Starting phenix.real_space_refine on Mon Mar 11 02:21:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_8910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_8910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_8910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_8910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dso_8910/03_2024/6dso_8910.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.18, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 6.241A pdb=" N PHE A 2 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE C 5 " --> pdb=" O PHE A 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 4 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY C 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 6 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE C 2 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE E 5 " --> pdb=" O PHE C 2 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER C 4 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY E 7 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 6 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE E 2 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE G 5 " --> pdb=" O PHE E 2 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER E 4 " --> pdb=" O PHE G 5 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLY G 7 " --> pdb=" O SER E 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE E 6 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE G 2 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE I 5 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER G 4 " --> pdb=" O PHE I 5 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLY I 7 " --> pdb=" O SER G 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE G 6 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE I 2 " --> pdb=" O PHE K 3 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE K 5 " --> pdb=" O PHE I 2 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER I 4 " --> pdb=" O PHE K 5 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY K 7 " --> pdb=" O SER I 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE I 6 " --> pdb=" O GLY K 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.332A pdb=" N TYR A 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR C 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR E 20 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 20 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR I 20 " --> pdb=" O THR K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.808A pdb=" N TRP A 28 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP C 28 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP E 28 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP G 28 " --> pdb=" O LYS I 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP I 28 " --> pdb=" O LYS K 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 38 removed outlier: 6.555A pdb=" N LYS C 33 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS E 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE C 35 " --> pdb=" O HIS E 36 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG E 38 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 37 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS I 33 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N HIS K 36 " --> pdb=" O LYS I 33 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 35 " --> pdb=" O HIS K 36 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ARG K 38 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA I 37 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.145A pdb=" N VAL A 51 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 51 " --> pdb=" O TRP E 52 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL E 51 " --> pdb=" O TRP G 52 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL G 51 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL I 51 " --> pdb=" O TRP K 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.416A pdb=" N LYS A 56 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS G 56 " --> pdb=" O ILE I 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 8 removed outlier: 6.237A pdb=" N PHE B 2 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N PHE D 5 " --> pdb=" O PHE B 2 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER B 4 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY D 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE B 6 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE D 2 " --> pdb=" O PHE F 3 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE F 5 " --> pdb=" O PHE D 2 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER D 4 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY F 7 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE D 6 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE F 2 " --> pdb=" O PHE H 3 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE H 5 " --> pdb=" O PHE F 2 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F 4 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY H 7 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE F 6 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 