B 29 LYS cc_start: 0.8885 (tttt) cc_final: 0.8412 (ttpt) REVERT: B 38 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7702 (ttm-80) REVERT: B 45 GLN cc_start: 0.8616 (mt0) cc_final: 0.8326 (mt0) REVERT: C 22 ASP cc_start: 0.8319 (t0) cc_final: 0.7862 (t0) REVERT: C 23 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8260 (mtm) REVERT: C 24 LYS cc_start: 0.8016 (mttt) cc_final: 0.7300 (mtpp) REVERT: C 25 GLU cc_start: 0.8646 (mp0) cc_final: 0.8218 (mp0) REVERT: C 45 GLN cc_start: 0.8430 (mt0) cc_final: 0.8129 (mt0) REVERT: D 24 LYS cc_start: 0.7653 (mttt) cc_final: 0.7182 (mtpm) REVERT: D 45 GLN cc_start: 0.8458 (mt0) cc_final: 0.8081 (mt0) REVERT: D 56 LYS cc_start: 0.8291 (mttt) cc_final: 0.7775 (ttmm) REVERT: D 66 GLU cc_start: 0.8717 (pt0) cc_final: 0.8376 (pt0) REVERT: E 24 LYS cc_start: 0.7669 (mttt) cc_final: 0.7178 (mtpm) REVERT: E 33 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8073 (mmtp) REVERT: F 23 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: F 24 LYS cc_start: 0.7486 (mttt) cc_final: 0.7021 (mtpm) REVERT: F 34 TYR cc_start: 0.8104 (m-80) cc_final: 0.7833 (m-80) REVERT: F 38 ARG cc_start: 0.7358 (ttt180) cc_final: 0.6962 (ttt180) REVERT: G 24 LYS cc_start: 0.7590 (mttt) cc_final: 0.7135 (mtpm) REVERT: G 29 LYS cc_start: 0.7971 (tttt) cc_final: 0.7554 (tttm) REVERT: G 45 GLN cc_start: 0.7998 (mt0) cc_final: 0.7525 (mt0) REVERT: H 22 ASP cc_start: 0.8480 (t0) cc_final: 0.8085 (t0) REVERT: H 24 LYS cc_start: 0.8170 (mttt) cc_final: 0.7131 (mtpm) REVERT: H 25 GLU cc_start: 0.8250 (mp0) cc_final: 0.7019 (mp0) REVERT: H 45 GLN cc_start: 0.8074 (mt0) cc_final: 0.7798 (mt0) REVERT: I 24 LYS cc_start: 0.7921 (mttt) cc_final: 0.7040 (mtpm) REVERT: I 25 GLU cc_start: 0.8786 (mp0) cc_final: 0.7687 (mp0) REVERT: J 24 LYS cc_start: 0.7521 (mttt) cc_final: 0.6827 (mtpt) REVERT: J 25 GLU cc_start: 0.8725 (mp0) cc_final: 0.8416 (mp0) REVERT: K 24 LYS cc_start: 0.7887 (mttt) cc_final: 0.7099 (mtpm) REVERT: K 38 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7360 (tpp-160) REVERT: K 55 GLU cc_start: 0.8161 (tt0) cc_final: 0.5898 (pm20) REVERT: L 16 MET cc_start: 0.8866 (mtt) cc_final: 0.8474 (mtp) REVERT: L 22 ASP cc_start: 0.8969 (t0) cc_final: 0.8344 (t0) REVERT: L 23 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8498 (mtm) REVERT: L 24 LYS cc_start: 0.7998 (mttt) cc_final: 0.7144 (mtpm) REVERT: L 55 GLU cc_start: 0.8207 (tt0) cc_final: 0.6344 (pm20) REVERT: L 56 LYS cc_start: 0.8341 (mttt) cc_final: 0.7984 (mttt) REVERT: L 62 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8544 (mt-10) outliers start: 16 outliers final: 7 residues processed: 156 average time/residue: 2.1224 time to fit residues: 343.6467 Evaluate side-chains 156 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.107286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093492 restraints weight = 9874.895| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.57 r_work: 0.3549 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6804 Z= 0.188 Angle : 0.501 5.419 9108 Z= 0.290 