Starting phenix.real_space_refine on Sun Mar 10 17:52:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/03_2024/8a7t_15225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/03_2024/8a7t_15225.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/8a7t_15225/03_2024/8a7t_15225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/03_2024/8a7t_15225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/03_2024/8a7t_15225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/03_2024/8a7t_15225.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= 0.000 sd= 0.004 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 12 5.16 5 C 2370 2.51 5 N 600 2.21 5 O 720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3702 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "B" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 530 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "C" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "D" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 530 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "E" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 530 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Time building chain proxies: 2.44, per 1000 atoms: 0.66 Number of scatterers: 3702 At special positions: 0 Unit cell: (104.58, 108.73, 34.86, 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 12 16.00 O 720 8.00 N 600 7.00 C 2370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " distance=2.03 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: 1.22 Conformation dependent library (CDL) restraints added in 658.6 milliseconds 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.813A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.226A pdb=" N GLU A 16 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C 16 " --> pdb=" O ASN E 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.648A pdb=" N SER A 20 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU C 23 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 22 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER C 20 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU E 23 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE C 22 " --> pdb=" O LEU E 23 " (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 39 removed outlier: 6.985A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.767A pdb=" N GLY C 43 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.243A pdb=" N VAL C 49 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS C 51 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL E 49 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU C 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N HIS E 51 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.279A pdb=" N TRP A 60 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 63 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 62 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N LEU C 65 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N LEU A 64 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TRP C 60 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR E 63 " --> pdb=" O TRP C 60 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE C 62 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N LEU E 65 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N LEU C 64 " --> pdb=" O LEU E 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 removed outlier: 6.440A pdb=" N GLU C 69 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU E 69 " --> pdb=" O PHE C 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.529A pdb=" N GLU C 74 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 88 Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 24 removed outlier: 7.067A pdb=" N LEU B 23 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 23 " --> pdb=" O ASN F 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.782A pdb=" N ILE B 35 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASP D 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 37 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE D 35 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP F 38 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 37 " --> pdb=" O ASP F 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 53 removed outlier: 6.912A pdb=" N GLY B 43 " --> pdb=" O