2 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHE J 5 " --> pdb=" O PHE H 2 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER H 4 " --> pdb=" O PHE J 5 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLY J 7 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE H 6 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE J 2 " --> pdb=" O PHE L 3 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE L 5 " --> pdb=" O PHE J 2 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER J 4 " --> pdb=" O PHE L 5 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY L 7 " --> pdb=" O SER J 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE J 6 " --> pdb=" O GLY L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.296A pdb=" N TYR B 20 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR D 20 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR F 20 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR H 20 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR J 20 " --> pdb=" O THR L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.805A pdb=" N TRP B 28 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP D 28 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP F 28 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 28 " --> pdb=" O LYS J 29 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP J 28 " --> pdb=" O LYS L 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 38 removed outlier: 6.566A pdb=" N LYS D 33 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS F 36 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 35 " --> pdb=" O HIS F 36 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG F 38 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA D 37 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS J 33 " --> pdb=" O TYR L 34 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N HIS L 36 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE J 35 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG L 38 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA J 37 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53 removed outlier: 6.134A pdb=" N VAL B 51 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 51 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL F 51 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL H 51 " --> pdb=" O TRP J 52 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL J 51 " --> pdb=" O TRP L 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.414A pdb=" N LYS B 56 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS H 56 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 68 82 hydrogen bonds defined for protein. 246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.68 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: 99.13 - 106.10: 84 106.10 - 113.07: 3070 113.07 - 120.04: 2424 120.04 - 127.01: 3422 127.01 - 133.98: 108 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 2.520 nonbonded pdb=" O GLY B 49 " pdb=" NH2 ARG D 46 " model vdw 2.435 2.520 nonbonded pdb=" O GLY E 49 " pdb=" NH2 ARG G 46 " model vdw 2.436 2.520 nonbonded pdb=" O GLY I 49 " pdb=" NH2 ARG K 46 " model vdw 2.437 2.520 nonbonded pdb=" O GLY C 49 " pdb=" NH2 ARG E 46 " model vdw 2.437 2.520 ... (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 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: 0.490 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: 3.240 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.710 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.749 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: 1.5974 time to fit residues: 324.3248 Evaluate side-chains 140 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 G 11 GLN K 11 GLN L 40 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6804 Z= 0.164 Angle : 0.498 5.144 9108 Z= 0.290 Chirality : 0.042 0.117 744 Planarity : 0.003 0.029 1236 Dihedral : 4.679 17.668 900 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.26 % Allowed : 11.98 % Favored : 85.76 % 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 0.001 0.001 HIS J 36 PHE 0.013 0.001 PHE B 5 TYR 0.009 0.001 TYR K 34 ARG 0.003 0.001 ARG J 18 *********************** 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 182 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8449 (mtt) cc_final: 0.8227 (mtt) REVERT: A 24 LYS cc_start: 0.8198 (mttt) cc_final: 0.7786 (mtpm) REVERT: B 24 LYS cc_start: 0.8261 (mttt) cc_final: 0.7608 (mtpp) REVERT: B 45 GLN cc_start: 0.8308 (mt0) cc_final: 0.7702 (mt0) REVERT: C 22 ASP cc_start: 0.8162 (t0) cc_final: 0.7686 (t0) REVERT: C 24 LYS cc_start: 0.7960 (mttt) cc_final: 0.7326 (mtpp) REVERT: C 25 GLU cc_start: 0.8469 (mp0) cc_final: 0.8165 (mp0) REVERT: C 45 GLN cc_start: 0.7970 (mt0) cc_final: 0.7659 (mt0) REVERT: D 11 GLN cc_start: 0.8698 (mt0) cc_final: 0.8498 (mt0) REVERT: D 22 ASP cc_start: 0.8384 (t0) cc_final: 0.7988 (t0) REVERT: D 24 LYS cc_start: 0.7878 (mttt) cc_final: 0.7497 (mtpm) REVERT: D 45 GLN cc_start: 0.8145 (mt0) cc_final: 0.7796 (mt0) REVERT: D 56 LYS cc_start: 0.8057 (mttt) cc_final: 0.7805 (ttmt) REVERT: D 66 GLU cc_start: 0.8002 (pt0) cc_final: 0.7783 (pt0) REVERT: E 24 