Chirality : 0.042 0.121 744 Planarity : 0.002 0.028 1236 Dihedral : 4.287 14.172 900 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 15.80 % 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: -4.09 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 28 HIS 0.002 0.001 HIS I 36 PHE 0.010 0.001 PHE B 5 TYR 0.011 0.001 TYR F 34 ARG 0.002 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 160 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8414 (mttt) cc_final: 0.7993 (mtpm) REVERT: B 24 LYS cc_start: 0.8342 (mttt) cc_final: 0.7654 (mtpp) REVERT: B 25 GLU cc_start: 0.8904 (mp0) cc_final: 0.8633 (mp0) REVERT: B 38 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7661 (ttm-80) REVERT: B 45 GLN cc_start: 0.8627 (mt0) cc_final: 0.8344 (mt0) REVERT: C 22 ASP cc_start: 0.8247 (t0) cc_final: 0.7816 (t0) REVERT: C 24 LYS cc_start: 0.7956 (mttt) cc_final: 0.6882 (mtpp) REVERT: C 25 GLU cc_start: 0.8675 (mp0) cc_final: 0.7352 (mp0) REVERT: C 45 GLN cc_start: 0.8269 (mt0) cc_final: 0.7862 (mt0) REVERT: D 24 LYS cc_start: 0.7691 (mttt) cc_final: 0.7234 (mtpm) REVERT: D 45 GLN cc_start: 0.8376 (mt0) cc_final: 0.7933 (mt0) REVERT: D 56 LYS cc_start: 0.8271 (mttt) cc_final: 0.7741 (ttmm) REVERT: D 66 GLU cc_start: 0.8579 (pt0) cc_final: 0.8294 (pt0) REVERT: E 24 LYS cc_start: 0.7587 (mttt) cc_final: 0.7035 (mtpm) REVERT: F 23 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: F 24 LYS cc_start: 0.7421 (mttt) cc_final: 0.6954 (mtpm) REVERT: F 34 TYR cc_start: 0.8013 (m-80) cc_final: 0.7754 (m-80) REVERT: F 38 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6971 (ttt90) REVERT: G 24 LYS cc_start: 0.7611 (mttt) cc_final: 0.7097 (mtpm) REVERT: G 29 LYS cc_start: 0.7996 (tttt) cc_final: 0.7596 (tttp) REVERT: G 45 GLN cc_start: 0.7945 (mt0) cc_final: 0.7352 (mt0) REVERT: H 22 ASP cc_start: 0.8466 (t0) cc_final: 0.8058 (t0) REVERT: H 24 LYS cc_start: 0.8226 (mttt) cc_final: 0.7135 (mtpm) REVERT: H 25 GLU cc_start: 0.8184 (mp0) cc_final: 0.6943 (mp0) REVERT: H 45 GLN cc_start: 0.7945 (mt0) cc_final: 0.7678 (mt0) REVERT: I 24 LYS cc_start: 0.7896 (mttt) cc_final: 0.7285 (mtpm) REVERT: I 25 GLU cc_start: 0.8713 (mp0) cc_final: 0.8330 (mp0) REVERT: I 56 LYS cc_start: 0.8345 (mttt) cc_final: 0.7846 (ttmm) REVERT: J 24 LYS cc_start: 0.7461 (mttt) cc_final: 0.6745 (mtpt) REVERT: J 25 GLU cc_start: 0.8718 (mp0) cc_final: 0.8410 (mp0) REVERT: J 66 GLU cc_start: 0.8441 (pt0) cc_final: 0.8131 (pt0) REVERT: K 23 MET cc_start: 0.9222 (mtm) cc_final: 0.8999 (mpp) REVERT: K 24 LYS cc_start: 0.7735 (mttt) cc_final: 0.6876 (mtpt) REVERT: K 55 GLU cc_start: 0.8102 (tt0) cc_final: 0.5803 (pm20) REVERT: L 16 MET cc_start: 0.8857 (mtt) cc_final: 0.8470 (mtp) REVERT: L 22 ASP cc_start: 0.8897 (t0) cc_final: 0.8269 (t0) REVERT: L 23 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8413 (mtm) REVERT: L 24 LYS cc_start: 0.7915 (mttt) cc_final: 0.7073 (mtpm) REVERT: L 55 GLU cc_start: 0.8160 (tt0) cc_final: 0.6300 (pm20) outliers start: 13 outliers final: 6 residues processed: 150 average time/residue: 