GLU D 44 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 46 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ARG B 45 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS D 48 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B 47 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLU D 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 49 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HIS B 51 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY D 43 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE F 46 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ARG D 45 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N LYS F 48 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU D 47 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU F 50 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL D 49 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N HIS D 51 " --> pdb=" O SER F 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 66 removed outlier: 9.790A pdb=" N ASP B 59 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N PHE D 62 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER B 61 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU D 64 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR B 63 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR D 66 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 65 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N ASP D 59 " --> pdb=" O TRP F 60 " (cutoff:3.500A) removed outlier: 9.840A pdb=" N PHE F 62 " --> pdb=" O ASP D 59 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER D 61 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU F 64 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR D 63 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR F 66 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 65 " --> pdb=" O TYR F 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 70 removed outlier: 6.455A pdb=" N GLU D 69 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU F 69 " --> pdb=" O PHE D 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AB9, first strand: chain 'B' and resid 77 through 78 41 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1179 1.34 - 1.46: 950 1.46 - 1.58: 1666 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 3807 Sorted by residual: bond pdb=" C ASN F 42 " pdb=" N GLY F 43 " ideal model delta sigma weight residual 1.333 1.324 0.010 1.22e-02 6.72e+03 6.72e-01 bond pdb=" C ASN D 42 " pdb=" N GLY D 43 " ideal model delta sigma weight residual 1.333 1.324 0.010 1.22e-02 6.72e+03 6.39e-01 bond pdb=" N GLY F 43 " pdb=" CA GLY F 43 " ideal model delta sigma weight residual 1.444 1.451 -0.008 1.02e-02 9.61e+03 5.60e-01 bond pdb=" C ASN B 42 " pdb=" N GLY B 43 " ideal model delta sigma weight residual 1.333 1.324 0.009 1.22e-02 6.72e+03 5.49e-01 bond pdb=" N GLY B 43 " pdb=" CA GLY B 43 " ideal model delta sigma weight residual 1.444 1.451 -0.007 1.02e-02 9.61e+03 4.66e-01 ... (remaining 3802 not shown) Histogram of bond angle deviations from ideal: 102.56 - 108.84: 346 108.84 - 115.11: 1975 115.11 - 121.39: 1780 121.39 - 127.67: 1014 127.67 - 133.94: 42 Bond angle restraints: 5157 Sorted by residual: angle pdb=" NE ARG A 12 " pdb=" CZ ARG A 12 " pdb=" NH1 ARG A 12 " ideal model delta sigma weight residual 121.50 119.96 1.54 1.00e+00 1.00e+00 2.38e+00 angle pdb=" NE ARG B 45 " pdb=" CZ ARG B 45 " pdb=" NH1 ARG B 45 " ideal model delta sigma weight residual 121.50 119.97 1.53 1.00e+00 1.00e+00 2.34e+00 angle pdb=" NE ARG C 12 " pdb=" CZ ARG C 12 " pdb=" NH1 ARG C 12 " ideal model delta sigma weight residual 121.50 120.00 1.50 1.00e+00 1.00e+00 2.26e+00 angle pdb=" NE ARG B 81 " pdb=" CZ ARG B 81 " pdb=" NH1 ARG B 81 " ideal model delta sigma weight residual 121.50 120.00 1.50 1.00e+00 1.00e+00 2.25e+00 angle pdb=" NE ARG A 45 " pdb=" CZ ARG A 45 " pdb=" NH1 ARG A 45 " ideal model delta sigma weight residual 121.50 120.01 1.49 1.00e+00 1.00e+00 2.22e+00 ... (remaining 5152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.61: 2056 10.61 - 21.21: 161 21.21 - 31.82: 21 31.82 - 42.42: 9 42.42 - 53.03: 6 Dihedral angle restraints: 2253 sinusoidal: 924 harmonic: 1329 Sorted by residual: dihedral pdb=" CA LEU D 39 " pdb=" CB LEU D 39 " pdb=" CG LEU D 39 " pdb=" CD1 LEU D 39 " ideal model delta sinusoidal sigma weight