LYS cc_start: 0.7824 (mttt) cc_final: 0.7364 (mtpm) REVERT: E 56 LYS cc_start: 0.8148 (mttt) cc_final: 0.7889 (mttt) REVERT: F 24 LYS cc_start: 0.7784 (mttt) cc_final: 0.7260 (mtpp) REVERT: G 22 ASP cc_start: 0.8407 (t0) cc_final: 0.7751 (t0) REVERT: G 24 LYS cc_start: 0.7642 (mttt) cc_final: 0.7424 (mttp) REVERT: G 45 GLN cc_start: 0.7926 (mt0) cc_final: 0.7448 (mt0) REVERT: H 24 LYS cc_start: 0.8151 (mttt) cc_final: 0.7094 (mtpm) REVERT: H 25 GLU cc_start: 0.8179 (mp0) cc_final: 0.6958 (mp0) REVERT: I 56 LYS cc_start: 0.8150 (mttt) cc_final: 0.7607 (ttmm) REVERT: J 24 LYS cc_start: 0.7627 (mttt) cc_final: 0.6900 (mtpt) REVERT: J 25 GLU cc_start: 0.8502 (mp0) cc_final: 0.7804 (mp0) REVERT: K 16 MET cc_start: 0.8534 (mtt) cc_final: 0.8043 (mtp) REVERT: K 24 LYS cc_start: 0.7758 (mttt) cc_final: 0.7090 (mtpt) REVERT: K 46 ARG cc_start: 0.8029 (tpt90) cc_final: 0.5589 (mtt-85) REVERT: L 11 GLN cc_start: 0.8991 (mt0) cc_final: 0.8652 (mt0) REVERT: L 16 MET cc_start: 0.8435 (mtt) cc_final: 0.8161 (mtp) REVERT: L 24 LYS cc_start: 0.8116 (mttt) cc_final: 0.7331 (mtpp) REVERT: L 46 ARG cc_start: 0.8000 (tpt90) cc_final: 0.5640 (mtt-85) REVERT: L 56 LYS cc_start: 0.8217 (mttt) cc_final: 0.8008 (mttt) REVERT: L 62 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8098 (mt-10) outliers start: 13 outliers final: 0 residues processed: 173 average time/residue: 1.7861 time to fit residues: 319.0589 Evaluate side-chains 147 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6804 Z= 0.301 Angle : 0.545 4.016 9108 Z= 0.317 Chirality : 0.042 0.117 744 Planarity : 0.003 0.021 1236 Dihedral : 4.589 15.167 900 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.12 % Allowed : 12.85 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), 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 0.005 0.001 TRP G 17 HIS 0.003 0.001 HIS K 36 PHE 0.015 0.002 PHE G 5 TYR 0.011 0.002 TYR A 34 ARG 0.003 0.001 ARG C 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 180 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8280 (mttt) cc_final: 0.7839 (mtpm) REVERT: B 24 LYS cc_start: 0.8259 (mttt) cc_final: 0.7651 (mtpp) REVERT: B 29 LYS cc_start: 0.8707 (tttt) cc_final: 0.8280 (ttpt) REVERT: B 45 GLN cc_start: 0.8328 (mt0) cc_final: 0.7693 (mt0) REVERT: C 22 ASP cc_start: 0.8179 (t0) cc_final: 0.7750 (t0) REVERT: C 24 LYS cc_start: 0.8048 (mttt) cc_final: 0.7411 (mtpp) REVERT: C 25 GLU cc_start: 0.8469 (mp0) cc_final: 0.8155 (mp0) REVERT: C 45 GLN cc_start: 0.8085 (mt0) cc_final: 0.7773 (mt0) REVERT: D 22 ASP cc_start: 0.8282 (t0) cc_final: 0.7969 (t0) REVERT: D 24 LYS cc_start: 0.7882 (mttt) cc_final: 0.7459 (mtpm) REVERT: D 45 GLN cc_start: 0.8215 (mt0) cc_final: 0.7777 (mt0) REVERT: D 56 LYS cc_start: 0.8139 (mttt) cc_final: 0.7845 (ttmt) REVERT: D 61 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: D 66 GLU cc_start: 0.8107 (pt0) cc_final: 0.7782 (pt0) REVERT: E 24 LYS cc_start: 0.7883 (mttt) cc_final: 0.7396 (mtpm) REVERT: F 23 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8484 (mtt) REVERT: F 24 LYS cc_start: 0.7825 (mttt) cc_final: 0.7377 (mtpt) REVERT: F 38 ARG cc_start: 0.6976 (ttt180) cc_final: 0.6510 (ttt90) REVERT: G 24 LYS cc_start: 0.7653 (mttt) cc_final: 0.7219 (mtpm) REVERT: G 45 GLN cc_start: 0.7944 (mt0) cc_final: 0.7420 (mt0) REVERT: H 24 LYS cc_start: 0.8241 (mttt) cc_final: 0.7161 (mtpm) REVERT: H 25 GLU cc_start: 0.8208 (mp0) cc_final: 0.6850 (mp0) REVERT: H 46 ARG cc_start: 0.8502 (tpt90) cc_final: 0.8180 (tpt90) REVERT: I 24 LYS cc_start: 0.7963 (mttt) cc_final: 0.7170 (mtpm) REVERT: I 25 GLU cc_start: 0.8543 (mp0) cc_final: 0.7584 (mp0) REVERT: I 56 LYS cc_start: 0.8062 (mttt) cc_final: 0.7548 (ttmm) REVERT: J 24 LYS cc_start: 0.7736 (mttt) cc_final: 0.6869 (mtpt) REVERT: J 25 GLU cc_start: 0.8525 (mp0) cc_final: 0.7797 (mp0) REVERT: K 16 MET cc_start: 0.8527 (mtt) cc_final: 0.8204 (mtt) REVERT: K 24 LYS cc_start: 0.7907 (mttt) cc_final: 0.7168 (mtpt) REVERT: K 38 ARG cc_start: 0.7376 (ttt180) cc_final: 0.6997 (ttt-90) REVERT: K 46 ARG cc_start: 0.8215 (tpt90) cc_final: 0.5387 (mpt-90) REVERT: K 55 GLU cc_start: 0.7796 (tt0) cc_final: 0.5700 (pm20) REVERT: L 16 MET cc_start: 0.8570 (mtt) cc_final: 0.8231 (mtp) REVERT: L 22 ASP cc_start: 0.8726 (t0) cc_final: 0.8150 (t0) REVERT: L 23 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8236 (mtm) REVERT: L 24 LYS cc_start: 0.8083 (mttt) cc_final: 0.7205 (mtpm) REVERT: L 46 ARG cc_start: 0.8340 (tpt90) cc_final: 0.5811 (mtt-85) REVERT: L 62 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8169 (mt-10) outliers start: 18 outliers final: 2 residues processed: 166 average time/residue: 1.7778 time to fit residues: 304.6963 Evaluate side-chains 153 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain I residue 63 SER 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 64 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN E 11 GLN G 11 GLN G 40 ASN H 45 GLN I 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6804 Z= 0.411 Angle : 0.591 3.895 9108 Z= 0.345 Chirality : 0.044 0.119 744 Planarity : 0.003 0.025 1236 Dihedral : 4.756 16.265 900 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.99 % Allowed : 15.10 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.14 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.004 0.002 HIS L 36 PHE 0.018 0.002 PHE F 5 TYR 0.011 0.002 TYR F 34 ARG 0.004 0.001 ARG F 61 *********************** 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 178 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8333 (mttt) cc_final: 0.7906 (mtpm) REVERT: A 29 LYS cc_start: 0.8676 (tttt) cc_final: 0.8469 (ttpt) REVERT: B 24 LYS cc_start: 0.8282 (mttt) cc_final: 0.7665 (mtpp) REVERT: B 29 LYS cc_start: 0.8819 (tttt) cc_final: 0.8393 (ttpt) REVERT: B 38 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7516 (ttm-80) REVERT: B 45 GLN cc_start: 0.8290 (mt0) cc_final: 0.7987 (mt0) REVERT: C 22 ASP cc_start: 0.8192 (t0) cc_final: 0.7744 (t0) REVERT: C 23 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8033 (mtm) REVERT: C 24 LYS cc_start: 0.8152 (mttt) cc_final: 0.7463 (mtpp) REVERT: C 25 GLU cc_start: 0.8509 (mp0) cc_final: 0.8110 (mp0) REVERT: C 45 GLN cc_start: 0.8047 (mt0) cc_final: 0.7679 (mt0) REVERT: D 24 LYS cc_start: 0.7863 (mttt) cc_final: 0.7455 (mtpm) REVERT: D 45 GLN cc_start: 0.8178 (mt0) cc_final: 0.7782 (mt0) REVERT: D 56 LYS cc_start: 0.8163 (mttt) cc_final: 0.7614 (ttmm) REVERT: D 66 GLU cc_start: 0.8148 (pt0) cc_final: 0.7817 (pt0) REVERT: E 24 LYS cc_start: 0.7886 (mttt) cc_final: 0.7404 (mtpm) REVERT: E 33 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7785 (mptt) REVERT: F 23 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: F 24 LYS cc_start: 0.7857 (mttt) cc_final: 0.7394 (mtpm) REVERT: F 34 TYR cc_start: 0.8043 (m-80) cc_final: 0.7792 (m-80) REVERT: F 38 ARG cc_start: 0.7239 (ttt180) cc_final: 0.7026 (ttt180) REVERT: F 59 ASP cc_start: 0.8710 (m-30) cc_final: 0.8388 (m-30) REVERT: G 23 MET cc_start: 0.8146 (mtt) cc_final: 0.7931 (mtt) REVERT: G 24 LYS cc_start: 0.7797 (mttt) cc_final: 0.7373 (mtpm) REVERT: G 45 GLN cc_start: 0.7754 (mt0) cc_final: 0.7245 (mt0) REVERT: H 22 ASP cc_start: 0.8358 (t0) cc_final: 0.7951 (t0) REVERT: H 24 LYS cc_start: 0.8327 (mttt) cc_final: 0.7289 (mtpm) REVERT: H 25 GLU cc_start: 0.8153 (mp0) cc_final: 0.6913 (mp0) REVERT: I 24 LYS cc_start: 0.7884 (mttt) cc_final: 0.7412 (mtpm) REVERT: I 25 GLU cc_start: 0.8558 (mp0) cc_final: 0.8259 (mp0) REVERT: J 24 LYS cc_start: 0.7746 (mttt) cc_final: 0.6923 (mtpt) REVERT: J 25 GLU cc_start: 0.8530 (mp0) cc_final: 0.7843 (mp0) REVERT: K 24 LYS cc_start: 0.7976 (mttt) cc_final: 0.7198 (mtpt) REVERT: K 38 ARG cc_start: 0.7709 (ttt180) cc_final: 0.7300 (tpp-160) REVERT: K 46 ARG cc_start: 0.8144 (tpt90) cc_final: 0.5343 (mpt-90) REVERT: K 55 GLU cc_start: 0.7800 (tt0) cc_final: 0.5696 (pm20) REVERT: L 16 MET cc_start: 0.8607 (mtt) cc_final: 0.8219 (mtp) REVERT: L 22 ASP cc_start: 0.8798 (t0) cc_final: 0.8211 (t0) REVERT: L 23 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8294 (mtm) REVERT: L 24 LYS cc_start: 0.8070 (mttt) cc_final: 0.7236 (mtpm) REVERT: L 46 ARG cc_start: 0.8490 (tpt90) cc_final: 0.5911 (mtt-85) REVERT: L 55 GLU cc_start: 0.7703 (tt0) cc_final: 0.5987 (pm20) REVERT: L 62 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8124 (mt-10) outliers start: 23 outliers final: 4 residues processed: 166 average time/residue: 1.8186 time to fit residues: 311.6144 Evaluate side-chains 158 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 MET Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain L residue 23 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN D 40 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 6804 Z= 0.492 Angle : 0.633 4.471 9108 Z= 0.368 Chirality : 0.046 0.120 744 Planarity : 0.003 0.031 1236 Dihedral : 4.886 16.038 900 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.95 % Allowed : 16.49 % Favored : 80.56 % 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: -4.26 (0.15), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 17 HIS 0.005 0.002 HIS L 36 PHE 0.020 0.002 PHE F 5 TYR 0.015 0.002 TYR B 34 ARG 0.005 0.001 ARG L 18 *********************** 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 167 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: A 24 LYS cc_start: 0.8342 (mttt) cc_final: 0.7902 (mtpm) REVERT: A 29 LYS cc_start: 0.8679 (tttt) cc_final: 0.8474 (ttpt) REVERT: B 24 LYS cc_start: 0.8480 (mttt) cc_final: 0.7852 (mtpp) REVERT: B 29 LYS cc_start: 0.8812 (tttt) cc_final: 0.8371 (ttpt) REVERT: B 38 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7566 (ttm-80) REVERT: C 22 ASP cc_start: 0.8229 (t0) cc_final: 0.7788 (t0) REVERT: C 23 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7923 (mtm) REVERT: C 24 LYS cc_start: 0.8211 (mttt) cc_final: 0.7519 (mtpp) REVERT: C 25 GLU cc_start: 0.8502 (mp0) cc_final: 0.8108 (mp0) REVERT: C 45 GLN cc_start: 0.8154 (mt0) cc_final: 0.7820 (mt0) REVERT: D 24 LYS cc_start: 0.7811 (mttt) cc_final: 0.7409 (mtpm) REVERT: D 45 GLN cc_start: 0.8167 (mt0) cc_final: 0.7794 (mt0) REVERT: D 56 LYS cc_start: 0.8186 (mttt) cc_final: 0.7630 (ttmm) REVERT: D 66 GLU cc_start: 0.8217 (pt0) cc_final: 0.7908 (pt0) REVERT: E 24 LYS cc_start: 0.7822 (mttt) cc_final: 0.7345 (mtpm) REVERT: E 33 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7978 (mptt) REVERT: F 23 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8029 (mtm) REVERT: F 24 LYS cc_start: 0.7877 (mttt) cc_final: 0.7423 (mtpm) REVERT: F 34 TYR cc_start: 0.8033 (m-80) cc_final: 0.7780 (m-80) REVERT: F 38 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6921 (ttt180) REVERT: F 59 ASP cc_start: 0.8725 (m-30) cc_final: 0.8420 (m-30) REVERT: G 23 MET cc_start: 0.8202 (mtt) cc_final: 0.7917 (mtt) REVERT: G 24 LYS cc_start: 0.7844 (mttt) cc_final: 0.7354 (mtpm) REVERT: G 29 LYS cc_start: 0.7899 (tttt) cc_final: 0.7445 (tttm) REVERT: G 45 GLN cc_start: 0.7727 (mt0) cc_final: 0.7231 (mt0) REVERT: H 22 ASP cc_start: 0.8376 (t0) cc_final: 0.7988 (t0) REVERT: H 24 LYS cc_start: 0.8341 (mttt) cc_final: 0.7335 (mtpm) REVERT: H 25 GLU cc_start: 0.8156 (mp0) cc_final: 0.6951 (mp0) REVERT: I 24 LYS cc_start: 0.8006 (mttt) cc_final: 0.7437 (mtpm) REVERT: I 25 GLU cc_start: 0.8583 (mp0) cc_final: 0.8352 (mp0) REVERT: J 24 LYS cc_start: 0.7749 (mttt) cc_final: 0.7094 (mtpt) REVERT: J 25 GLU cc_start: 0.8505 (mp0) cc_final: 0.8174 (mp0) REVERT: J 46 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7257 (tmt-80) REVERT: K 24 LYS cc_start: 0.8064 (mttt) cc_final: 0.7308 (mtpm) REVERT: K 38 ARG cc_start: 0.7688 (ttt180) cc_final: 0.7369 (tpp-160) REVERT: K 46 ARG cc_start: 0.8181 (tpt90) cc_final: 0.5398 (mpt-90) REVERT: K 55 GLU cc_start: 0.7804 (tt0) cc_final: 0.5699 (pm20) REVERT: L 16 MET cc_start: 0.8604 (mtt) cc_final: 0.8192 (mtp) REVERT: L 22 ASP cc_start: 0.8872 (t0) cc_final: 0.8283 (t0) REVERT: L 23 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: L 24 LYS cc_start: 0.8121 (mttt) cc_final: 0.7299 (mtpm) REVERT: L 46 ARG cc_start: 0.8482 (tpt90) cc_final: 0.5747 (mpt-90) REVERT: L 55 GLU cc_start: 0.7757 (tt0) cc_final: 0.6098 (pm20) REVERT: L 62 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8122 (mt-10) outliers start: 17 outliers final: 8 residues processed: 156 average time/residue: 1.9358 time to fit residues: 311.2785 Evaluate side-chains 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain B residue 18 ARG 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 23 MET Chi-restraints excluded: chain G residue 18 ARG 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 J residue 46 ARG Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3082 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= 0.217 Angle : 0.502 4.003 9108 Z= 0.293 Chirality : 0.042 0.122 744 Planarity : 0.002 0.023 1236 Dihedral : 4.351 14.464 900 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.60 % Allowed : 16.49 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.21 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (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 H 36 PHE 0.016 0.001 PHE F 67 TYR 0.010 0.001 TYR L 34 ARG 0.002 0.000 ARG J 18 *********************** 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 167 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8762 (mtm) cc_final: 0.8539 (mtm) REVERT: A 24 LYS cc_start: 0.8324 (mttt) cc_final: 0.7949 (mtpm) REVERT: B 24 LYS cc_start: 0.8459 (mttt) cc_final: 0.7837 (mtpp) REVERT: B 38 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7549 (ttm-80) REVERT: C 22 ASP cc_start: 0.8123 (t0) cc_final: 0.7699 (t0) REVERT: C 24 LYS cc_start: 0.8146 (mttt) cc_final: 0.7471 (mtpp) REVERT: C 25 GLU cc_start: 0.8506 (mp0) cc_final: 0.8112 (mp0) REVERT: C 45 GLN cc_start: 0.8015 (mt0) cc_final: 0.7643 (mt0) REVERT: D 24 LYS cc_start: 0.7899 (mttt) cc_final: 0.7482 (mtpm) REVERT: D 45 GLN cc_start: 0.8137 (mt0) cc_final: 0.7689 (mt0) REVERT: D 56 LYS cc_start: 0.8157 (mttt) cc_final: 0.7592 (ttmm) REVERT: D 66 GLU cc_start: 0.8109 (pt0) cc_final: 0.7831 (pt0) REVERT: E 24 LYS cc_start: 0.7817 (mttt) cc_final: 0.7328 (mtpm) REVERT: F 23 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7922 (mtm) REVERT: F 24 LYS cc_start: 0.7750 (mttt) cc_final: 0.7267 (mtpm) REVERT: F 34 TYR cc_start: 0.8049 (m-80) cc_final: 0.7804 (m-80) REVERT: F 38 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6852 (ttt180) REVERT: G 24 LYS cc_start: 0.7669 (mttt) cc_final: 0.7252 (mtpm) REVERT: G 45 GLN cc_start: 0.7729 (mt0) cc_final: 0.7139 (mt0) REVERT: H 22 ASP cc_start: 0.8349 (t0) cc_final: 0.7971 (t0) REVERT: H 24 LYS cc_start: 0.8370 (mttt) cc_final: 0.7336 (mtpm) REVERT: H 25 GLU cc_start: 0.8093 (mp0) cc_final: 0.6907 (mp0) REVERT: I 24 LYS cc_start: 0.7902 (mttt) cc_final: 0.7434 (mtpm) REVERT: I 25 GLU cc_start: 0.8575 (mp0) cc_final: 0.8224 (mp0) REVERT: J 24 LYS cc_start: 0.7693 (mttt) cc_final: 0.7015 (mtpt) REVERT: J 25 GLU cc_start: 0.8551 (mp0) cc_final: 0.8232 (mp0) REVERT: J 46 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6881 (tmt-80) REVERT: J 66 GLU cc_start: 0.7922 (pt0) cc_final: 0.7620 (pt0) REVERT: K 23 MET cc_start: 0.8944 (mtm) cc_final: 0.8478 (mpp) REVERT: K 24 LYS cc_start: 0.7925 (mttt) cc_final: 0.7126 (mtpt) REVERT: K 38 ARG cc_start: 0.7687 (ttt180) cc_final: 0.7332 (tpp-160) REVERT: K 46 ARG cc_start: 0.8079 (tpt90) cc_final: 0.5399 (mpt-90) REVERT: K 55 GLU cc_start: 0.7730 (tt0) cc_final: 0.5647 (pm20) REVERT: L 11 GLN cc_start: 0.9023 (mt0) cc_final: 