Starting phenix.real_space_refine on Thu Dec 7 18:58:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/12_2023/8a7t_15225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/12_2023/8a7t_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_15225/12_2023/8a7t_15225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/12_2023/8a7t_15225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/12_2023/8a7t_15225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7t_15225/12_2023/8a7t_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.49, per 1000 atoms: 0.67 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: 1.17 Conformation dependent library (CDL) restraints added in 660.6 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: 0.55 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: 0.85 Time building geometry restraints manager: 1.32 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.700 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- 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 : 0.452 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.2262 time to fit residues: 158.6424 Evaluate side-chains 115 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6003 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 C 83 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN E 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.005 0.036 3807 Z= 0.362 Angle : 0.602 4.548 5157 Z= 0.313 Chirality : 0.046 0.139 534 Planarity : 0.003 0.020 666 Dihedral : 4.600 13.781 486 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.86 % Allowed : 13.33 % Favored : 83.81 % 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: -4.20 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.22), 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 13 PHE 0.015 0.002 PHE F 30 TYR 0.013 0.002 TYR B 66 ARG 0.002 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 139 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 133 average time/residue: 1.3916 time to fit residues: 189.5169 Evaluate side-chains 128 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.0371 time to fit residues: 0.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN C 51 HIS ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN F 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3807 Z= 0.350 Angle : 0.595 4.501 5157 Z= 0.309 Chirality : 0.046 0.137 534 Planarity : 0.003 0.019 666 Dihedral : 4.719 14.183 486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.71 % Allowed : 16.43 % 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: -4.15 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (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 E 13 PHE 0.012 0.002 PHE F 30 TYR 0.015 0.002 TYR B 67 ARG 0.002 0.001 ARG E 12 *********************** 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 146 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.438 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 129 average time/residue: 1.3618 time to fit residues: 180.0197 Evaluate side-chains 130 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.0345 time to fit residues: 0.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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** F 24 ASN F 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 3807 Z= 0.428 Angle : 0.633 4.663 5157 Z= 0.330 Chirality : 0.047 0.149 534 Planarity : 0.003 0.024 666 Dihedral : 5.030 14.295 486 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.71 % Allowed : 17.14 % Favored : 77.14 % 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: -4.17 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.005 0.002 HIS A 31 PHE 0.014 0.002 PHE D 30 TYR 0.018 0.002 TYR B 67 ARG 0.003 0.001 ARG E 45 *********************** 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 139 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.366 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 1.3448 time to fit residues: 169.4895 Evaluate side-chains 129 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 113 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.5529 time to fit residues: 5.8601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 83 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4953 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= 0.286 Angle : 0.587 8.400 5157 Z= 0.298 Chirality : 0.045 0.150 534 Planarity : 0.003 0.022 666 Dihedral : 4.808 13.856 486 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.29 % Allowed : 19.76 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.30), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (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 0.011 0.002 PHE D 30 TYR 0.017 0.001 TYR B 67 ARG 0.003 0.000 ARG C 12 *********************** 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: 18 poor density : 118 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 1.3160 time to fit residues: 168.7571 Evaluate side-chains 127 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.415 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.2787 time to fit residues: 2.4215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- 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 89 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3807 Z= 0.374 Angle : 0.638 7.871 5157 Z= 0.325 Chirality : 0.047 0.144 534 Planarity : 0.003 0.025 666 Dihedral : 4.972 14.159 486 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.48 % Allowed : 19.05 % Favored : 75.48 % 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: -4.08 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.22), 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 0.001 ARG E 45 *********************** 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 139 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.464 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 1.3577 time to fit residues: 172.5423 Evaluate side-chains 132 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.3388 