residual 180.00 141.26 38.74 3 1.50e+01 4.44e-03 6.83e+00 dihedral pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " pdb=" CG LEU B 39 " pdb=" CD1 LEU B 39 " ideal model delta sinusoidal sigma weight residual 180.00 141.27 38.73 3 1.50e+01 4.44e-03 6.83e+00 dihedral pdb=" CA LEU F 39 " pdb=" CB LEU F 39 " pdb=" CG LEU F 39 " pdb=" CD1 LEU F 39 " ideal model delta sinusoidal sigma weight residual 180.00 141.27 38.73 3 1.50e+01 4.44e-03 6.83e+00 ... (remaining 2250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 262 0.025 - 0.051: 203 0.051 - 0.076: 24 0.076 - 0.101: 9 0.101 - 0.127: 36 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 531 not shown) Planarity restraints: 666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 71 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO E 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 71 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 71 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO C 72 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " -0.016 5.00e-02 4.00e+02 ... (remaining 663 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 994 2.82 - 3.34: 2839 3.34 - 3.86: 5703 3.86 - 4.38: 6386 4.38 - 4.90: 10666 Nonbonded interactions: 26588 Sorted by model distance: nonbonded pdb=" OE2 GLU C 16 " pdb=" NH2 ARG C 81 " model vdw 2.302 2.520 nonbonded pdb=" OE2 GLU A 16 " pdb=" NH2 ARG A 81 " model vdw 2.302 2.520 nonbonded pdb=" OE2 GLU E 16 " pdb=" NH2 ARG E 81 " model vdw 2.303 2.520 nonbonded pdb=" O LYS A 58 " pdb=" N LYS C 58 " model vdw 2.305 2.520 nonbonded pdb=" O LYS C 58 " pdb=" N LYS E 58 " model vdw 2.392 2.520 ... (remaining 26583 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.550 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.003 0.019 3807 Z= 0.193 Angle : 0.465 3.534 5157 Z= 0.266 Chirality : 0.042 0.127 534 Planarity : 0.003 0.030 666 Dihedral : 8.475 53.030 1377 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.48 (0.28), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 60 HIS 0.002 0.001 HIS A 13 PHE 0.007 0.001 PHE A 70 TYR 0.008 0.001 TYR F 63 ARG 0.001 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.5860 (mttt) cc_final: 0.5630 (mptt) REVERT: A 12 ARG cc_start: 0.7894 (ttt180) cc_final: 0.5563 (tpm-80) REVERT: A 50 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7834 (mt-10) REVERT: C 36 GLU cc_start: 0.7582 (tt0) cc_final: 0.6991 (mt-10) REVERT: C 38 ASP cc_start: 0.7971 (p0) cc_final: 0.7700 (p0) REVERT: C 50 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7806 (mt-10) REVERT: C 51 HIS cc_start: 0.7738 (m90) cc_final: 0.7146 (m-70) REVERT: D 36 GLU cc_start: 0.7744 (tt0) cc_final: 0.7473 (mt-10) REVERT: D 38 ASP cc_start: 0.8802 (p0) cc_final: 0.8448 (p0) REVERT: D 45 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7753 (mtp85) REVERT: E 6 LYS cc_start: 0.6277 (mttt) cc_final: 0.6077 (mptt) REVERT: E 19 LYS cc_start: 0.8955 (pttt) cc_final: 0.8742 (pttm) REVERT: E 36 GLU cc_start: 0.7577 (tt0) cc_final: 0.6903 (mt-10) REVERT: E 48 LYS cc_start: 0.7635 (mttt) cc_final: 0.7405 (mmpt) REVERT: E 50 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7524 (mp0) REVERT: E 77 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8046 (mt-10) REVERT: F 34 ASP cc_start: 0.8311 (m-30) cc_final: 0.8060 (m-30) REVERT: F 36 GLU cc_start: 0.7684 (tt0) cc_final: 0.7439 (tt0) REVERT: F 38 ASP cc_start: 0.8341 (p0) cc_final: 0.8118 (p0) REVERT: F 75 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7868 (mtpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.2599 time to fit residues: 163.0875 Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3807 Z= 0.276 Angle : 0.552 4.616 5157 Z= 0.286 Chirality : 0.045 0.137 534 Planarity : 0.003 0.017 666 Dihedral : 4.371 12.569 486 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.62 % Allowed : 9.76 % Favored : 87.62 % 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 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 60 HIS 0.004 0.001 HIS C 13 PHE 0.013 0.002 PHE F 30 TYR 0.012 0.002 TYR A 63 ARG 0.001 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.480 Fit side-chains REVERT: A 12 ARG cc_start: 0.7959 (ttt180) cc_final: 0.5720 (tpm-80) REVERT: A 36 GLU cc_start: 0.7855 (tt0) cc_final: 0.7218 (mt-10) REVERT: A 38 ASP cc_start: 0.7722 (p0) cc_final: 0.7438 (p0) REVERT: A 