1.9813 time to fit residues: 306.5906 Evaluate side-chains 150 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN D 40 ASN E 40 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.087187 restraints weight = 10497.298| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.54 r_work: 0.3430 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.057 6804 Z= 0.712 Angle : 0.742 5.901 9108 Z= 0.429 Chirality : 0.050 0.130 744 Planarity : 0.005 0.037 1236 Dihedral : 5.147 15.181 900 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.95 % Allowed : 17.53 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), 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 0.017 0.002 TRP F 17 HIS 0.006 0.002 HIS L 36 PHE 0.025 0.003 PHE E 3 TYR 0.022 0.002 TYR B 34 ARG 0.005 0.001 ARG F 61 *********************** 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 170 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8641 (mp) REVERT: A 24 LYS cc_start: 0.8344 (mttt) cc_final: 0.7974 (mtpm) REVERT: B 23 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8588 (mtm) REVERT: B 24 LYS cc_start: 0.8400 (mttt) cc_final: 0.7726 (mtpp) REVERT: B 29 LYS cc_start: 0.8907 (tttt) cc_final: 0.8423 (ttpt) REVERT: B 38 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7664 (ttm-80) REVERT: B 45 GLN cc_start: 0.8583 (mt0) cc_final: 0.8358 (mt0) REVERT: C 22 ASP cc_start: 0.8499 (t0) cc_final: 0.8021 (t0) REVERT: C 23 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8237 (mtm) REVERT: C 24 LYS cc_start: 0.8167 (mttt) cc_final: 0.7057 (mtpp) REVERT: C 25 GLU cc_start: 0.8665 (mp0) cc_final: 0.7479 (mp0) REVERT: C 45 GLN cc_start: 0.8345 (mt0) cc_final: 0.8015 (mt0) REVERT: D 24 LYS cc_start: 0.7795 (mttt) cc_final: 0.7333 (mtpm) REVERT: D 45 GLN cc_start: 0.8504 (mt0) cc_final: 0.8149 (mt0) REVERT: D 66 GLU cc_start: 0.8815 (pt0) cc_final: 0.8468 (pt0) REVERT: E 24 LYS cc_start: 0.7722 (mttt) cc_final: 0.7161 (mtpm) REVERT: E 29 LYS cc_start: 0.8376 (tttt) cc_final: 0.8054 (ttpp) REVERT: F 23 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: F 24 LYS cc_start: 0.7675 (mttt) cc_final: 0.7204 (mtpm) REVERT: F 34 TYR cc_start: 0.8175 (m-80) cc_final: 0.7879 (m-80) REVERT: F 38 ARG cc_start: 0.7614 (ttt180) cc_final: 0.7246 (ttt90) REVERT: F 59 ASP cc_start: 0.8992 (m-30) cc_final: 0.8713 (m-30) REVERT: G 24 LYS cc_start: 0.7784 (mttt) cc_final: 0.7301 (mtpm) REVERT: G 29 LYS cc_start: 0.8034 (tttt) cc_final: 0.7620 (tttm) REVERT: G 45 GLN cc_start: 0.8096 (mt0) cc_final: 0.7601 (mt0) REVERT: H 22 ASP cc_start: 0.8596 (t0) cc_final: 0.8214 (t0) REVERT: H 24 LYS cc_start: 0.8224 (mttt) cc_final: 0.7199 (mtpm) REVERT: H 25 GLU cc_start: 0.8308 (mp0) cc_final: 0.7143 (mp0) REVERT: H 45 GLN cc_start: 0.8137 (mt0) cc_final: 0.7878 (mt0) REVERT: I 24 LYS cc_start: 0.7903 (mttt) cc_final: 0.7073 (mtpm) REVERT: I 25 GLU cc_start: 0.8838 (mp0) cc_final: 0.7778 (mp0) REVERT: I 38 ARG cc_start: 0.7498 (ttt180) cc_final: 0.7214 (ttt180) REVERT: J 24 LYS cc_start: 0.7680 (mttt) cc_final: 0.6981 (mtpt) REVERT: J 