time to fit residues: 4.2435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- 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 ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3807 Z= 0.288 Angle : 0.618 8.114 5157 Z= 0.308 Chirality : 0.045 0.148 534 Planarity : 0.003 0.026 666 Dihedral : 4.881 14.719 486 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.81 % Allowed : 20.95 % Favored : 75.24 % 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: -4.05 (0.29), residues: 432 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (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 D 30 TYR 0.018 0.001 TYR B 67 ARG 0.004 0.001 ARG C 12 *********************** 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 133 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 126 average time/residue: 1.4185 time to fit residues: 183.3332 Evaluate side-chains 128 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.0382 time to fit residues: 0.9373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3807 Z= 0.408 Angle : 0.671 10.492 5157 Z= 0.335 Chirality : 0.047 0.145 534 Planarity : 0.004 0.035 666 Dihedral : 5.112 15.015 486 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.81 % Allowed : 20.95 % Favored : 75.24 % 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: -4.08 (0.30), 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 0.004 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 0.007 0.001 ARG D 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 139 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.471 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 1.4030 time to fit residues: 186.8870 Evaluate side-chains 133 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.434 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.0362 time to fit residues: 0.9084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 ASN ** 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: 0.8350 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3807 Z= 0.288 Angle : 0.617 7.343 5157 Z= 0.311 Chirality : 0.045 0.136 534 Planarity : 0.003 0.036 666 Dihedral : 4.943 14.610 486 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.57 % Allowed : 21.43 % Favored : 75.00 % 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: -4.10 (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 0.002 0.001 TRP C 60 HIS 0.004 0.001 HIS C 31 PHE 0.010 0.002 PHE D 30 TYR 0.018 0.002 TYR B 67 ARG 0.007 0.001 ARG D 45 *********************** 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 134 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.462 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 126 average time/residue: 1.3984 time to fit residues: 180.5101 Evaluate side-chains 126 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0315 time to fit residues: 0.6073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3807 Z= 0.287 Angle : 0.641 9.771 5157 Z= 0.321 Chirality : 0.045 0.131 534 Planarity : 0.003 0.035 666 Dihedral : 4.994 14.987 486 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.38 % Allowed : 22.62 % Favored : 75.00 % 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: -4.11 (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 0.002 0.001 TRP C 60 HIS 0.004 0.001 HIS D 31 PHE 0.011 0.002 PHE D 30 TYR 0.018 0.002 TYR B 67 ARG 0.008 0.001 ARG D 45 ********************** 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 126 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.442 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 123 average time/residue: 1.4329 time to fit residues: 180.4091 Evaluate side-chains 125 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0372 time to fit residues: 0.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.9079 > 50: distance: 126 - 131: 4.014 distance: 131 - 132: 11.351 distance: 132 - 133: 10.823 distance: 132 - 135: 4.802 distance: 133 - 134: 29.566 distance: 133 - 145: 25.645 distance: 135 - 136: 6.382 distance: 136 - 137: 14.147 distance: 136 - 138: 7.398 distance: 137 - 139: 3.523 distance: 138 - 140: 3.612 distance: 138 - 141: 3.677 distance: 139 - 140: 3.520 distance: 141 - 143: 4.254 distance: 142 - 144: 4.624 distance: 143 - 144: 3.148 distance: 145 - 146: 21.537 distance: 146 - 147: 14.685 distance: 146 - 149: 24.381 distance: 147 - 148: 6.564 distance: 147 - 151: 12.964 distance: 149 - 150: 26.164 distance: 151 - 152: 3.560 distance: 152 - 153: 3.404 distance: 153 - 154: 4.874 distance: 153 - 162: 5.227 distance: 155 - 156: 3.188 distance: 157 - 159: 3.649 distance: 158 - 160: 3.977 distance: 159 - 161: 3.830 distance: 160 - 161: 5.618 distance: 164 - 165: 4.464 distance: 168 - 170: 4.341 distance: 169 - 171: 3.196 distance: 172 - 173: 3.289 distance: 176 - 177: 6.417 distance: 179 - 181: 5.464 distance: 182 - 183: 4.918 distance: 183 - 184: 5.501 distance: 183 - 186: 5.919 distance: 184 - 185: 5.415 distance: 184 - 190: 6.501 distance: 187 - 188: 5.931 distance: 187 - 189: 9.302 distance: 190 - 191: 6.232 distance: 191 - 192: 6.814 distance: 191 - 194: 3.463 distance: 192 - 193: 9.614 distance: 192 - 202: 8.872 distance: 194 - 195: 3.498 distance: 195 - 196: 5.914 distance: 195 - 197: 3.410 distance: 196 - 198: 6.759 distance: 199 - 200: 3.383 distance: 200 - 201: 6.789 distance: 202 - 203: 6.825 distance: 203 - 204: 13.554 distance: 203 - 206: 6.670 distance: 204 - 205: 4.541 distance: 204 - 214: 6.540 distance: 207 - 208: 6.667 distance: 207 - 209: 6.179 distance: 208 - 210: 8.476 distance: 209 - 211: 8.710 distance: 210 - 212: 5.303 distance: 211 - 212: 4.160 distance: 212 - 213: 6.460 distance: 214 - 215: 4.071 distance: 215 - 216: 6.453 distance: 215 - 218: 3.532 distance: 216 - 217: 13.099 distance: 216 - 221: 3.185 distance: 218 - 220: 14.358 distance: 221 - 222: 6.810 distance: 222 - 225: 6.353 distance: 223 - 224: 9.399 distance: 223 - 230: 5.550 distance: 225 - 226: 4.572 distance: 226 - 227: 7.837 distance: 227 - 228: 8.412 distance: 227 - 229: 5.157