Starting phenix.real_space_refine on Mon May 26 01:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ert_28560/05_2025/8ert_28560_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ert_28560/05_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_28560/05_2025/8ert_28560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ert_28560/05_2025/8ert_28560.map" model { file = "/net/cci-nas-00/data/ceres_data/8ert_28560/05_2025/8ert_28560_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ert_28560/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.83, per 1000 atoms: 0.54 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: 3.91 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: 1.32 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: 4.24 Time building geometry restraints manager: 4.57 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 34.640 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- 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 : 1.778 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: 0.3635 time to fit residues: 276.8752 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 : 1.806 ------------------------------------------------------------------------------- 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 = 0.119943 restraints weight = 20094.268| |-----------------------------------------------------------------------------| 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 : 1.836 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7656 (tpt) cc_final: 0.7027 (tmm) REVERT: A 31 ASP cc_start: 0.8520 (m-30) cc_final: 0.8142 (m-30) REVERT: A 45 GLN cc_start: 0.8239 (mt0) cc_final: 0.7929 (mt0) REVERT: C 1 MET cc_start: 0.6667 (ttp) cc_final: 0.6354 (ttp) REVERT: C 30 GLU cc_start: 0.7465 (mp0) cc_final: 0.7002 (mp0) REVERT: D 1 MET cc_start: 0.8225 (tmm) cc_final: 0.7719 (tpp) REVERT: D 45 GLN cc_start: 0.8706 (mt0) cc_final: 0.8477 (mt0) REVERT: D 62 ASN cc_start: 0.8643 (m110) cc_final: 0.8438 (m110) REVERT: E 1 MET cc_start: 0.7118 (tmm) cc_final: 0.6554 (ppp) REVERT: F 15 GLU cc_start: 0.8064 (tt0) cc_final: 0.7810 (tt0) REVERT: G 45 GLN cc_start: 0.8849 (mp10) cc_final: 0.8540 (mp10) REVERT: I 62 ASN cc_start: 0.8788 (m110) cc_final: 0.8510 (m110) REVERT: J 31 ASP cc_start: 0.8427 (m-30) cc_final: 0.8218 (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: 0.7594 (mp0) cc_final: 0.7296 (mp0) REVERT: L 15 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7986 (mm-30) REVERT: M 1 MET cc_start: 0.6770 (tmm) cc_final: 0.6301 (ppp) REVERT: M 13 TYR cc_start: 0.8738 (m-10) cc_final: 0.8370 (m-10) REVERT: N 1 MET cc_start: 0.7345 (tmm) cc_final: 0.6700 (tpp) REVERT: O 64 GLU cc_start: 0.8108 (mp0) cc_final: 0.7788 (mt-10) REVERT: O 79 ASN cc_start: 0.7780 (m-40) cc_final: 0.7428 (m110) REVERT: R 1 MET cc_start: 0.7025 (tmm) cc_final: 0.6289 (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: 0.8806 (mp10) cc_final: 0.8562 (mp10) REVERT: S 66 LYS cc_start: 0.8340 (mmtp) cc_final: 0.8101 (mmtp) REVERT: U 1 MET cc_start: 0.7634 (tpp) cc_final: 0.7105 (tmm) REVERT: U 58 MET cc_start: 0.8815 (mtp) cc_final: 0.8579 (ttm) REVERT: U 66 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8254 (mmtt) REVERT: U 70 MET cc_start: 0.8376 (mtp) cc_final: 0.8162 (mtp) REVERT: W 30 GLU cc_start: 0.7563 (mp0) cc_final: 0.7007 (mp0) REVERT: X 27 MET cc_start: 0.8894 (ttp) cc_final: 0.8465 (ttm) outliers start: 10 outliers final: 3 residues processed: 548 average time/residue: 0.3652 time to fit residues: 270.9934 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 : 2.087 ------------------------------------------------------------------------------- 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: 0.0050 chunk 39 optimal weight: 4.9990 