0.8579 (mt0) REVERT: L 16 MET cc_start: 0.8499 (mtt) cc_final: 0.8123 (mtp) REVERT: L 22 ASP cc_start: 0.8767 (t0) cc_final: 0.8126 (t0) REVERT: L 24 LYS cc_start: 0.8082 (mttt) cc_final: 0.7268 (mtpm) REVERT: L 46 ARG cc_start: 0.8412 (tpt90) cc_final: 0.5813 (mtt-85) REVERT: L 55 GLU cc_start: 0.7731 (tt0) cc_final: 0.6039 (pm20) outliers start: 15 outliers final: 5 residues processed: 155 average time/residue: 1.8869 time to fit residues: 301.7677 Evaluate side-chains 155 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 46 ARG 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 7 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6804 Z= 0.375 Angle : 0.576 4.345 9108 Z= 0.335 Chirality : 0.044 0.120 744 Planarity : 0.003 0.018 1236 Dihedral : 4.575 15.044 900 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.08 % Allowed : 18.92 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 17 HIS 0.003 0.001 HIS L 36 PHE 0.016 0.002 PHE F 5 TYR 0.009 0.001 TYR F 34 ARG 0.003 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8434 (mtm) REVERT: A 24 LYS cc_start: 0.8339 (mttt) cc_final: 0.7965 (mtpm) REVERT: B 24 LYS cc_start: 0.8435 (mttt) cc_final: 0.7856 (mtpp) REVERT: B 29 LYS cc_start: 0.8774 (tttt) cc_final: 0.8374 (ttpt) REVERT: B 38 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7576 (ttm-80) REVERT: C 22 ASP cc_start: 0.8131 (t0) cc_final: 0.7710 (t0) REVERT: C 24 LYS cc_start: 0.8184 (mttt) cc_final: 0.7495 (mtpp) REVERT: C 25 GLU cc_start: 0.8485 (mp0) cc_final: 0.8079 (mp0) REVERT: C 45 GLN cc_start: 0.8143 (mt0) cc_final: 0.7830 (mt0) REVERT: D 24 LYS cc_start: 0.7865 (mttt) cc_final: 0.7343 (mtpp) REVERT: D 45 GLN cc_start: 0.8140 (mt0) cc_final: 0.7717 (mt0) REVERT: D 56 LYS cc_start: 0.8176 (mttt) cc_final: 0.7611 (ttmm) REVERT: D 66 GLU cc_start: 0.8136 (pt0) cc_final: 0.7918 (pt0) REVERT: E 24 LYS cc_start: 0.7841 (mttt) cc_final: 0.7300 (mtpm) REVERT: E 33 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7874 (mptt) REVERT: F 23 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7983 (mtm) REVERT: F 24 LYS cc_start: 0.7738 (mttt) cc_final: 0.7270 (mtpm) REVERT: F 34 TYR cc_start: 0.8039 (m-80) cc_final: 0.7731 (m-80) REVERT: F 38 ARG cc_start: 0.7327 (ttt180) cc_final: 0.7098 (ttt180) REVERT: G 24 LYS cc_start: 0.7745 (mttt) cc_final: 0.7325 (mtpm) REVERT: G 29 LYS cc_start: 0.8002 (tttt) cc_final: 0.7588 (tttm) REVERT: G 45 GLN cc_start: 0.7746 (mt0) cc_final: 0.7145 (mt0) REVERT: H 22 ASP cc_start: 0.8337 (t0) cc_final: 0.7950 (t0) REVERT: H 24 LYS cc_start: 0.8343 (mttt) cc_final: 0.7321 (mtpm) REVERT: H 25 GLU cc_start: 0.8073 (mp0) cc_final: 0.6903 (mp0) REVERT: I 24 LYS cc_start: 0.8012 (mttt) cc_final: 0.7444 (mtpm) REVERT: I 25 GLU cc_start: 0.8569 (mp0) cc_final: 0.8236 (mp0) REVERT: J 24 LYS cc_start: 0.7696 (mttt) cc_final: 0.7023 (mtpt) REVERT: J 25 GLU cc_start: 0.8543 (mp0) cc_final: 0.8245 (mp0) REVERT: J 46 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7062 (tmt-80) REVERT: K 24 LYS cc_start: 0.7899 (mttt) cc_final: 0.7132 (mtpm) REVERT: K 38 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7365 (tpp-160) REVERT: K 46 ARG cc_start: 0.8163 (tpt90) cc_final: 0.5403 (mpt-90) REVERT: K 55 GLU cc_start: 0.7781 (tt0) cc_final: 0.5657 (pm20) REVERT: L 11 GLN cc_start: 0.9034 (mt0) cc_final: 0.8544 (mt0) REVERT: L 16 MET cc_start: 0.8591 (mtt) cc_final: 0.8187 (mtp) REVERT: L 22 ASP cc_start: 0.8857 (t0) cc_final: 0.8233 (t0) REVERT: L 23 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: L 24 LYS cc_start: 0.8118 (mttt) cc_final: 0.7294 (mtpm) REVERT: L 46 ARG cc_start: 0.8507 (tpt90) cc_final: 0.5776 (mpt-90) REVERT: L 55 GLU cc_start: 0.7749 (tt0) cc_final: 0.6047 (pm20) outliers start: 12 outliers final: 4 residues processed: 155 average time/residue: 1.9889 time to fit residues: 317.5670 Evaluate side-chains 159 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 23 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 46 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 20 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6804 Z= 0.374 Angle : 0.576 4.290 9108 Z= 0.335 Chirality : 0.044 0.121 744 Planarity : 0.002 0.016 1236 Dihedral : 4.617 14.807 900 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.60 % Allowed : 19.10 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.003 0.001 HIS L 36 PHE 0.016 0.002 PHE F 67 TYR 0.009 0.001 TYR B 34 ARG 0.003 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: A 24 LYS cc_start: 0.8349 (mttt) cc_final: 0.7959 (mtpm) REVERT: B 24 LYS cc_start: 0.8441 (mttt) cc_final: 0.7877 (mtpp) REVERT: B 29 LYS cc_start: 0.8776 (tttt) cc_final: 0.8358 (ttpt) REVERT: B 38 ARG cc_start: 0.7828 (ttt180) cc_final: 0.7572 (ttm-80) REVERT: C 22 ASP cc_start: 0.8116 (t0) cc_final: 0.7677 (t0) REVERT: C 24 LYS cc_start: 0.8175 (mttt) cc_final: 0.7074 (mtpp) REVERT: C 25 GLU cc_start: 0.8498 (mp0) cc_final: 0.7237 (mp0) REVERT: C 45 GLN cc_start: 0.7967 (mt0) cc_final: 0.7611 (mt0) REVERT: D 24 LYS cc_start: 0.7954 (mttt) cc_final: 0.7459 (mtpp) REVERT: D 45 GLN cc_start: 0.8145 (mt0) cc_final: 0.7735 (mt0) REVERT: D 66 GLU cc_start: 0.8235 (pt0) cc_final: 0.7878 (pt0) REVERT: E 24 LYS cc_start: 0.7834 (mttt) cc_final: 0.7280 (mtpm) REVERT: E 33 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7906 (mptt) REVERT: F 23 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7977 (mtm) REVERT: F 24 LYS cc_start: 0.7745 (mttt) cc_final: 0.7262 (mtpm) REVERT: F 34 TYR cc_start: 0.8045 (m-80) cc_final: 0.7736 (m-80) REVERT: F 38 ARG cc_start: 0.7334 (ttt180) cc_final: 0.7109 (ttt180) REVERT: F 46 ARG cc_start: 0.8574 (tmt170) cc_final: 0.8209 (tpt90) REVERT: G 24 LYS cc_start: 0.7750 (mttt) cc_final: 0.7313 (mtpm) REVERT: G 29 LYS cc_start: 0.8003 (tttt) cc_final: 0.7594 (tttm) REVERT: G 45 GLN cc_start: 0.7737 (mt0) cc_final: 0.7123 (mt0) REVERT: H 22 ASP cc_start: 0.8378 (t0) cc_final: 0.8001 (t0) REVERT: H 24 LYS cc_start: 0.8371 (mttt) cc_final: 0.7336 (mtpm) REVERT: H 25 GLU cc_start: 0.8089 (mp0) cc_final: 0.6916 (mp0) REVERT: I 24 LYS cc_start: 0.7985 (mttt) cc_final: 0.7174 (mtpm) REVERT: I 25 GLU cc_start: 0.8421 (mp0) cc_final: 0.7398 (mp0) REVERT: J 24 LYS cc_start: 0.7695 (mttt) cc_final: 0.7024 (mtpt) REVERT: J 25 GLU cc_start: 0.8542 (mp0) cc_final: 0.8246 (mp0) REVERT: J 46 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7022 (tmt-80) REVERT: K 23 MET cc_start: 0.8972 (mtm) cc_final: 0.8505 (mpp) REVERT: K 24 LYS cc_start: 0.7915 (mttt) cc_final: 0.7149 (mtpt) REVERT: K 38 ARG cc_start: 0.7715 (ttt180) cc_final: 0.7390 (tpp-160) REVERT: K 46 ARG cc_start: 0.8105 (tpt90) cc_final: 0.5532 (mtt90) REVERT: K 55 GLU cc_start: 0.7774 (tt0) cc_final: 0.5650 (pm20) REVERT: K 62 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8235 (mt-10) REVERT: L 11 GLN cc_start: 0.9031 (mt0) cc_final: 0.8530 (mt0) REVERT: L 16 MET cc_start: 0.8615 (mtt) cc_final: 0.8220 (mtp) REVERT: L 22 ASP cc_start: 0.8861 (t0) cc_final: 0.8207 (t0) REVERT: L 23 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8329 (mtm) REVERT: L 24 LYS cc_start: 0.8123 (mttt) cc_final: 0.7305 (mtpm) REVERT: L 46 ARG cc_start: 0.8501 (tpt90) cc_final: 0.5732 (mpt-90) REVERT: L 55 GLU cc_start: 0.7742 (tt0) cc_final: 0.6042 (pm20) outliers start: 15 outliers final: 7 residues processed: 154 average time/residue: 1.9144 time to fit residues: 303.7897 Evaluate side-chains 161 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 23 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 63 SER 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 J residue 46 ARG Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.0770 chunk 41 optimal weight: 7.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6804 Z= 0.402 Angle : 0.595 4.642 9108 Z= 0.345 Chirality : 0.045 0.122 744 Planarity : 0.003 0.021 1236 Dihedral : 4.696 15.763 900 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.78 % Allowed : 19.62 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -3.38 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.004 0.002 HIS L 36 PHE 0.016 0.002 PHE F 67 TYR 0.010 0.001 TYR B 34 ARG 0.003 0.001 ARG L 18 *********************** 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 164 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8485 (mtm) REVERT: A 24 LYS cc_start: 0.8308 (mttt) cc_final: 0.7936 (mtpm) REVERT: B 24 LYS cc_start: 0.8447 (mttt) cc_final: 0.7886 (mtpp) REVERT: B 29 LYS cc_start: 0.8752 (tttt) cc_final: 0.8338 (ttpt) REVERT: B 38 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7572 (ttm-80) REVERT: B 66 GLU cc_start: 0.8453 (pt0) cc_final: 0.8240 (pt0) REVERT: C 22 ASP cc_start: 0.8163 (t0) cc_final: 0.7764 (t0) REVERT: C 23 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7878 (mtm) REVERT: C 24 LYS cc_start: 0.8188 (mttt) cc_final: 0.7085 (mtpp) REVERT: C 25 GLU cc_start: 0.8502 (mp0) cc_final: 0.7250 (mp0) REVERT: C 45 GLN cc_start: 0.7977 (mt0) cc_final: 0.7624 (mt0) REVERT: D 24 LYS cc_start: 0.7945 (mttt) cc_final: 0.7454 (mtpp) REVERT: D 45 GLN cc_start: 0.8179 (mt0) cc_final: 0.7784 (mt0) REVERT: E 24 LYS cc_start: 0.7848 (mttt) cc_final: 0.7291 (mtpm) REVERT: E 33 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7948 (mptt) REVERT: F 23 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: F 24 LYS cc_start: 0.7746 (mttt) cc_final: 0.7268 (mtpm) REVERT: F 34 TYR cc_start: 0.8052 (m-80) cc_final: 0.7795 (m-80) REVERT: F 46 ARG cc_start: 0.8424 (tmt170) cc_final: 0.8220 (tpt90) REVERT: G 24 LYS cc_start: 0.7779 (mttt) cc_final: 0.7368 (mtpm) REVERT: G 29 LYS cc_start: 0.8002 (tttt) cc_final: 0.7596 (tttp) REVERT: G 45 GLN cc_start: 0.7734 (mt0) cc_final: 0.7109 (mt0) REVERT: H 22 ASP cc_start: 0.8410 (t0) cc_final: 0.8025 (t0) REVERT: H 24 LYS cc_start: 0.8381 (mttt) cc_final: 0.7350 (mtpm) REVERT: H 25 GLU cc_start: 0.8092 (mp0) cc_final: 0.6911 (mp0) REVERT: I 24 LYS cc_start: 0.8018 (mttt) cc_final: 0.7215 (mtpm) REVERT: I 25 GLU cc_start: 0.8420 (mp0) cc_final: 0.7399 (mp0) REVERT: J 24 LYS cc_start: 0.7698 (mttt) cc_final: 0.7032 (mtpt) REVERT: J 25 GLU cc_start: 0.8543 (mp0) cc_final: 0.8257 (mp0) REVERT: J 46 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7369 (tmt-80) REVERT: K 24 LYS cc_start: 0.8007 (mttt) cc_final: 0.7274 (mtpm) REVERT: K 38 ARG cc_start: 0.7703 (ttt180) cc_final: 0.7375 (tpp-160) REVERT: K 46 ARG