Starting phenix.real_space_refine on Mon Jun 23 20:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560.map" model { file = "/net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ert_28560/06_2025/8ert_28560_neut.cif" } resolution = 3.3 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= 0.012 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14994 atoms to isotropic. 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 147 5.16 5 C 10437 2.51 5 N 2835 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16359 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "B" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "G" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "J" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "K" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "M" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "N" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "O" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "Q" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "R" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "S" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "W" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "X" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Time building chain proxies: 9.88, per 1000 atoms: 0.60 Number of scatterers: 16359 At special positions: 0 Unit cell: (94.34, 96.46, 128.26, 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 147 16.00 O 2940 8.00 N 2835 7.00 C 10437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.9 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 0 sheets defined 69.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.659A pdb=" N LEU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 51 through 78 removed outlier: 7.736A pdb=" N GLU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N GLU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.575A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 51 through 78 removed outlier: 7.576A pdb=" N GLU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N GLU B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'C' and resid 5 through 17 removed outlier: 3.555A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.569A pdb=" N ASP C 31 " --> pdb=" O MET C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 78 removed outlier: 3.577A pdb=" N ALA C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'D' and resid 5 through 17 removed outlier: 3.534A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 Processing helix chain 'D' and resid 51 through 78 removed outlier: 3.545A pdb=" N ALA D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N GLU D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'E' and resid 5 through 17 removed outlier: 3.596A pdb=" N LEU E 17 " --> pdb=" O TYR E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 31 Processing helix chain 'E' and resid 51 through 78 removed outlier: 3.574A pdb=" N ALA E 55 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 66 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.577A pdb=" N LEU F 17 " --> pdb=" O TYR F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.708A pdb=" N ALA F 55 " --> pdb=" O HIS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 Processing helix chain 'F' and resid 80 through 90 Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.528A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 31 Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.603A pdb=" N ALA G 55 " --> pdb=" O HIS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 78 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'I' and resid 5 through 17 removed outlier: 3.592A pdb=" N LEU I 17 " --> pdb=" O TYR I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 Processing helix chain 'I' and resid 51 through 63 Processing helix chain 'I' and resid 63 through 78 Processing helix chain 'I' and resid 80 through 90 Processing helix chain 'J' and resid 5 through 17 removed outlier: 3.600A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 31 Processing helix chain 'J' and resid 51 through 78 removed outlier: 7.588A pdb=" N GLU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS J 66 " --> pdb=" O ASN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 5 through 17 removed outlier: 3.687A pdb=" N LEU K 17 " --> pdb=" O TYR K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.574A pdb=" N ASP K 31 " --> pdb=" O MET K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 78 removed outlier: 3.534A pdb=" N ALA K 55 " --> pdb=" O HIS K 51 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS K 66 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'L' and resid 5 through 16 Processing helix chain 'L' and resid 18 through 31 Processing helix chain 'L' and resid 51 through 78 removed outlier: 3.840A pdb=" N ALA L 55 " --> pdb=" O HIS L 51 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N GLU L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS L 66 " --> pdb=" O ASN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 Processing helix chain 'M' and resid 5 through 17 removed outlier: 3.699A pdb=" N LEU M 17 " --> pdb=" O TYR M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 31 Processing helix chain 'M' and resid 51 through 78 removed outlier: 3.638A pdb=" N ALA M 55 " --> pdb=" O HIS M 51 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N GLU M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS M 66 " --> pdb=" O ASN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 5 through 17 removed outlier: 3.589A pdb=" N LEU N 17 " --> pdb=" O TYR N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 Processing helix chain 'N' and resid 51 through 78 removed outlier: 3.739A pdb=" N ALA N 55 " --> pdb=" O HIS N 51 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N GLU N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS N 66 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'O' and