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: 0.9396 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.146641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118108 restraints weight = 20020.699| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.34 r_work: 0.3243 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1468 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= 0.122 Angle : 0.554 8.158 22491 Z= 0.296 Chirality : 0.039 0.175 2310 Planarity : 0.004 0.035 2877 Dihedral : 3.787 16.950 2163 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.82 % Allowed : 10.76 % Favored : 88.42 % 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: 0.62 (0.18), residues: 1953 helix: 1.19 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.43 (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 0.019 0.001 TYR I 84 ARG 0.009 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 939) hydrogen bonds : angle 4.51545 ( 2817) covalent geometry : bond 0.00265 (16737) covalent geometry : angle 0.55365 (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 : 1.810 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7611 (tpt) cc_final: 0.7003 (tmm) REVERT: A 31 ASP cc_start: 0.8638 (m-30) cc_final: 0.8148 (m-30) REVERT: A 64 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7413 (mm-30) REVERT: C 1 MET cc_start: 0.6680 (ttp) cc_final: 0.6343 (ttp) REVERT: C 30 GLU cc_start: 0.7506 (mp0) cc_final: 0.7130 (mp0) REVERT: D 1 MET cc_start: 0.8263 (tmm) cc_final: 0.7754 (tpp) REVERT: D 31 ASP cc_start: 0.7979 (t0) cc_final: 0.7754 (t70) REVERT: D 62 ASN cc_start: 0.8676 (m110) cc_final: 0.8399 (m110) REVERT: D 86 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7938 (mmtm) REVERT: E 1 MET cc_start: 0.7252 (tmm) cc_final: 0.6705 (ppp) REVERT: E 13 TYR cc_start: 0.8719 (m-10) cc_final: 0.8164 (m-80) REVERT: F 15 GLU cc_start: 0.8045 (tt0) cc_final: 0.7775 (tt0) REVERT: G 45 GLN cc_start: 0.8902 (mp10) cc_final: 0.8572 (mp10) REVERT: G 62 ASN cc_start: 0.9036 (m110) cc_final: 0.8708 (m110) REVERT: I 62 ASN cc_start: 0.8778 (m110) cc_final: 0.8458 (m110) REVERT: J 32 TYR cc_start: 0.8844 (t80) cc_final: 0.8606 (t80) REVERT: K 1 MET cc_start: 0.6694 (tmm) cc_final: 0.5352 (pmm) REVERT: K 30 GLU cc_start: 0.7520 (mp0) cc_final: 0.7292 (mp0) REVERT: L 31 ASP cc_start: 0.8311 (t0) cc_final: 0.8110 (t0) REVERT: M 1 MET cc_start: 0.6900 (tmm) cc_final: 0.6446 (ppp) REVERT: M 13 TYR cc_start: 0.8791 (m-10) cc_final: 0.8134 (m-80) REVERT: O 62 ASN cc_start: 0.8864 (m-40) cc_final: 0.8449 (m110) REVERT: O 79 ASN cc_start: 0.7674 (m-40) cc_final: 0.7394 (m110) REVERT: R 66 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8252 (mttm) REVERT: U 1 MET cc_start: 0.7703 (tpp) cc_final: 0.7092 (tmm) REVERT: U 58 MET cc_start: 0.8837 (mtp) cc_final: 0.8530 (ttm) REVERT: W 30 GLU cc_start: 0.7452 (mp0) cc_final: 0.6821 (mp0) REVERT: X 27 MET cc_start: 0.8899 (ttp) cc_final: 0.8545 (ttm) outliers start: 14 outliers final: 8 residues processed: 545 average time/residue: 0.3531 time to fit residues: 261.0711 Evaluate side-chains 534 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 526 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116993 restraints weight = 20139.836| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.36 r_work: 0.3228 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16737 Z= 0.132 Angle : 0.567 8.711 22491 Z= 0.301 Chirality : 0.039 0.190 2310 Planarity : 0.004 0.036 2877 Dihedral : 3.746 17.208 2163 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.94 % Allowed : 11.99 % Favored : 87.07 % 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: 0.68 (0.18), residues: 1953 helix: 1.23 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.36 (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 R 51 PHE 