cc_start: 0.8110 (tpt90) cc_final: 0.5539 (mtt90) REVERT: K 55 GLU cc_start: 0.7789 (tt0) cc_final: 0.5652 (pm20) REVERT: K 62 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8232 (mt-10) REVERT: L 11 GLN cc_start: 0.9029 (mt0) cc_final: 0.8519 (mt0) REVERT: L 16 MET cc_start: 0.8614 (mtt) cc_final: 0.8220 (mtp) REVERT: L 22 ASP cc_start: 0.8877 (t0) cc_final: 0.8225 (t0) REVERT: L 23 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: L 24 LYS cc_start: 0.8127 (mttt) cc_final: 0.7310 (mtpm) REVERT: L 46 ARG cc_start: 0.8505 (tpt90) cc_final: 0.5737 (mpt-90) REVERT: L 55 GLU cc_start: 0.7742 (tt0) cc_final: 0.6044 (pm20) outliers start: 16 outliers final: 7 residues processed: 151 average time/residue: 1.8797 time to fit residues: 292.7788 Evaluate side-chains 160 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain G residue 63 SER 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 J residue 46 ARG Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6804 Z= 0.277 Angle : 0.540 4.358 9108 Z= 0.314 Chirality : 0.043 0.123 744 Planarity : 0.002 0.017 1236 Dihedral : 4.521 16.101 900 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.08 % Allowed : 20.31 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.44 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 28 HIS 0.002 0.001 HIS H 36 PHE 0.018 0.001 PHE F 67 TYR 0.011 0.001 TYR B 34 ARG 0.002 0.000 ARG L 18 ********************** 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 163 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 23 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8438 (mtm) REVERT: A 24 LYS cc_start: 0.8345 (mttt) cc_final: 0.7955 (mtpm) REVERT: B 24 LYS cc_start: 0.8441 (mttt) cc_final: 0.7870 (mtpp) REVERT: B 29 LYS cc_start: 0.8767 (tttt) cc_final: 0.8361 (ttpt) REVERT: B 38 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7553 (ttm-80) REVERT: B 66 GLU cc_start: 0.8350 (pt0) cc_final: 0.8145 (pt0) REVERT: C 22 ASP cc_start: 0.8063 (t0) cc_final: 0.7664 (t0) REVERT: C 24 LYS cc_start: 0.8276 (mttt) cc_final: 0.7188 (mtpp) REVERT: C 25 GLU cc_start: 0.8498 (mp0) cc_final: 0.7218 (mp0) REVERT: C 45 GLN cc_start: 0.7958 (mt0) cc_final: 0.7603 (mt0) REVERT: D 24 LYS cc_start: 0.7963 (mttt) cc_final: 0.7463 (mtpp) REVERT: D 45 GLN cc_start: 0.8147 (mt0) cc_final: 0.7724 (mt0) REVERT: D 56 LYS cc_start: 0.8262 (mttt) cc_final: 0.7922 (ttmt) REVERT: E 24 LYS cc_start: 0.7834 (mttt) cc_final: 0.7277 (mtpm) REVERT: F 23 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: F 24 LYS cc_start: 0.7731 (mttt) cc_final: 0.7231 (mtpm) REVERT: F 34 TYR cc_start: 0.8045 (m-80) cc_final: 0.7754 (m-80) REVERT: G 24 LYS cc_start: 0.8036 (mttt) cc_final: 0.7551 (mtpm) REVERT: G 29 LYS cc_start: 0.8021 (tttt) cc_final: 0.7625 (tttp) REVERT: G 45 GLN cc_start: 0.7711 (mt0) cc_final: 0.7108 (mt0) REVERT: H 22 ASP cc_start: 0.8446 (t0) cc_final: 0.8079 (t0) REVERT: H 24 LYS cc_start: 0.8382 (mttt) cc_final: 0.7333 (mtpm) REVERT: H 25 GLU cc_start: 0.8103 (mp0) cc_final: 0.6897 (mp0) REVERT: I 24 LYS cc_start: 0.8002 (mttt) cc_final: 0.7471 (mtpm) REVERT: I 25 GLU cc_start: 0.8394 (mp0) cc_final: 0.8057 (mp0) REVERT: J 24 LYS cc_start: 0.7800 (mttt) cc_final: 0.7144 (mtpt) REVERT: J 25 GLU cc_start: 0.8543 (mp0) cc_final: 0.8238 (mp0) REVERT: K 23 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8647 (mpp) REVERT: K 24 LYS cc_start: 0.7968 (mttt) cc_final: 0.7094 (mtpm) REVERT: K 38 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7418 (tpp-160) REVERT: K 46 ARG cc_start: 0.8119 (tpt90) cc_final: 0.5567 (mtt90) REVERT: K 55 GLU cc_start: 0.7750 (tt0) cc_final: 0.5660 (pm20) REVERT: L 11 GLN cc_start: 0.9030 (mt0) cc_final: 0.8560 (mt0) REVERT: L 16 MET cc_start: 0.8538 (mtt) cc_final: 0.8152 (mtp) REVERT: L 22 ASP cc_start: 0.8812 (t0) cc_final: 0.8148 (t0) REVERT: L 24 LYS cc_start: 0.8127 (mttt) cc_final: 0.7310 (mtpm) REVERT: L 46 ARG cc_start: 0.8484 (tpt90) cc_final: 0.5743 (mpt-90) REVERT: L 55 GLU cc_start: 0.7717 (tt0) cc_final: 0.6034 (pm20) outliers start: 12 outliers final: 4 residues processed: 152 average time/residue: 1.8645 time to fit residues: 292.4010 Evaluate side-chains 155 residues out of total 576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain L residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.104096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.090591 restraints weight = 10063.134| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.60 r_work: 0.3499 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6804 Z= 0.343 Angle : 0.572 5.265 9108 Z= 0.332 Chirality : 0.044 0.122 744 Planarity : 0.003 0.033 1236 Dihedral : 4.665 16.053 900 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.74 % Allowed : 21.53 % Favored : 76.74 % 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: -4.49 (0.16), residues: 804 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.12), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 17 HIS 0.003 0.001 HIS L 36 PHE 0.016 0.002 PHE K 67 TYR 0.012 0.001 TYR B 34 ARG 0.004 0.001 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.23 seconds wall clock time: 77 minutes 48.85 seconds (4668.85 seconds total)