resid 5 through 17 removed outlier: 3.545A pdb=" N LYS O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 17 " --> pdb=" O TYR O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 31 Processing helix chain 'O' and resid 51 through 78 removed outlier: 3.656A pdb=" N ALA O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N GLU O 65 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS O 66 " --> pdb=" O ASN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'Q' and resid 5 through 17 removed outlier: 3.629A pdb=" N LEU Q 17 " --> pdb=" O TYR Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 31 Processing helix chain 'Q' and resid 51 through 78 removed outlier: 3.683A pdb=" N ALA Q 55 " --> pdb=" O HIS Q 51 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N GLU Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 Processing helix chain 'R' and resid 5 through 17 removed outlier: 3.586A pdb=" N LEU R 17 " --> pdb=" O TYR R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 31 Processing helix chain 'R' and resid 51 through 63 removed outlier: 3.724A pdb=" N ALA R 55 " --> pdb=" O HIS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 78 Processing helix chain 'R' and resid 80 through 90 Processing helix chain 'S' and resid 5 through 17 removed outlier: 3.584A pdb=" N LYS S 9 " --> pdb=" O SER S 5 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU S 17 " --> pdb=" O TYR S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 31 Processing helix chain 'S' and resid 34 through 38 removed outlier: 3.955A pdb=" N GLY S 37 " --> pdb=" O PRO S 34 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS S 38 " --> pdb=" O GLN S 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 34 through 38' Processing helix chain 'S' and resid 51 through 78 removed outlier: 3.624A pdb=" N ALA S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU S 64 " --> pdb=" O ASP S 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU S 65 " --> pdb=" O PHE S 61 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS S 66 " --> pdb=" O ASN S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 Processing helix chain 'U' and resid 5 through 17 removed outlier: 3.673A pdb=" N LEU U 17 " --> pdb=" O TYR U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 31 Processing helix chain 'U' and resid 51 through 78 removed outlier: 7.716A pdb=" N GLU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU U 65 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 90 Processing helix chain 'V' and resid 5 through 17 removed outlier: 3.592A pdb=" N LYS V 9 " --> pdb=" O SER V 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU V 17 " --> pdb=" O TYR V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 31 Processing helix chain 'V' and resid 51 through 78 removed outlier: 3.515A pdb=" N ALA V 55 " --> pdb=" O HIS V 51 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N GLU V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 90 Processing helix chain 'W' and resid 5 through 17 removed outlier: 3.502A pdb=" N LYS W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU W 17 " --> pdb=" O TYR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 31 removed outlier: 3.636A pdb=" N ASP W 31 " --> pdb=" O MET W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 78 removed outlier: 7.737A pdb=" N GLU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLU W 65 " --> pdb=" O PHE W 61 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 90 Processing helix chain 'X' and resid 5 through 17 removed outlier: 3.609A pdb=" N LYS X 9 " --> pdb=" O SER X 5 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU X 17 " --> pdb=" O TYR X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 Processing helix chain 'X' and resid 51 through 78 removed outlier: 3.649A pdb=" N ALA X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU X 64 " --> pdb=" O ASP X 60 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLU X 65 " --> pdb=" O PHE X 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 90 939 hydrogen bonds defined for protein. 2817 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: 4.18 Time building geometry restraints manager: 4.60 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: 5313 1.34 - 1.46: 3488 1.46 - 1.58: 7684 1.58 - 1.70: 0 1.70 - 1.81: 252 Bond restraints: 16737 Sorted by residual: bond pdb=" CG LYS I 88 " pdb=" CD LYS I 88 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CE LYS I 88 " pdb=" NZ LYS I 88 " ideal model delta sigma weight residual 1.489 1.446 0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CG ARG E 89 " pdb=" CD ARG E 89 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA ILE L 39 " pdb=" C ILE L 39 " ideal model delta sigma weight residual 1.528 1.519 0.009 8.50e-03 1.38e+04 1.05e+00 bond pdb=" CG ARG L 89 " pdb=" CD ARG L 89 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 21948 1.66 - 3.32: 451 3.32 - 4.98: 67 4.98 - 6.64: 18 6.64 - 8.30: 7 Bond angle restraints: 22491 Sorted by residual: angle pdb=" CG LYS I 88 " pdb=" CD LYS I 88 " pdb=" CE LYS I 88 " ideal model delta sigma weight residual 111.30 103.00 8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N LYS I 88 " pdb=" CA LYS I 88 " pdb=" CB LYS I 88 " ideal model delta sigma weight residual 110.01 114.39 -4.38 1.45e+00 4.76e-01 9.13e+00 angle pdb=" C ALA I 87 " pdb=" N LYS I 88 " pdb=" CA LYS I 88 " ideal model delta sigma weight residual 120.44 116.76 3.68 1.30e+00 5.92e-01 8.00e+00 angle pdb=" CA TYR X 84 " pdb=" CB TYR X 84 " pdb=" CG TYR X 84 " ideal model delta sigma weight residual 113.90 118.88 -4.98 1.80e+00 3.09e-01 7.65e+00 angle pdb=" CB MET I 3 " pdb=" CG MET I 3 " pdb=" SD MET I 3 " ideal model delta sigma weight residual 112.70 120.79 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 22486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9182 17.75 - 35.51: 935 35.51 - 53.26: 196 53.26 - 71.02: 16 71.02 - 88.77: 