25 GLU cc_start: 0.8646 (mp0) cc_final: 0.8380 (mp0) REVERT: K 24 LYS cc_start: 0.7936 (mttt) cc_final: 0.7221 (mtpm) REVERT: K 38 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7436 (tpp-160) REVERT: K 55 GLU cc_start: 0.8277 (tt0) cc_final: 0.6136 (pm20) REVERT: L 16 MET cc_start: 0.8911 (mtt) cc_final: 0.8492 (mtp) REVERT: L 22 ASP cc_start: 0.9039 (t0) cc_final: 0.8423 (t0) REVERT: L 23 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8517 (mtm) REVERT: L 24 LYS cc_start: 0.8006 (mttt) cc_final: 0.7003 (mtpm) REVERT: L 25 GLU cc_start: 0.8758 (mp0) cc_final: 0.7880 (mp0) REVERT: L 55 GLU cc_start: 0.8175 (tt0) cc_final: 0.6495 (pm20) REVERT: L 62 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8602 (mt-10) outliers start: 17 outliers final: 8 residues processed: 160 average time/residue: 1.9363 time to fit residues: 319.2519 Evaluate side-chains 164 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 15 ASP Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** F 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 = 0.3843 r_free = 0.3843 target = 0.107038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.093293 restraints weight = 9923.805| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.57 r_work: 0.3545 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6804 Z= 0.180 Angle : 0.506 4.460 9108 Z= 0.294 Chirality : 0.042 0.124 744 Planarity : 0.003 0.035 1236 Dihedral : 4.350 15.085 900 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.08 % Allowed : 18.40 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.27 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 17 HIS 0.002 0.001 HIS H 36 PHE 0.010 0.001 PHE F 5 TYR 0.011 0.001 TYR F 34 ARG 0.003 0.000 ARG E 46 *********************** 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 156 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8448 (mttt) cc_final: 0.8070 (mtpm) REVERT: B 24 LYS cc_start: 0.8310 (mttt) cc_final: 0.7651 (mtpp) REVERT: B 25 GLU cc_start: 0.8863 (mp0) cc_final: 0.8613 (mp0) REVERT: B 38 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7624 (ttm-80) REVERT: C 22 ASP cc_start: 0.8244 (t0) cc_final: 0.7804 (t0) REVERT: C 24 LYS cc_start: 0.7982 (mttt) cc_final: 0.7298 (mtpp) REVERT: C 25 GLU cc_start: 0.8658 (mp0) cc_final: 0.8150 (mp0) REVERT: C 45 GLN cc_start: 0.8296 (mt0) cc_final: 0.7856 (mt0) REVERT: D 24 LYS cc_start: 0.7744 (mttt) cc_final: 0.7181 (mtpp) REVERT: D 45 GLN cc_start: 0.8360 (mt0) cc_final: 0.7934 (mt0) REVERT: E 24 LYS cc_start: 0.7578 (mttt) cc_final: 0.6955 (mtpm) REVERT: E 29 LYS cc_start: 0.8276 (tttt) cc_final: 0.7932 (ttpp) REVERT: E 33 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7733 (mmtp) REVERT: F 23 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8175 (mtm) REVERT: F 24 LYS cc_start: 0.7449 (mttt) cc_final: 0.6921 (mtpm) REVERT: F 34 TYR cc_start: 0.8037 (m-80) cc_final: 0.7785 (m-80) REVERT: F 38 ARG cc_start: 0.7428 (ttt180) cc_final: 0.7081 (ttt90) REVERT: F 59 ASP cc_start: 0.8971 (m-30) cc_final: 0.8658 (m-30) REVERT: G 24 LYS cc_start: 0.7884 (mttt) cc_final: 0.7399 (mtpm) REVERT: G 29 LYS cc_start: 0.7964 (tttt) cc_final: 0.7564 (tttp) REVERT: G 45 GLN cc_start: 0.7878 (mt0) cc_final: 0.7367 (mt0) REVERT: H 22 ASP cc_start: 0.8566 (t0) cc_final: 0.8200 (t0) REVERT: H 24 LYS cc_start: 0.8193 (mttt) cc_final: 0.7144 (mtpm) REVERT: H 25 GLU cc_start: 0.8191 (mp0) cc_final: 0.7007 (mp0) REVERT: I 16 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8226 (mtp) REVERT: I 24 LYS cc_start: 0.7924 (mttt) cc_final: 0.7108 (mtpm) REVERT: I 25 GLU cc_start: 0.8764 (mp0) cc_final: 0.7639 (mp0) REVERT: I 33 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7764 (mttm) REVERT: I 66 GLU cc_start: 0.8414 (pt0) cc_final: 0.8187 (pt0) REVERT: J 24 LYS cc_start: 0.7511 (mttt) cc_final: 0.6805 (mtpt) REVERT: J 25 GLU cc_start: 0.8738 (mp0) cc_final: 0.8438 (mp0) REVERT: J 66 GLU cc_start: 0.8464 (pt0) cc_final: 0.8166 (pt0) REVERT: K 24 LYS cc_start: 0.7749 (mttt) cc_final: 0.6806 (mtpm) REVERT: K 55 GLU cc_start: 0.8106 (tt0) cc_final: 0.5822 (pm20) REVERT: L 16 MET cc_start: 0.8875 (mtt) cc_final: 0.8514 (mtp) REVERT: L 22 ASP cc_start: 0.8952 (t0) cc_final: 0.8303 (t0) REVERT: L 24 LYS cc_start: 0.7974 (mttt) cc_final: 0.7129 (mtpm) REVERT: L 55 GLU cc_start: 0.8194 (tt0) cc_final: 0.6405 (pm20) outliers start: 12 outliers final: 3 residues processed: 146 average time/residue: 1.8527 time to fit residues: 279.3021 Evaluate side-chains 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 16 MET Chi-restraints excluded: chain J residue 16 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: 6.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.102761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.089399 restraints weight = 10387.757| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.59 r_work: 0.3475 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6804 Z= 0.416 Angle : 0.605 5.557 9108 Z= 0.350 Chirality : 0.045 0.125 744 Planarity : 0.003 0.033 1236 Dihedral : 4.686 15.872 900 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.91 % Allowed : 18.92 % Favored : 79.17 % 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: -4.36 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.004 0.002 HIS L 36 PHE 0.015 0.002 PHE F 5 TYR 0.014 0.001 TYR B 34 ARG 0.003 0.001 ARG E 46 *********************** 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 156 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8335 (mttt) cc_final: 0.7941 (mtpm) REVERT: B 24 LYS cc_start: 0.8359 (mttt) cc_final: 0.7708 (mtpp) REVERT: B 29 LYS cc_start: 0.8844 (tttt) cc_final: 0.8400 (ttpt) REVERT: B 38 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7686 (ttm-80) REVERT: C 22 ASP cc_start: 0.8261 (t0) cc_final: 0.7850 (t0) REVERT: C 24 LYS cc_start: 0.8223 (mttt) cc_final: 0.7116 (mtpp) REVERT: C 25 GLU cc_start: 0.8668 (mp0) cc_final: 0.7369 (mp0) REVERT: C 45 GLN cc_start: 0.8268 (mt0) cc_final: 0.7904 (mt0) REVERT: D 24 LYS cc_start: 0.7788 (mttt) cc_final: 0.7236 (mtpp) REVERT: D 45 GLN cc_start: 0.8503 (mt0) cc_final: 0.8098 (mt0) REVERT: D 56 LYS cc_start: 0.8497 (mttt) cc_final: 0.8204 (ttmt) REVERT: E 24 LYS cc_start: 0.7628 (mttt) cc_final: 0.7061 (mtpt) REVERT: E 29 LYS cc_start: 0.8380 (tttt) cc_final: 0.8049 (ttpp) REVERT: F 23 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: F 24 LYS cc_start: 0.7486 (mttt) cc_final: 0.6997 (mtpm) REVERT: F 34 TYR cc_start: 0.8191 (m-80) cc_final: 0.7923 (m-80) REVERT: F 38 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7095 (ttt90) REVERT: G 24 LYS cc_start: 0.7738 (mttt) cc_final: 0.7315 (mtpm) REVERT: G 29 LYS cc_start: 0.7972 (tttt) cc_final: 0.7572 (tttm) REVERT: G 45 GLN cc_start: 0.8005 (mt0) cc_final: 0.7509 (mt0) REVERT: H 22 ASP cc_start: 0.8542 (t0) cc_final: 0.8177 (t0) REVERT: H 24 LYS cc_start: 0.8220 (mttt) cc_final: 0.7187 (mtpm) REVERT: H 25 GLU cc_start: 0.8229 (mp0) cc_final: 0.7037 (mp0) REVERT: H 45 GLN cc_start: 0.8092 (mt0) cc_final: 0.7820 (mt0) REVERT: I 24 LYS cc_start: 0.7924 (mttt) cc_final: 0.7128 (mtpm) REVERT: I 25 GLU cc_start: 0.8781 (mp0) cc_final: 0.7706 (mp0) REVERT: J 24 LYS cc_start: 0.7548 (mttt) cc_final: 0.6868 (mtpt) REVERT: J 25 GLU cc_start: 0.8746 (mp0) cc_final: 0.8464 (mp0) REVERT: K 24 LYS cc_start: 0.7932 (mttt) cc_final: 0.7152 (mtpm) REVERT: K 38 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7328 (tpp-160) REVERT: K 55 GLU cc_start: 0.8179 (tt0) cc_final: 0.5935 (pm20) REVERT: L 16 MET cc_start: 0.8939 (mtt) cc_final: 0.8554 (mtp) REVERT: L 24 LYS cc_start: 0.8032 (mttt) cc_final: 0.7207 (mtpm) REVERT: L 55 GLU cc_start: 0.8229 (tt0) cc_final: 0.6436 (pm20) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 1.8987 time to fit residues: 287.9179 Evaluate side-chains 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain K residue 38 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 45 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.102579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.089231 restraints weight = 10561.865| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.59 r_work: 0.3469 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6804 Z= 0.452 Angle : 0.632 5.410 9108 Z= 0.365 Chirality : 0.046 0.125 744 Planarity : 0.003 0.032 1236 Dihedral : 4.852 17.013 900 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.91 % Allowed : 19.10 % 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: -4.45 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 17 HIS 0.004 0.002 HIS L 36 PHE 0.016 0.002 PHE F 5 TYR 0.015 0.002 TYR B 34 ARG 0.004 0.001 ARG A 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 158 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 23 MET cc_start: 0.9043 (mtm) cc_final: 0.8612 (mtm) REVERT: A 24 LYS cc_start: 0.8346 (mttt) cc_final: 0.7951 (mtpm) REVERT: B 24 LYS cc_start: 0.8361 (mttt) cc_final: 0.7734 (mtpp) REVERT: B 29 LYS cc_start: 0.8902 (tttt) cc_final: 0.8454 (ttpt) REVERT: B 38 ARG cc_start: 0.7981 (ttt180) cc_final: 0.7682 (ttm-80) REVERT: C 22 ASP cc_start: 0.8450 (t0) cc_final: 0.7985 (t0) REVERT: C 24 