0.008 0.001 PHE N 25 TYR 0.017 0.001 TYR C 32 ARG 0.010 0.001 ARG L 89 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 939) hydrogen bonds : angle 4.46192 ( 2817) covalent geometry : bond 0.00296 (16737) covalent geometry : angle 0.56712 (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: 16 poor density : 540 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7580 (tpt) cc_final: 0.7021 (tmm) REVERT: C 15 GLU cc_start: 0.8226 (tt0) cc_final: 0.8013 (tt0) REVERT: C 30 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7209 (mp0) REVERT: D 1 MET cc_start: 0.8104 (tmm) cc_final: 0.7606 (tpp) REVERT: D 31 ASP cc_start: 0.7991 (t0) cc_final: 0.7770 (t70) REVERT: D 70 MET cc_start: 0.8830 (mtp) cc_final: 0.8332 (mtp) REVERT: D 86 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7926 (mmtm) REVERT: E 1 MET cc_start: 0.7324 (tmm) cc_final: 0.6705 (ppp) REVERT: E 3 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5483 (tmm) REVERT: F 60 ASP cc_start: 0.7774 (t0) cc_final: 0.7535 (t0) REVERT: F 62 ASN cc_start: 0.8948 (m110) cc_final: 0.8582 (m110) REVERT: G 62 ASN cc_start: 0.9051 (m110) cc_final: 0.8738 (m110) REVERT: G 79 ASN cc_start: 0.7682 (m-40) cc_final: 0.7462 (m110) REVERT: I 62 ASN cc_start: 0.8761 (m110) cc_final: 0.8509 (m110) REVERT: K 1 MET cc_start: 0.6786 (tmm) cc_final: 0.5451 (pmm) REVERT: K 3 MET cc_start: 0.6833 (ppp) cc_final: 0.6457 (ppp) REVERT: K 30 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7294 (mp0) REVERT: L 8 CYS cc_start: 0.8599 (m) cc_final: 0.8365 (m) REVERT: M 1 MET cc_start: 0.6977 (tmm) cc_final: 0.6484 (ppp) REVERT: N 1 MET cc_start: 0.7162 (tmm) cc_final: 0.6742 (mtp) REVERT: O 62 ASN cc_start: 0.8841 (m-40) cc_final: 0.8437 (m110) REVERT: O 64 GLU cc_start: 0.8154 (mp0) cc_final: 0.7767 (mt-10) REVERT: O 65 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8207 (mm-30) REVERT: O 79 ASN cc_start: 0.7701 (m-40) cc_final: 0.7450 (m110) REVERT: R 1 MET cc_start: 0.7082 (tmm) cc_final: 0.6283 (tpp) REVERT: S 62 ASN cc_start: 0.9011 (m110) cc_final: 0.8400 (m110) REVERT: S 64 GLU cc_start: 0.8187 (mp0) cc_final: 0.7933 (mt-10) REVERT: S 66 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7923 (mmtt) REVERT: U 1 MET cc_start: 0.7734 (tpp) cc_final: 0.6778 (ppp) REVERT: U 58 MET cc_start: 0.8833 (mtp) cc_final: 0.8523 (ttm) REVERT: V 70 MET cc_start: 0.8387 (mtp) cc_final: 0.8182 (mtp) REVERT: W 30 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7154 (mp0) REVERT: X 15 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8107 (mm-30) REVERT: X 27 MET cc_start: 0.8946 (ttp) cc_final: 0.8567 (ttm) outliers start: 16 outliers final: 12 residues processed: 542 average time/residue: 0.3653 time to fit residues: 268.8045 Evaluate side-chains 538 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 525 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 V 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: 0.3980 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 0.0170 chunk 40 optimal weight: 0.0030 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6830 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118949 restraints weight = 20347.444| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.39 r_work: 0.3235 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1869 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= 0.118 Angle : 0.560 8.571 22491 Z= 0.299 Chirality : 0.039 0.205 2310 Planarity : 0.004 0.051 2877 Dihedral : 3.707 17.887 2163 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.00 % Allowed : 13.58 % Favored : 85.42 % 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: 1.24 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.33 (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 R 51 PHE 0.008 0.001 PHE N 25 