50 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7990 (mt-10) REVERT: A 58 LYS cc_start: 0.7982 (mmtt) cc_final: 0.6039 (pmtt) REVERT: C 16 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 36 GLU cc_start: 0.7240 (tt0) cc_final: 0.6463 (mt-10) REVERT: C 44 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6179 (mm-30) REVERT: C 48 LYS cc_start: 0.7684 (mttt) cc_final: 0.7380 (mmtp) REVERT: C 50 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7631 (mt-10) REVERT: C 51 HIS cc_start: 0.7453 (m90) cc_final: 0.6844 (m-70) REVERT: D 36 GLU cc_start: 0.7658 (tt0) cc_final: 0.7330 (mt-10) REVERT: D 47 GLU cc_start: 0.7912 (tp30) cc_final: 0.7217 (mm-30) REVERT: E 6 LYS cc_start: 0.6232 (mttt) cc_final: 0.5924 (mptt) REVERT: E 36 GLU cc_start: 0.7312 (tt0) cc_final: 0.6530 (mt-10) REVERT: E 48 LYS cc_start: 0.7614 (mttt) cc_final: 0.7380 (mmpt) REVERT: E 50 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7525 (mt-10) REVERT: F 75 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7848 (mtpp) outliers start: 11 outliers final: 9 residues processed: 128 average time/residue: 1.3558 time to fit residues: 177.7882 Evaluate side-chains 124 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 61 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN A 89 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN E 89 GLN F 24 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3807 Z= 0.174 Angle : 0.497 3.962 5157 Z= 0.259 Chirality : 0.043 0.134 534 Planarity : 0.003 0.018 666 Dihedral : 4.229 14.238 486 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.38 % Allowed : 13.57 % Favored : 84.05 % 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: -4.07 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 60 HIS 0.004 0.001 HIS C 13 PHE 0.008 0.001 PHE D 30 TYR 0.014 0.001 TYR B 67 ARG 0.002 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7939 (ttt180) cc_final: 0.5786 (tpm-80) REVERT: A 36 GLU cc_start: 0.7838 (tt0) cc_final: 0.7110 (mt-10) REVERT: A 38 ASP cc_start: 0.7658 (p0) cc_final: 0.7389 (p0) REVERT: A 44 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 50 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8062 (mt-10) REVERT: A 58 LYS cc_start: 0.8028 (mmtt) cc_final: 0.6069 (pmtt) REVERT: B 45 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7861 (mtp85) REVERT: C 6 LYS cc_start: 0.5886 (mptp) cc_final: 0.5025 (tttt) REVERT: C 16 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 36 GLU cc_start: 0.7288 (tt0) cc_final: 0.6554 (mt-10) REVERT: C 48 LYS cc_start: 0.7654 (mttt) cc_final: 0.7336 (mmtp) REVERT: C 50 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 77 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: D 36 GLU cc_start: 0.7678 (tt0) cc_final: 0.7472 (mp0) REVERT: D 47 GLU cc_start: 0.7719 (tp30) cc_final: 0.7411 (tp30) REVERT: E 6 LYS cc_start: 0.6411 (mttt) cc_final: 0.6206 (mptp) REVERT: E 36 GLU cc_start: 0.7372 (tt0) cc_final: 0.6583 (mt-10) REVERT: E 50 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7985 (mt-10) REVERT: F 36 GLU cc_start: 0.7533 (tt0) cc_final: 0.7286 (tt0) REVERT: F 75 LYS cc_start: 0.8120 (mtmt) cc_final: 0.7868 (mtpp) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 1.3255 time to fit residues: 169.8616 Evaluate side-chains 126 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 69 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3807 Z= 0.413 Angle : 0.617 6.665 5157 Z= 0.319 Chirality : 0.046 0.145 534 Planarity : 0.003 0.027 666 Dihedral : 4.760 15.424 486 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.52 % Allowed : 13.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 60 HIS 0.005 0.002 HIS C 13 PHE 0.014 0.002 PHE F 30 TYR 0.017 0.002 TYR B 67 ARG 0.003 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8005 (ttt180) cc_final: 0.5816 (tpm170) REVERT: A 36 GLU cc_start: 0.7809 (tt0) cc_final: 0.7091 (mt-10) REVERT: A 50 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8066 (mt-10) REVERT: A 58 LYS cc_start: 0.7974 (mmtt) cc_final: 0.6122 (pptt) REVERT: A 74 GLU cc_start: 0.8027 (pt0) cc_final: 0.7456 (pt0) REVERT: B 36 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 81 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7019 (pmt-80) REVERT: C 16 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 36 GLU cc_start: 0.7278 (tt0) cc_final: 