LYS cc_start: 0.8243 (mttt) cc_final: 0.7130 (mtpp) REVERT: C 25 GLU cc_start: 0.8663 (mp0) cc_final: 0.7364 (mp0) REVERT: C 45 GLN cc_start: 0.8433 (mt0) cc_final: 0.8114 (mt0) REVERT: D 24 LYS cc_start: 0.7836 (mttt) cc_final: 0.7284 (mtpp) REVERT: D 45 GLN cc_start: 0.8469 (mt0) cc_final: 0.8085 (mt0) REVERT: D 56 LYS cc_start: 0.8460 (mttt) cc_final: 0.8169 (ttmt) REVERT: E 24 LYS cc_start: 0.7651 (mttt) cc_final: 0.7088 (mtpt) REVERT: E 29 LYS cc_start: 0.8365 (tttt) cc_final: 0.8055 (ttpp) REVERT: F 23 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8200 (mtm) REVERT: F 24 LYS cc_start: 0.7504 (mttt) cc_final: 0.7009 (mtpm) REVERT: F 34 TYR cc_start: 0.8182 (m-80) cc_final: 0.7876 (m-80) REVERT: F 38 ARG cc_start: 0.7502 (ttt180) cc_final: 0.7111 (ttt90) REVERT: G 24 LYS cc_start: 0.7777 (mttt) cc_final: 0.7342 (mtpm) REVERT: G 29 LYS cc_start: 0.7962 (tttt) cc_final: 0.7564 (tttm) REVERT: G 45 GLN cc_start: 0.7998 (mt0) cc_final: 0.7398 (mt0) REVERT: H 22 ASP cc_start: 0.8636 (t0) cc_final: 0.8246 (t0) REVERT: H 24 LYS cc_start: 0.8248 (mttt) cc_final: 0.7234 (mtpm) REVERT: H 25 GLU cc_start: 0.8247 (mp0) cc_final: 0.7052 (mp0) REVERT: H 45 GLN cc_start: 0.8084 (mt0) cc_final: 0.7812 (mt0) REVERT: I 8 GLU cc_start: 0.8843 (tt0) cc_final: 0.8625 (mt-10) REVERT: I 24 LYS cc_start: 0.7910 (mttt) cc_final: 0.7112 (mtpm) REVERT: I 25 GLU cc_start: 0.8618 (mp0) cc_final: 0.7580 (mp0) REVERT: I 33 LYS cc_start: 0.8579 (mmtt) cc_final: 0.7991 (mttm) REVERT: J 24 LYS cc_start: 0.7561 (mttt) cc_final: 0.6892 (mtpt) REVERT: J 25 GLU cc_start: 0.8696 (mp0) cc_final: 0.8425 (mp0) REVERT: K 23 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8866 (mpp) REVERT: K 24 LYS cc_start: 0.7807 (mttt) cc_final: 0.7043 (mtpm) REVERT: K 38 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7363 (tpp-160) REVERT: K 55 GLU cc_start: 0.8242 (tt0) cc_final: 0.6045 (pm20) REVERT: L 16 MET cc_start: 0.8938 (mtt) cc_final: 0.8543 (mtp) REVERT: L 24 LYS cc_start: 0.8059 (mttt) cc_final: 0.7291 (mtpm) REVERT: L 55 GLU cc_start: 0.8224 (tt0) cc_final: 0.6412 (pm20) outliers start: 11 outliers final: 7 residues processed: 150 average time/residue: 1.9306 time to fit residues: 299.3366 Evaluate side-chains 155 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 38 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 45 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.090884 restraints weight = 10335.260| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.61 r_work: 0.3511 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6804 Z= 0.245 Angle : 0.557 5.007 9108 Z= 0.321 Chirality : 0.043 0.127 744 Planarity : 0.003 0.038 1236 Dihedral : 4.634 16.398 900 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.91 % Allowed : 20.14 % Favored : 77.95 % 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: -4.39 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 F 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: 6225.89 seconds wall clock time: 106 minutes 21.35 seconds (6381.35 seconds total)