3 Dihedral angle restraints: 10332 sinusoidal: 4473 harmonic: 5859 Sorted by residual: dihedral pdb=" CA GLU X 47 " pdb=" C GLU X 47 " pdb=" N LYS X 48 " pdb=" CA LYS X 48 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE O 61 " pdb=" C PHE O 61 " pdb=" N ASN O 62 " pdb=" CA ASN O 62 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE I 61 " pdb=" C PHE I 61 " pdb=" N ASN I 62 " pdb=" CA ASN I 62 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 10329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1330 0.028 - 0.056: 723 0.056 - 0.084: 131 0.084 - 0.111: 97 0.111 - 0.139: 29 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA GLU X 85 " pdb=" N GLU X 85 " pdb=" C GLU X 85 " pdb=" CB GLU X 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LYS I 36 " pdb=" N LYS I 36 " pdb=" C LYS I 36 " pdb=" CB LYS I 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA GLU L 85 " pdb=" N GLU L 85 " pdb=" C GLU L 85 " pdb=" CB GLU L 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2307 not shown) Planarity restraints: 2877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 84 " -0.013 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR I 84 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR I 84 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR I 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 84 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 84 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR I 84 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 84 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 89 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.97e+00 pdb=" NE ARG L 89 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 89 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG L 89 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 89 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 89 " 0.133 9.50e-02 1.11e+02 6.00e-02 2.87e+00 pdb=" NE ARG A 89 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 89 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 89 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 89 " 0.000 2.00e-02 2.50e+03 ... (remaining 2874 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1810 2.74 - 3.28: 16426 3.28 - 3.82: 26610 3.82 - 4.36: 31261 4.36 - 4.90: 54350 Nonbonded interactions: 130457 Sorted by model distance: nonbonded pdb=" OG1 THR I 6 " pdb=" OE2 GLU I 64 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG M 43 " pdb=" OE2 GLU U 18 " model vdw 2.243 3.120 nonbonded pdb=" NZ LYS I 24 " pdb=" OE1 GLU M 15 " model vdw 2.265 3.120 nonbonded pdb=" OE2 GLU C 15 " pdb=" NE2 GLN S 45 " model vdw 2.268 3.120 nonbonded pdb=" OE2 GLU G 30 " pdb=" OG1 THR G 46 " model vdw 2.273 3.040 ... (remaining 130452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.570 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 0.050 16737 Z= 0.136 Angle : 0.588 8.296 22491 Z= 0.324 Chirality : 0.038 0.139 2310 Planarity : 0.005 0.062 2877 Dihedral : 14.141 88.773 6510 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 1953 helix: 0.79 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 68 HIS 0.011 0.001 HIS I 51 PHE 0.009 0.001 PHE C 61 TYR 0.039 0.002 TYR I 84 ARG 0.015 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.11054 ( 939) hydrogen bonds : angle 5.60570 ( 2817) covalent geometry : bond 0.00285 (16737) covalent geometry : angle 0.58779 (22491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7218 (tpt) cc_final: 0.6898 (tmm) REVERT: A 16 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t70) REVERT: A 31 ASP cc_start: 0.8139 (m-30) cc_final: 0.7910 (m-30) REVERT: C 1 MET cc_start: 0.6679 (ttp) cc_final: 0.6355 (ttp) REVERT: E 1 MET cc_start: 0.6697 (tmm) cc_final: 0.6243 (ppp) REVERT: G 15 GLU cc_start: 0.7463 (tt0) cc_final: 0.7178 (tt0) REVERT: K 70 MET cc_start: 0.8468 (mtp) cc_final: 0.8258 (mtm) REVERT: M 1 MET cc_start: 0.6300 (tmm) cc_final: 0.5964 (ppp) REVERT: N 46 THR cc_start: 0.8276 (p) cc_final: 0.8035 (p) REVERT: S 9 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8205 (mttp) REVERT: S 45 GLN cc_start: 0.8394 (mp10) cc_final: 0.8191 (mp10) REVERT: S 66 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7983 (mmtp) REVERT: U 1 MET cc_start: 0.7259 (tpp) cc_final: 0.6985 (tmm) REVERT: U 58 MET cc_start: 0.8720 (mtp) cc_final: 0.8457 (ttm) REVERT: V 70 MET cc_start: 0.8195 (mtp) cc_final: 0.7555 (mtp) REVERT: X 27 MET cc_start: 0.9014 (ttp) cc_final: 0.8414 (ttm) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3820 time to fit residues: 292.2435 Evaluate side-chains 537 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 0.0870 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119944 restraints weight = 20094.267| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.23 r_work: 0.3214 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16737 Z= 0.126 Angle : 0.566 8.014 22491 Z= 0.301 Chirality : 0.039 0.162 2310 Planarity : 0.005 0.045 2877 Dihedral : 3.857 18.686 2163 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.59 % Allowed : 7.58 % Favored : 91.83 % 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: 0.51 (0.18), residues: 1953 helix: 1.13 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 94 HIS 0.013 0.001 HIS N 51 PHE 0.009 0.001 PHE N 25 TYR 0.024 0.001 TYR I 84 ARG 0.008 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 939) hydrogen bonds : angle 4.59400 ( 2817) covalent geometry : bond 0.00270 (16737) covalent geometry : angle 0.56619 (22491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 547 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7654 (tpt) cc_final: 0.7026 (tmm) REVERT: A 31 ASP cc_start: 0.8521 (m-30) cc_final: 0.8142 (m-30) REVERT: A 45 GLN cc_start: 0.8238 (mt0) cc_final: 0.7929 (mt0) REVERT: C 1 MET cc_start: 0.6666 (ttp) cc_final: 0.6353 (ttp) REVERT: C 30 GLU cc_start: 0.7465 (mp0) cc_final: 0.7000 (mp0) REVERT: D 1 MET cc_start: 0.8224 (tmm) cc_final: 0.7718 (tpp) REVERT: D 45 GLN cc_start: 0.8706 (mt0) cc_final: 0.8478 (mt0) REVERT: D 62 ASN cc_start: 0.8644 (m110) cc_final: 0.8439 (m110) REVERT: E 1 MET cc_start: 0.7117 (tmm) cc_final: 0.6553 (ppp) REVERT: F 15 GLU cc_start: 0.8067 (tt0) cc_final: 0.7811 (tt0) REVERT: G 45 GLN cc_start: 0.8850 (mp10) cc_final: 0.8541 (mp10) REVERT: I 62 ASN cc_start: 0.8789 (m110) cc_final: 0.8510 (m110) REVERT: J 31 ASP cc_start: 0.8427 (m-30) cc_final: 0.8219 (m-30) REVERT: J 32 TYR cc_start: 0.8834 (t80) cc_final: 0.8605 (t80) REVERT: K 9 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8449 (mttm) REVERT: K 30 GLU cc_start: 0.7595 (mp0) cc_final: 0.7298 (mp0) REVERT: L 15 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7984 (mm-30) REVERT: M 1 MET cc_start: 0.6770 (tmm) cc_final: 0.6301 (ppp) REVERT: M 13 TYR cc_start: 0.8739 (m-10) cc_final: 0.8371 (m-10) REVERT: N 1 MET cc_start: 0.7341 (tmm) cc_final: 0.6697 (tpp) REVERT: O 64 GLU cc_start: 0.8106 (mp0) cc_final: 0.7786 (mt-10) REVERT: O 79 ASN cc_start: 0.7781 (m-40) cc_final: 0.7429 (m110) REVERT: R 1 MET cc_start: 0.7022 (tmm) cc_final: 0.6286 (tpp) REVERT: R 66 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8168 (mttm) REVERT: S 9 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8440 (mttp) REVERT: S 45 GLN cc_start: 0.8805 (mp10) cc_final: 0.8561 (mp10) REVERT: S 66 LYS cc_start: 0.8340 (mmtp) cc_final: 0.8101 (mmtp) REVERT: U 1 MET cc_start: 0.7633 (tpp) cc_final: 0.7105 (tmm) REVERT: U 58 MET cc_start: 0.8815 (mtp) cc_final: 0.8578 (ttm) REVERT: U 66 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8254 (mmtt) REVERT: U 70 MET cc_start: 0.8377 (mtp) cc_final: 0.8161 (mtp) REVERT: W 30 GLU cc_start: 0.7564 (mp0) cc_final: 0.7008 (mp0) REVERT: X 27 MET cc_start: 0.8895 (ttp) cc_final: 0.8465 (ttm) outliers start: 10 outliers final: 3 residues processed: 548 average time/residue: 0.3644 time to fit residues: 271.1778 Evaluate side-chains 532 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain W residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118233 restraints weight = 20004.232| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.33 r_work: 0.3266 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16737 Z= 0.123 Angle : 0.555 7.948 22491 Z= 0.297 Chirality : 0.039 0.179 2310 Planarity : 0.004 0.034 2877 Dihedral : 3.778 16.830 2163 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.82 % Allowed : 10.70 % Favored : 88.48 % 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: 0.61 (0.18), residues: 1953 helix: 1.19 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 94 HIS 0.015 0.001 HIS F 51 PHE 0.008 0.001 PHE N 25 TYR 0.018 0.001 TYR I 84 ARG 0.009 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 939) hydrogen bonds : angle 4.49995 ( 2817) covalent geometry : bond 0.00265 (16737) covalent geometry : angle 0.55454 (22491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 543 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7666 (tpt) cc_final: 0.6968 (tmm) REVERT: A 31 ASP cc_start: 0.8711 (m-30) cc_final: 0.8134 (m-30) REVERT: A 64 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7493 (mm-30) REVERT: C 1 MET cc_start: 0.6727 (ttp) cc_final: 0.6407 (ttp) REVERT: C 30 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7102 (mp0) REVERT: D 1 MET cc_start: 0.8322 (tmm) cc_final: 0.7794 (tpp) REVERT: D 31 ASP cc_start: 0.7918 (t0) cc_final: 0.7689 (t70) REVERT: D 70 MET cc_start: 0.8693 (mtp) cc_final: 0.8447 (mtp) REVERT: D 86 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7801 (mmtm) REVERT: E 1 MET cc_start: 0.7296 (tmm) cc_final: 0.6724 (ppp) REVERT: E 13 TYR cc_start: 0.8713 (m-10) cc_final: 0.8141 (m-80) REVERT: F 15 GLU cc_start: 0.8179 (tt0) cc_final: 0.7883 (tt0) REVERT: G 45 GLN cc_start: 0.8935 (mp10) cc_final: 0.8549 (mp10) REVERT: G 62 ASN cc_start: 0.8959 (m110) cc_final: 0.8635 (m110) REVERT: I 62 ASN cc_start: 0.8720 (m110) cc_final: 0.8386 (m110) REVERT: J 32 TYR cc_start: 0.8894 (t80) cc_final: 0.8630 (t80) REVERT: K 1 MET cc_start: 0.6781 (tmm) cc_final: 0.5418 (pmm) REVERT: K 3 MET cc_start: 0.6752 (ptm) cc_final: 0.6510 (ppp) REVERT: K 30 GLU cc_start: 0.7522 (mp0) cc_final: 0.7272 (mp0) REVERT: M 1 MET cc_start: 0.6937 (tmm) cc_final: 0.6450 (ppp) REVERT: M 13 TYR cc_start: 0.8764 (m-10) cc_final: 0.8087 (m-80) REVERT: M 31 ASP cc_start: 0.8454 (m-30) cc_final: 0.8245 (m-30) REVERT: O 79 ASN cc_start: 0.7692 (m-40) cc_final: 0.7410 (m110) REVERT: R 66 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8151 (mttm) REVERT: S 66 LYS cc_start: 0.8244 (mmtp) cc_final: 0.8013 (mmtp) REVERT: U 1 MET cc_start: 0.7762 (tpp) cc_final: 0.7083 (tmm) REVERT: U 58 MET cc_start: 0.8873 (mtp) cc_final: 0.8586 (ttm) REVERT: W 30 GLU cc_start: 0.7456 (mp0) cc_final: 0.6802 (mp0) REVERT: X 15 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8361 (mm-30) REVERT: X 27 MET cc_start: 0.8782 (ttp) cc_final: 0.8427 (ttm) outliers start: 14 outliers final: 8 residues processed: 545 average time/residue: 0.3825 time to fit residues: 283.9184 Evaluate side-chains 533 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 525 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 126 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116053 restraints weight = 20215.175| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.23 r_work: 0.3217 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16737 Z= 0.148 Angle : 0.573 8.947 22491 Z= 0.304 Chirality : 0.040 0.190 2310 Planarity : 0.004 0.036 2877 Dihedral : 3.765 17.164 2163 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.00 % Allowed : 11.99 % Favored : 87.01 % 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: 0.69 (0.18), residues: 1953 helix: 1.23 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 94 HIS 0.013 0.001 HIS R 51 PHE 0.008 0.001 PHE K 25 TYR 0.017 0.002 TYR C 32 ARG 0.011 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 