0.6581 (mt-10) REVERT: C 50 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 58 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7336 (mmtt) REVERT: C 77 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: D 38 ASP cc_start: 0.8613 (p0) cc_final: 0.8330 (p0) REVERT: E 6 LYS cc_start: 0.6556 (mttt) cc_final: 0.6111 (mptp) REVERT: E 36 GLU cc_start: 0.7454 (tt0) cc_final: 0.6650 (mt-10) REVERT: F 36 GLU cc_start: 0.7618 (tt0) cc_final: 0.7219 (tt0) REVERT: F 38 ASP cc_start: 0.8774 (p0) cc_final: 0.8462 (p0) REVERT: F 45 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7429 (mtt-85) REVERT: F 75 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7921 (mtpp) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 1.4311 time to fit residues: 184.8866 Evaluate side-chains 129 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 61 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3807 Z= 0.353 Angle : 0.590 8.171 5157 Z= 0.300 Chirality : 0.045 0.139 534 Planarity : 0.003 0.019 666 Dihedral : 4.787 15.410 486 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.76 % Allowed : 15.95 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.005 0.001 HIS C 31 PHE 0.012 0.002 PHE F 30 TYR 0.018 0.002 TYR B 67 ARG 0.003 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 12 ARG cc_start: 0.7964 (ttt180) cc_final: 0.5841 (tpm170) REVERT: A 36 GLU cc_start: 0.7780 (tt0) cc_final: 0.7005 (mt-10) REVERT: A 50 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 58 LYS cc_start: 0.7993 (mmtt) cc_final: 0.6090 (pmtt) REVERT: A 74 GLU cc_start: 0.8047 (pt0) cc_final: 0.7521 (pt0) REVERT: B 45 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7946 (mtp85) REVERT: B 81 ARG cc_start: 0.7360 (mtt180) cc_final: 0.6976 (pmt-80) REVERT: C 16 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 36 GLU cc_start: 0.7319 (tt0) cc_final: 0.6666 (mt-10) REVERT: C 48 LYS cc_start: 0.7753 (tptm) cc_final: 0.7336 (tppp) REVERT: C 50 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 77 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: E 6 LYS cc_start: 0.6494 (mttt) cc_final: 0.6094 (mptp) REVERT: E 36 GLU cc_start: 0.7458 (tt0) cc_final: 0.6746 (mt-10) REVERT: E 48 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.3866 (tptt) REVERT: F 45 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7409 (mtt-85) REVERT: F 75 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7884 (mtpp) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 1.3463 time to fit residues: 171.1868 Evaluate side-chains 127 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3807 Z= 0.337 Angle : 0.589 7.685 5157 Z= 0.298 Chirality : 0.045 0.141 534 Planarity : 0.003 0.021 666 Dihedral : 4.796 14.733 486 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.24 % Allowed : 16.19 % Favored : 78.57 % 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: -4.10 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS C 31 PHE 0.013 0.002 PHE F 30 TYR 0.018 0.002 TYR B 67 ARG 0.002 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.5968 (mptp) cc_final: 0.5183 (mmmm) REVERT: A 12 ARG cc_start: 0.7918 (ttt180) cc_final: 0.5865 (tpm170) REVERT: A 36 GLU cc_start: 0.7749 (tt0) cc_final: 0.6977 (mt-10) REVERT: A 50 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8257 (mt-10) REVERT: A 58 LYS cc_start: 0.7970 (mmtt) cc_final: 0.6088 (pmtt) REVERT: A 74 GLU cc_start: 0.8046 (pt0) cc_final: 0.7560 (pt0) REVERT: B 45 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7978 (mtp85) REVERT: B 81 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6981 (pmt-80) REVERT: C 16 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 36 GLU cc_start: 0.7331 (tt0) cc_final: 0.6684 (mt-10) REVERT: C 48 LYS cc_start: 0.7724 (tptm) cc_final: 0.7328 (tppp) REVERT: C 50 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7815 (mt-10) REVERT: C 77 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: D 74 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: E 6 LYS cc_start: 0.6413 (mttt) cc_final: 0.6082 (mptp) REVERT: E 36 GLU cc_start: 0.7444 (tt0) cc_final: 0.6758 (mt-10) REVERT: E 48 LYS cc_start: 0.4383 (OUTLIER) cc_final: 0.4032 (tptt) REVERT: F 45 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7343 (mtt-85) REVERT: F 74 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: F 75 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7912 (mtpp) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 1.3073 time to fit residues: 166.2670 Evaluate side-chains 130 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 74 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3807 Z= 0.266 Angle : 0.572 8.134 5157 Z= 0.285 Chirality : 0.045 0.140 534 Planarity : 0.003 0.020 666 Dihedral : 4.663 14.630 486 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.24 % Allowed : 16.90 % Favored : 77.86 % 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: -4.04 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.001 HIS C 31 PHE 0.010 0.002 PHE F 30 TYR 0.017 0.001 TYR B 67 ARG 0.001 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6041 (mptp) cc_final: 0.5233 (mmmm) REVERT: A 12 ARG cc_start: 0.7911 (ttt180) cc_final: 0.5905 (tpm170) REVERT: A 36 GLU cc_start: 0.7767 (tt0) cc_final: 0.7011 (mt-10) REVERT: A 50 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 58 LYS cc_start: 0.7981 (mmtt) cc_final: 0.6095 (pmtt) REVERT: A 74 GLU cc_start: 0.8039 (pt0) cc_final: 0.7601 (pt0) REVERT: B 45 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7976 (mtp85) REVERT: B 81 ARG cc_start: 0.7451 (mtt180) cc_final: 0.6984 (pmt-80) REVERT: C 16 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 36 GLU cc_start: 0.7309 (tt0) cc_final: 0.6724 (mt-10) REVERT: C 48 LYS cc_start: 0.7715 (tptm) cc_final: 0.7344 (tppp) REVERT: C 50 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 77 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: D 74 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: E 6 LYS cc_start: 0.6453 (mttt) cc_final: 0.6091 (mptp) REVERT: E 36 GLU cc_start: 0.7435 (tt0) cc_final: 0.6739 (mt-10) REVERT: E 48 LYS cc_start: 0.4240 (OUTLIER) cc_final: 0.4024 (tptt) REVERT: F 45 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7310 (mtt-85) REVERT: F 74 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: F 75 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7836 (mtpp) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 1.4577 time to fit residues: 189.7320 Evaluate side-chains 135 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3807 Z= 0.225 Angle : 0.566 10.299 5157 Z= 0.280 Chirality : 0.044 0.139 534 Planarity : 0.002 0.018 666 Dihedral : 4.522 14.170 486 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.29 % Allowed : 17.14 % Favored : 78.57 % 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: -3.97 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 60 HIS 0.003 0.001 HIS C 31 PHE 0.010 0.001 PHE F 30 TYR 0.017 0.001 TYR E 10 ARG 0.002 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6039 (mptp) cc_final: 0.5218 (mmmm) REVERT: A 12 ARG cc_start: 0.7904 (ttt180) cc_final: 0.5907 (tpm170) REVERT: A 16 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 36 GLU cc_start: 0.7764 (tt0) cc_final: 0.7005 (mt-10) REVERT: A 50 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 58 LYS cc_start: 0.7955 (mmtt) cc_final: 0.6043 (pmtt) REVERT: A 74 GLU cc_start: 0.8047 (pt0) cc_final: 0.7742 (pt0) REVERT: B 45 ARG cc_start: 0.8263 (mtp85) cc_final: 0.7985 (mtp85) REVERT: B 81 ARG cc_start: 0.7456 (mtt180) cc_final: 0.6986 (pmt-80) REVERT: C 6 LYS cc_start: 0.6063 (mptp) cc_final: 0.5219 (mmmm) REVERT: C 36 GLU cc_start: 0.7319 (tt0) cc_final: 0.6741 (mt-10) REVERT: C 48 LYS cc_start: 0.7714 (tptm) cc_final: 0.7350 (tppp) REVERT: C 50 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 77 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: D 74 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: E 6 LYS cc_start: 0.6469 (mttt) cc_final: 0.6125 (mptp) REVERT: E 36 GLU cc_start: 0.7418 (tt0) cc_final: 0.6712 (mt-10) REVERT: E 48 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.4040 (tptt) REVERT: F 74 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: F 75 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7805 (mtpp) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 1.4079 time to fit residues: 176.1396 Evaluate side-chains 131 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 74 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3807 Z= 0.269 Angle : 0.566 7.188 5157 Z= 0.286 Chirality : 0.044 0.142 534 Planarity : 0.002 0.019 666 Dihedral : 4.569 13.965 486 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.81 % Allowed : 17.38 % Favored : 78.81 % 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: -3.96 (0.31), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 PHE 0.011 0.002 PHE F 30 TYR 0.018 0.002 TYR B 67 ARG 0.001 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.6001 (mptp) cc_final: 0.5200 (mmmm) REVERT: A 12 ARG cc_start: 0.7851 (ttt180) cc_final: 0.5801 (tpm170) REVERT: A 16 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 36 GLU cc_start: 0.7737 (tt0) cc_final: 0.7009 (mt-10) REVERT: A 50 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 58 LYS cc_start: 0.7950 (mmtt) cc_final: 0.6053 (pmtt) REVERT: A 74 GLU cc_start: 0.8023 (pt0) cc_final: 0.7730 (pt0) REVERT: B 45 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7988 (mtp85) REVERT: B 81 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6971 (pmt-80) REVERT: C 6 LYS cc_start: 0.6188 (mptp) cc_final: 0.5186 (mmmm) REVERT: C 36 GLU cc_start: 0.7354 (tt0) cc_final: 0.6750 (mt-10) REVERT: C 48 LYS cc_start: 0.7705 (tptm) cc_final: 0.7339 (tppp) REVERT: C 50 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 74 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: E 6 LYS cc_start: 0.6550 (mttt) cc_final: 0.6212 (mptp) REVERT: E 36 GLU cc_start: 0.7423 (tt0) cc_final: 0.6716 (mt-10) REVERT: E 48 LYS cc_start: 0.4293 (OUTLIER) cc_final: 0.4055 (tptt) REVERT: F 74 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: F 75 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7866 (mtpp) outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 1.3875 time to fit residues: 180.5836 Evaluate side-chains 134 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3807 Z= 0.364 Angle : 0.619 7.054 5157 Z= 0.314 Chirality : 0.046 0.148 534 Planarity : 0.003 0.026 666 Dihedral : 4.775 13.871 486 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.29 % Allowed : 17.14 % Favored : 78.57 % 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: -4.02 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 60 HIS 0.004 0.002 HIS C 31 PHE 0.014 0.002 PHE F 30 TYR 0.020 0.002 TYR B 67 ARG 0.002 0.000 ARG A 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 6 LYS cc_start: 0.5982 (mptp) cc_final: 0.5155 (mmmm) REVERT: A 12 ARG cc_start: 0.7857 (ttt180) cc_final: 0.5810 (tpm170) REVERT: A 16 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 36 GLU cc_start: 0.7746 (tt0) cc_final: 0.7014 (mt-10) REVERT: A 58 LYS cc_start: 0.7932 (mmtt) cc_final: 0.6081 (pmtt) REVERT: A 74 GLU cc_start: 0.7997 (pt0) cc_final: 0.7708 (pt0) REVERT: B 81 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6910 (pmt-80) REVERT: C 6 LYS cc_start: 0.6130 (mptp) cc_final: 0.5139 (mmmm) REVERT: C 36 GLU cc_start: 0.7361 (tt0) cc_final: 0.6785 (mt-10) REVERT: C 48 LYS cc_start: 0.7673 (tptm) cc_final: 0.7337 (tppp) REVERT: C 50 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 74 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: E 6 LYS cc_start: 0.6551 (mttt) cc_final: 0.6244 (mptp) REVERT: E 36 GLU cc_start: 0.7406 (tt0) cc_final: 0.6748 (mt-10) REVERT: E 48 LYS cc_start: 0.4330 (OUTLIER) cc_final: 0.4069 (tptt) REVERT: F 74 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: F 75 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7895 (mtpp) outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 1.3710 time to fit residues: 179.8682 Evaluate side-chains 136 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 81 ARG Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0770 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.135146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113109 restraints weight = 4774.408| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.18 r_work: 0.3657 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3807 Z= 0.298 Angle : 0.617 7.622 5157 Z= 0.306 Chirality : 0.045 0.145 534 Planarity : 0.003 0.026 666 Dihedral : 4.688 13.401 486 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.29 % Allowed : 18.81 % Favored : 76.90 % 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: -4.03 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 60 HIS 0.004 0.001 HIS C 31 PHE 0.011 0.002 PHE F 30 TYR 0.019 0.002 TYR B 67 ARG 0.001 0.000 ARG D 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.91 seconds wall clock time: 49 minutes 10.76 seconds (2950.76 seconds total)