939) hydrogen bonds : angle 4.47860 ( 2817) covalent geometry : bond 0.00336 (16737) covalent geometry : angle 0.57318 (22491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 539 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7564 (tpt) cc_final: 0.7005 (tmm) REVERT: C 30 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7232 (mp0) REVERT: D 1 MET cc_start: 0.8082 (tmm) cc_final: 0.7589 (tpp) REVERT: D 31 ASP cc_start: 0.8035 (t0) cc_final: 0.7821 (t70) REVERT: D 70 MET cc_start: 0.8753 (mtp) cc_final: 0.8392 (mtp) REVERT: D 86 LYS cc_start: 0.8314 (mtpp) cc_final: 0.7915 (mmtm) REVERT: E 1 MET cc_start: 0.7319 (tmm) cc_final: 0.6656 (ppp) REVERT: E 3 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5496 (tmm) REVERT: F 60 ASP cc_start: 0.7785 (t0) cc_final: 0.7554 (t0) REVERT: F 62 ASN cc_start: 0.8996 (m110) cc_final: 0.8619 (m110) REVERT: G 43 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8604 (mtp180) REVERT: G 45 GLN cc_start: 0.8939 (mp10) cc_final: 0.8702 (mp10) REVERT: G 62 ASN cc_start: 0.9058 (m110) cc_final: 0.8715 (m110) REVERT: I 1 MET cc_start: 0.8072 (tpt) cc_final: 0.7863 (tpt) REVERT: I 62 ASN cc_start: 0.8785 (m110) cc_final: 0.8536 (m110) REVERT: K 1 MET cc_start: 0.6820 (tmm) cc_final: 0.5441 (pmm) REVERT: K 30 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7288 (mp0) REVERT: L 8 CYS cc_start: 0.8575 (m) cc_final: 0.8330 (m) REVERT: L 13 TYR cc_start: 0.8641 (m-80) cc_final: 0.8384 (m-80) REVERT: M 13 TYR cc_start: 0.8661 (m-10) cc_final: 0.8192 (m-80) REVERT: M 62 ASN cc_start: 0.8944 (m-40) cc_final: 0.8370 (m-40) REVERT: N 1 MET cc_start: 0.7118 (tmm) cc_final: 0.6752 (mtp) REVERT: O 62 ASN cc_start: 0.8840 (m-40) cc_final: 0.8421 (m110) REVERT: O 64 GLU cc_start: 0.8149 (mp0) cc_final: 0.7779 (mt-10) REVERT: O 65 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8188 (mm-30) REVERT: O 79 ASN cc_start: 0.7777 (m-40) cc_final: 0.7504 (m110) REVERT: R 1 MET cc_start: 0.7032 (tmm) cc_final: 0.6254 (tpp) REVERT: S 64 GLU cc_start: 0.8156 (mp0) cc_final: 0.7928 (mt-10) REVERT: U 1 MET cc_start: 0.7706 (tpp) cc_final: 0.7120 (tmm) REVERT: U 58 MET cc_start: 0.8853 (mtp) cc_final: 0.8522 (ttm) REVERT: W 30 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7169 (mp0) REVERT: X 15 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8405 (mm-30) REVERT: X 27 MET cc_start: 0.8955 (ttp) cc_final: 0.8566 (ttm) REVERT: X 51 HIS cc_start: 0.7564 (p90) cc_final: 0.7323 (p90) REVERT: X 66 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7365 (mmmt) outliers start: 17 outliers final: 11 residues processed: 542 average time/residue: 0.3725 time to fit residues: 274.5446 Evaluate side-chains 541 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 529 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 160 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN G 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118483 restraints weight = 20431.853| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.38 r_work: 0.3242 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16737 Z= 0.117 Angle : 0.565 8.758 22491 Z= 0.300 Chirality : 0.039 0.206 2310 Planarity : 0.004 0.052 2877 Dihedral : 3.726 18.026 2163 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.94 % Allowed : 14.23 % Favored : 84.83 % 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: 0.71 (0.18), residues: 1953 helix: 1.25 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 68 HIS 0.013 0.001 HIS F 51 PHE 0.008 0.001 PHE N 25 TYR 0.015 0.001 TYR C 32 ARG 0.010 0.001 ARG L 89 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 939) hydrogen bonds : angle 4.41467 ( 2817) covalent geometry : bond 0.00249 (16737) covalent geometry : angle 0.56465 (22491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 543 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7622 (tpt) cc_final: 0.7043 (tmm) REVERT: A 45 GLN cc_start: 0.8731 (mp10) cc_final: 0.8507 (mp10) REVERT: D 1 MET cc_start: 0.8111 (tmm) cc_final: 0.7628 (tpp) REVERT: D 62 ASN cc_start: 0.8666 (m110) cc_final: 0.8325 (m110) REVERT: D 86 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7810 (mmtm) REVERT: E 1 MET cc_start: 0.7374 (tmm) cc_final: 0.6725 (ppp) REVERT: E 3 MET cc_start: 0.5975 (OUTLIER) cc_final: 0.5579 (tmm) REVERT: F 45 GLN cc_start: 0.8573 (mp10) cc_final: 0.8344 (mp10) REVERT: G 45 GLN cc_start: 0.8926 (mp10) cc_final: 0.8638 (mp10) REVERT: G 62 ASN cc_start: 0.8967 (m-40) cc_final: 0.8674 (m110) REVERT: G 64 GLU cc_start: 0.8115 (mp0) cc_final: 0.7764 (mt-10) REVERT: I 62 ASN cc_start: 0.8812 (m110) cc_final: 0.8545 (m110) REVERT: K 1 MET cc_start: 0.6829 (tmm) cc_final: 0.5508 (pmm) REVERT: K 3 MET cc_start: 0.6838 (ppp) cc_final: 0.6515 (ppp) REVERT: K 9 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8490 (mttm) REVERT: K 26 LYS cc_start: 0.8560 (mttt) cc_final: 0.8017 (mttt) REVERT: K 30 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7261 (mp0) REVERT: L 8 CYS cc_start: 0.8601 (m) cc_final: 0.8340 (m) REVERT: L 13 TYR cc_start: 0.8651 (m-80) cc_final: 0.8337 (m-80) REVERT: N 1 MET cc_start: 0.7177 (tmm) cc_final: 0.6958 (mtp) REVERT: O 62 ASN cc_start: 0.8785 (m-40) cc_final: 0.8381 (m110) REVERT: O 64 GLU cc_start: 0.8178 (mp0) cc_final: 0.7779 (mt-10) REVERT: O 79 ASN cc_start: 0.7608 (m-40) cc_final: 0.7376 (m110) REVERT: Q 31 ASP cc_start: 0.8435 (m-30) cc_final: 0.8220 (m-30) REVERT: R 66 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8203 (mttm) REVERT: S 45 GLN cc_start: 0.8639 (mp10) cc_final: 0.8363 (mp10) REVERT: U 1 MET cc_start: 0.7799 (tpp) cc_final: 0.6857 (ppp) REVERT: U 58 MET cc_start: 0.8840 (mtp) cc_final: 0.8531 (ttm) REVERT: W 30 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7123 (mp0) REVERT: X 15 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8365 (mm-30) REVERT: X 27 MET cc_start: 0.8892 (ttp) cc_final: 0.8518 (ttm) REVERT: X 51 HIS cc_start: 0.7499 (p90) cc_final: 0.7222 (p90) outliers start: 16 outliers final: 9 residues processed: 545 average time/residue: 0.3702 time to fit residues: 274.8591 Evaluate side-chains 534 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 524 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128251 restraints weight = 19539.077| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.13 r_work: 0.3403 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16737 Z= 0.167 Angle : 0.605 9.304 22491 Z= 0.319 Chirality : 0.041 0.219 2310 Planarity : 0.005 0.060 2877 Dihedral : 3.779 16.936 2163 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.12 % Allowed : 15.40 % Favored : 83.48 % 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: 0.70 (0.18), residues: 1953 helix: 1.03 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -0.89 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 94 HIS 0.016 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.002 TYR C 32 ARG 0.012 0.001 ARG O 89 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 939) hydrogen bonds : angle 4.48519 ( 2817) covalent geometry : bond 0.00387 (16737) covalent geometry : angle 0.60451 (22491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 544 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7493 (tpt) cc_final: 0.7026 (tmm) REVERT: C 30 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7068 (mp0) REVERT: D 1 MET cc_start: 0.7986 (tmm) cc_final: 0.7506 (tpp) REVERT: D 66 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7579 (mmmt) REVERT: D 70 MET cc_start: 0.8832 (mtp) cc_final: 0.8569 (mtp) REVERT: E 3 MET cc_start: 0.6033 (tmm) cc_final: 0.5584 (tmm) REVERT: F 60 ASP cc_start: 0.7554 (t0) cc_final: 0.7322 (t0) REVERT: G 45 GLN cc_start: 0.8865 (mp10) cc_final: 0.8470 (mp10) REVERT: G 62 ASN cc_start: 0.9035 (m-40) cc_final: 0.8768 (m110) REVERT: I 1 MET cc_start: 0.8057 (tpt) cc_final: 0.7696 (tpp) REVERT: I 62 ASN cc_start: 0.8808 (m110) cc_final: 0.8585 (m110) REVERT: K 1 MET cc_start: 0.6824 (tmm) cc_final: 0.5579 (pmm) REVERT: K 3 MET cc_start: 0.6843 (ppp) cc_final: 0.6207 (ppp) REVERT: L 8 CYS cc_start: 0.8387 (m) cc_final: 0.8167 (m) REVERT: L 13 TYR cc_start: 0.8639 (m-80) cc_final: 0.8383 (m-80) REVERT: M 13 TYR cc_start: 0.8693 (m-10) cc_final: 0.8229 (m-80) REVERT: M 62 ASN cc_start: 0.8642 (m-40) cc_final: 0.8343 (m-40) REVERT: O 65 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8046 (mm-30) REVERT: O 79 ASN cc_start: 0.7787 (m-40) cc_final: 0.7525 (m110) REVERT: Q 31 ASP cc_start: 0.8332 (m-30) cc_final: 0.8099 (m-30) REVERT: R 45 GLN cc_start: 0.8509 (mp10) cc_final: 0.8262 (mp10) REVERT: S 65 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8108 (mm-30) REVERT: S 66 LYS cc_start: 0.8344 (mmtp) cc_final: 0.8074 (mmtt) REVERT: U 1 MET cc_start: 0.7591 (tpp) cc_final: 0.6871 (ppp) REVERT: U 58 MET cc_start: 0.8723 (mtp) cc_final: 0.8403 (ttm) REVERT: W 30 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7135 (mp0) REVERT: X 27 MET cc_start: 0.8904 (ttp) cc_final: 0.8531 (ttm) REVERT: X 51 HIS cc_start: 0.7389 (p90) cc_final: 0.7161 (p-80) REVERT: X 66 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7561 (mmmt) outliers start: 19 outliers final: 14 residues processed: 546 average time/residue: 0.3736 time to fit residues: 276.6473 Evaluate side-chains 545 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 531 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 131 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 85 optimal weight: 0.0570 chunk 169 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132796 restraints weight = 19442.238| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.14 r_work: 0.3439 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16737 Z= 0.122 Angle : 0.590 9.621 22491 Z= 0.313 Chirality : 0.039 0.232 2310 Planarity : 0.005 0.055 2877 Dihedral : 3.731 16.785 2163 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.88 % Allowed : 16.52 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 1953 helix: 1.23 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 94 HIS 0.014 0.001 HIS F 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR K 32 ARG 0.013 0.001 ARG M 89 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 939) hydrogen bonds : angle 4.40972 ( 2817) covalent geometry : bond 0.00263 (16737) covalent geometry : angle 0.59013 (22491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 544 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7422 (tpt) cc_final: 0.7088 (tmm) REVERT: D 1 MET cc_start: 0.7918 (tmm) cc_final: 0.7521 (tpp) REVERT: E 3 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5643 (tmm) REVERT: F 1 MET cc_start: 0.7115 (tmm) cc_final: 0.6486 (mtm) REVERT: G 45 GLN cc_start: 0.8787 (mp10) cc_final: 0.8428 (mp10) REVERT: G 62 ASN cc_start: 0.8997 (m-40) cc_final: 0.8758 (m110) REVERT: G 65 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7648 (mm-30) REVERT: I 1 MET cc_start: 0.7991 (tpt) cc_final: 0.7716 (tpp) REVERT: I 62 ASN cc_start: 0.8735 (m110) cc_final: 0.8512 (m110) REVERT: K 1 MET cc_start: 0.6818 (tmm) cc_final: 0.5732 (pmm) REVERT: K 3 MET cc_start: 0.6987 (ppp) cc_final: 0.6300 (ppp) REVERT: L 8 CYS cc_start: 0.8402 (m) cc_final: 0.8155 (m) REVERT: L 13 TYR cc_start: 0.8602 (m-80) cc_final: 0.8365 (m-80) REVERT: O 62 ASN cc_start: 0.8837 (m-40) cc_final: 0.8496 (m110) REVERT: O 79 ASN cc_start: 0.7525 (m-40) cc_final: 0.7296 (m110) REVERT: Q 31 ASP cc_start: 0.8250 (m-30) cc_final: 0.8004 (m-30) REVERT: Q 57 LEU cc_start: 0.8762 (tp) cc_final: 0.8462 (tp) REVERT: R 1 MET cc_start: 0.7031 (tmm) cc_final: 0.6701 (tmm) REVERT: R 66 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8249 (mttm) REVERT: S 45 GLN cc_start: 0.8492 (mp10) cc_final: 0.8270 (mp10) REVERT: U 1 MET cc_start: 0.7598 (tpp) cc_final: 0.6935 (ppp) REVERT: U 58 MET cc_start: 0.8646 (mtp) cc_final: 0.8338 (ttm) REVERT: W 30 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7060 (mp0) REVERT: X 15 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8196 (mm-30) REVERT: X 27 MET cc_start: 0.8870 (ttp) cc_final: 0.8520 (ttm) REVERT: X 43 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8546 (tpp80) REVERT: X 51 HIS cc_start: 0.7253 (p90) cc_final: 0.6790 (p90) outliers start: 15 outliers final: 10 residues processed: 546 average time/residue: 0.3871 time to fit residues: 288.9286 Evaluate side-chains 546 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 535 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 15 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131339 restraints weight = 19410.413| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.10 r_work: 0.3438 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16737 Z= 0.130 Angle : 0.611 8.730 22491 Z= 0.324 Chirality : 0.040 0.242 2310 Planarity : 0.005 0.054 2877 Dihedral : 3.716 17.143 2163 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.12 % Allowed : 16.11 % Favored : 82.77 % 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: 0.74 (0.18), residues: 1953 helix: 1.25 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 94 HIS 0.014 0.001 HIS F 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR C 32 ARG 0.014 0.001 ARG O 89 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 939) hydrogen bonds : angle 4.43447 ( 2817) covalent geometry : bond 0.00291 (16737) covalent geometry : angle 0.61082 (22491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 538 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7485 (tpt) cc_final: 0.7121 (tmm) REVERT: C 15 GLU cc_start: 0.8074 (tt0) cc_final: 0.7635 (tt0) REVERT: C 30 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7118 (mp0) REVERT: D 1 MET cc_start: 0.7941 (tmm) cc_final: 0.7563 (tpp) REVERT: D 30 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6817 (mp0) REVERT: D 62 ASN cc_start: 0.8729 (m110) cc_final: 0.8527 (m110) REVERT: E 3 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5547 (tmm) REVERT: G 45 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: G 62 ASN cc_start: 0.9033 (m-40) cc_final: 0.8793 (m110) REVERT: G 65 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7854 (mm-30) REVERT: I 1 MET cc_start: 0.7936 (tpt) cc_final: 0.7537 (tpp) REVERT: K 1 MET cc_start: 0.6834 (tmm) cc_final: 0.5875 (pmm) REVERT: K 3 MET cc_start: 0.7055 (ppp) cc_final: 0.6302 (ppp) REVERT: L 13 TYR cc_start: 0.8706 (m-80) cc_final: 0.8452 (m-80) REVERT: M 13 TYR cc_start: 0.8830 (m-10) cc_final: 0.8216 (m-80) REVERT: O 64 GLU cc_start: 0.8107 (mp0) cc_final: 0.7825 (mt-10) REVERT: O 65 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8213 (mm-30) REVERT: O 89 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7701 (mtm110) REVERT: Q 31 ASP cc_start: 0.8410 (m-30) cc_final: 0.8134 (m-30) REVERT: R 66 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8210 (mttm) REVERT: S 64 GLU cc_start: 0.8185 (mp0) cc_final: 0.7973 (mt-10) REVERT: S 65 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8233 (mm-30) REVERT: U 1 MET cc_start: 0.7681 (tpp) cc_final: 0.6987 (ppp) REVERT: U 58 MET cc_start: 0.8725 (mtp) cc_final: 0.8432 (ttm) REVERT: W 30 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7259 (mp0) REVERT: X 15 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8358 (mm-30) REVERT: X 27 MET cc_start: 0.8922 (ttp) cc_final: 0.8538 (ttm) REVERT: X 43 ARG cc_start: 0.8990 (tpp80) cc_final: 0.8777 (tpp80) REVERT: X 51 HIS cc_start: 0.7451 (p90) cc_final: 0.6961 (p90) REVERT: X 66 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7520 (mmmt) outliers start: 19 outliers final: 13 residues processed: 542 average time/residue: 0.3768 time to fit residues: 279.5051 Evaluate side-chains 542 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 527 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 15 GLU Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 180 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN I 62 ASN K 62 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125091 restraints weight = 19666.922| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.11 r_work: 0.3407 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16737 Z= 0.215 Angle : 0.679 10.179 22491 Z= 0.359 Chirality : 0.044 0.255 2310 Planarity : 0.005 0.057 2877 Dihedral : 3.909 17.359 2163 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.00 % Allowed : 17.28 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 1953 helix: 1.00 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 94 HIS 0.019 0.002 HIS L 51 PHE 0.009 0.001 PHE N 25 TYR 0.019 0.002 TYR K 32 ARG 0.014 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 939) hydrogen bonds : angle 4.63724 ( 2817) covalent geometry : bond 0.00510 (16737) covalent geometry : angle 0.67853 (22491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 544 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7512 (tpt) cc_final: 0.6975 (tmm) REVERT: D 1 MET cc_start: 0.7992 (tmm) cc_final: 0.7469 (tpp) REVERT: D 30 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7023 (mp0) REVERT: D 66 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7794 (mmmt) REVERT: E 3 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5520 (tmm) REVERT: F 1 MET cc_start: 0.7126 (tmm) cc_final: 0.6416 (mtm) REVERT: G 45 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: G 62 ASN cc_start: 0.9069 (m-40) cc_final: 0.8833 (m-40) REVERT: G 65 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7998 (mm-30) REVERT: I 1 MET cc_start: 0.8114 (tpt) cc_final: 0.7691 (tpp) REVERT: K 1 MET cc_start: 0.6801 (tmm) cc_final: 0.5906 (pmm) REVERT: K 3 MET cc_start: 0.6970 (ppp) cc_final: 0.6223 (ppp) REVERT: L 8 CYS cc_start: 0.8786 (m) cc_final: 0.8564 (m) REVERT: L 15 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8539 (mm-30) REVERT: O 64 GLU cc_start: 0.8206 (mp0) cc_final: 0.7872 (mt-10) REVERT: O 65 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8194 (mm-30) REVERT: O 89 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7730 (mtm110) REVERT: R 1 MET cc_start: 0.7417 (tmm) cc_final: 0.7010 (tmm) REVERT: R 45 GLN cc_start: 0.8531 (mp10) cc_final: 0.8237 (mp10) REVERT: R 66 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8463 (mttm) REVERT: S 64 GLU cc_start: 0.8289 (mp0) cc_final: 0.8045 (mt-10) REVERT: U 1 MET cc_start: 0.7713 (tpp) cc_final: 0.6866 (ppp) REVERT: U 58 MET cc_start: 0.8883 (mtp) cc_final: 0.8517 (ttm) REVERT: W 30 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7236 (mp0) REVERT: X 15 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8414 (mm-30) REVERT: X 27 MET cc_start: 0.8949 (ttp) cc_final: 0.8577 (ttm) REVERT: X 43 ARG cc_start: 0.8948 (tpp80) cc_final: 0.8742 (tpp80) REVERT: X 60 ASP cc_start: 0.7810 (t0) cc_final: 0.7516 (t0) REVERT: X 66 LYS cc_start: 0.8005 (mmtm) cc_final: 0.7618 (mmmt) outliers start: 17 outliers final: 12 residues processed: 544 average time/residue: 0.4348 time to fit residues: 321.7079 Evaluate side-chains 553 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 539 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 15 GLU Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** V 51 HIS ** 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 = 0.3868 r_free = 0.3868 target = 0.154581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.126496 restraints weight = 19565.603| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.18 r_work: 0.3424 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16737 Z= 0.178 Angle : 0.681 10.020 22491 Z= 0.361 Chirality : 0.042 0.264 2310 Planarity : 0.005 0.059 2877 Dihedral : 3.918 17.624 2163 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.71 % Allowed : 18.05 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 1953 helix: 0.81 (0.13), residues: 1407 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 94 HIS 0.017 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.018 0.001 TYR K 32 ARG 0.016 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 939) hydrogen bonds : angle 4.62266 ( 2817) covalent geometry : bond 0.00417 (16737) covalent geometry : angle 0.68133 (22491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 537 time to evaluate : 3.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7528 (tpt) cc_final: 0.6975 (tmm) REVERT: C 30 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7159 (mp0) REVERT: D 1 MET cc_start: 0.8022 (tmm) cc_final: 0.7493 (tpp) REVERT: D 66 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7721 (mmmt) REVERT: E 3 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5480 (tmm) REVERT: F 1 MET cc_start: 0.7133 (tmm) cc_final: 0.6455 (mtm) REVERT: G 45 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8561 (mp10) REVERT: G 62 ASN cc_start: 0.9042 (m-40) cc_final: 0.8785 (m110) REVERT: G 64 GLU cc_start: 0.8294 (mp0) cc_final: 0.8029 (mt-10) REVERT: G 65 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7974 (mm-30) REVERT: I 1 MET cc_start: 0.8167 (tpt) cc_final: 0.7745 (tpp) REVERT: I 43 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8584 (mmm-85) REVERT: K 1 MET cc_start: 0.6887 (tmm) cc_final: 0.5980 (pmm) REVERT: K 3 MET cc_start: 0.7014 (ppp) cc_final: 0.6208 (ppp) REVERT: L 8 CYS cc_start: 0.8799 (m) cc_final: 0.8572 (m) REVERT: M 13 TYR cc_start: 0.8896 (m-10) cc_final: 0.8451 (m-10) REVERT: M 43 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8495 (mtp-110) REVERT: O 64 GLU cc_start: 0.8249 (mp0) cc_final: 0.7862 (mt-10) REVERT: O 65 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8238 (mm-30) REVERT: Q 31 ASP cc_start: 0.8549 (m-30) cc_final: 0.8313 (m-30) REVERT: R 1 MET cc_start: 0.7386 (tmm) cc_final: 0.7018 (tmm) REVERT: R 45 GLN cc_start: 0.8506 (mp10) cc_final: 0.8199 (mp10) REVERT: R 66 LYS cc_start: 0.8662 (mmtp) cc_final: 0.8430 (mttm) REVERT: S 64 GLU cc_start: 0.8315 (mp0) cc_final: 0.8019 (mt-10) REVERT: S 65 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8222 (mm-30) REVERT: U 1 MET cc_start: 0.7770 (tpp) cc_final: 0.6865 (ppp) REVERT: U 58 MET cc_start: 0.8870 (mtp) cc_final: 0.8526 (ttm) REVERT: W 30 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7152 (mp0) REVERT: W 32 TYR cc_start: 0.9324 (t80) cc_final: 0.8917 (t80) REVERT: X 15 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8378 (mm-30) REVERT: X 27 MET cc_start: 0.9013 (ttp) cc_final: 0.8651 (ttm) REVERT: X 43 ARG cc_start: 0.8963 (tpp80) cc_final: 0.8720 (tpp80) REVERT: X 66 LYS cc_start: 0.7998 (mmtm) cc_final: 0.7564 (mmmt) outliers start: 12 outliers final: 10 residues processed: 538 average time/residue: 0.5786 time to fit residues: 430.4083 Evaluate side-chains 546 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 534 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain G residue 45 GLN Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 15 GLU Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 117 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130736 restraints weight = 19519.863| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.09 r_work: 0.3417 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16737 Z= 0.139 Angle : 0.663 10.009 22491 Z= 0.351 Chirality : 0.041 0.260 2310 Planarity : 0.005 0.058 2877 Dihedral : 3.841 17.647 2163 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.71 % Allowed : 17.99 % Favored : 81.31 % 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: 0.53 (0.18), residues: 1953 helix: 0.97 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 68 HIS 0.016 0.001 HIS F 51 PHE 0.007 0.001 PHE N 25 TYR 0.015 0.001 TYR K 32 ARG 0.015 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 939) hydrogen bonds : angle 4.56279 ( 2817) covalent geometry : bond 0.00312 (16737) covalent geometry : angle 0.66282 (22491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9070.34 seconds wall clock time: 160 minutes 26.50 seconds (9626.50 seconds total)