TYR 0.013 0.001 TYR X 84 ARG 0.010 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 939) hydrogen bonds : angle 4.41116 ( 2817) covalent geometry : bond 0.00251 (16737) covalent geometry : angle 0.56044 (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 561 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 544 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7666 (tpt) cc_final: 0.7025 (tmm) REVERT: D 1 MET cc_start: 0.8141 (tmm) cc_final: 0.7684 (tpp) REVERT: D 62 ASN cc_start: 0.8640 (m110) cc_final: 0.8348 (m110) REVERT: D 86 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7778 (mmtm) REVERT: E 1 MET cc_start: 0.7371 (tmm) cc_final: 0.6732 (ppp) REVERT: E 3 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5441 (tmm) REVERT: F 1 MET cc_start: 0.7070 (tmm) cc_final: 0.6213 (mtm) REVERT: G 62 ASN cc_start: 0.8998 (m110) cc_final: 0.8672 (m110) REVERT: G 64 GLU cc_start: 0.8127 (mp0) cc_final: 0.7754 (mt-10) REVERT: I 1 MET cc_start: 0.7969 (tpt) cc_final: 0.7687 (tpp) REVERT: I 62 ASN cc_start: 0.8803 (m110) cc_final: 0.8496 (m110) REVERT: K 1 MET cc_start: 0.6856 (tmm) cc_final: 0.5525 (pmm) REVERT: K 3 MET cc_start: 0.6812 (ppp) cc_final: 0.5961 (ppp) REVERT: K 26 LYS cc_start: 0.8549 (mttt) cc_final: 0.8005 (mttt) REVERT: K 30 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7260 (mp0) REVERT: L 8 CYS cc_start: 0.8615 (m) cc_final: 0.8351 (m) REVERT: L 13 TYR cc_start: 0.8605 (m-80) cc_final: 0.8273 (m-80) REVERT: M 1 MET cc_start: 0.7036 (tmm) cc_final: 0.6521 (ppp) REVERT: M 13 TYR cc_start: 0.8696 (m-10) cc_final: 0.8100 (m-80) REVERT: N 1 MET cc_start: 0.7119 (tmm) cc_final: 0.6862 (mtp) REVERT: O 62 ASN cc_start: 0.8770 (m-40) cc_final: 0.8379 (m110) REVERT: O 79 ASN cc_start: 0.7579 (m-40) cc_final: 0.7360 (m110) REVERT: R 1 MET cc_start: 0.7025 (tmm) cc_final: 0.6388 (tpp) REVERT: R 66 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8202 (mttm) REVERT: S 66 LYS cc_start: 0.8225 (mmtp) cc_final: 0.7767 (mmtt) REVERT: U 1 MET cc_start: 0.7760 (tpp) cc_final: 0.6819 (ppp) REVERT: U 58 MET cc_start: 0.8844 (mtp) cc_final: 0.8569 (ttm) REVERT: W 30 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7133 (mp0) REVERT: X 15 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8163 (mm-30) REVERT: X 27 MET cc_start: 0.8835 (ttp) cc_final: 0.8434 (ttm) outliers start: 17 outliers final: 10 residues processed: 546 average time/residue: 0.3614 time to fit residues: 268.1594 Evaluate side-chains 534 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 523 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain C residue 59 ILE 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: 0.8980 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN G 79 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115584 restraints weight = 20152.447| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.37 r_work: 0.3200 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16737 Z= 0.158 Angle : 0.598 9.356 22491 Z= 0.316 Chirality : 0.040 0.220 2310 Planarity : 0.005 0.062 2877 Dihedral : 3.757 17.009 2163 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.12 % Allowed : 15.34 % Favored : 83.54 % 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: 1.04 (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 0.010 0.001 TRP S 94 HIS 0.016 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR K 32 ARG 0.011 0.001 ARG Q 89 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 939) hydrogen bonds : angle 4.45936 ( 2817) covalent geometry : bond 0.00365 (16737) covalent geometry : angle 0.59750 (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 558 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 539 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7694 (tpt) cc_final: 0.7087 (tmm) REVERT: D 1 MET cc_start: 0.8105 (tmm) cc_final: 0.7596 (tpp) REVERT: D 70 MET cc_start: 0.8858 (mtp) cc_final: 0.8376 (mtp) REVERT: D 86 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7905 (mmtm) REVERT: E 1 MET cc_start: 0.7401 (tmm) cc_final: 0.6731 (ppp) REVERT: E 3 MET cc_start: 0.6033 (tmm) cc_final: 0.5565 (tmm) REVERT: E 13 TYR cc_start: 0.8750 (m-10) cc_final: 0.8025 (m-80) REVERT: E 45 GLN cc_start: 0.8403 (mt0) cc_final: 0.8166 (mt0) REVERT: G 62 ASN cc_start: 0.8990 (m-40) cc_final: 0.8705 (m110) REVERT: I 1 MET cc_start: 0.8070 (tpt) cc_final: 0.7719 (tpp) REVERT: I 62 ASN cc_start: 0.8851 (m110) cc_final: 0.8619 (m110) REVERT: K 1 MET cc_start: 0.6886 (tmm) cc_final: 0.5709 (pmm) REVERT: K 3 MET cc_start: 0.6740 (ppp) cc_final: 0.5831 (ppp) REVERT: L 8 CYS cc_start: 0.8569 (m) cc_final: 0.8325 (m) REVERT: M 62 ASN cc_start: 0.8656 (m-40) cc_final: 0.8341 (m-40) REVERT: N 1 MET cc_start: 0.7209 (tmm) cc_final: 0.7005 (mtp) REVERT: O 64 GLU cc_start: 0.8054 (mp0) cc_final: 0.7807 (mt-10) REVERT: O 65 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8200 (mm-30) REVERT: O 79 ASN cc_start: 0.7799 (m-40) cc_final: 0.7566 (m110) REVERT: R 45 GLN cc_start: 0.8611 (mp10) cc_final: 0.8339 (mp10) REVERT: S 64 GLU cc_start: 0.8222 (mp0) cc_final: 0.7909 (mt-10) REVERT: S 65 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8228 (mm-30) REVERT: S 66 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8016 (mmtt) REVERT: U 1 MET cc_start: 0.7856 (tpp) cc_final: 0.6914 (ppp) REVERT: U 58 MET cc_start: 0.8882 (mtp) cc_final: 0.8603 (ttm) REVERT: W 30 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7156 (mp0) REVERT: X 27 MET cc_start: 0.8966 (ttp) cc_final: 0.8569 (ttm) REVERT: X 66 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7408 (mmmt) outliers start: 19 outliers final: 13 residues processed: 541 average time/residue: 0.3779 time to fit residues: 277.5384 Evaluate side-chains 542 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 529 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain I residue 15 GLU 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 S residue 88 LYS 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: 0.9990 chunk 62 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 83 optimal weight: 0.0870 overall best weight: 0.7964 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132170 restraints weight = 19479.258| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.13 r_work: 0.3455 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2053 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= 0.125 Angle : 0.594 9.840 22491 Z= 0.315 Chirality : 0.039 0.233 2310 Planarity : 0.005 0.055 2877 Dihedral : 3.728 17.108 2163 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.12 % Allowed : 15.58 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 1953 helix: 1.25 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.31 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 94 HIS 0.020 0.002 HIS X 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR K 32 ARG 0.013 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 939) hydrogen bonds : angle 4.42376 ( 2817) covalent geometry : bond 0.00274 (16737) covalent geometry : angle 0.59360 (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 561 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 542 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7492 (tpt) cc_final: 0.7096 (tmm) REVERT: D 1 MET cc_start: 0.7955 (tmm) cc_final: 0.7550 (tpp) REVERT: D 62 ASN cc_start: 0.8733 (m110) cc_final: 0.8461 (m110) REVERT: E 1 MET cc_start: 0.7432 (tmm) cc_final: 0.6797 (ppp) REVERT: E 3 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5552 (tmm) REVERT: F 1 MET cc_start: 0.7204 (tmm) cc_final: 0.6419 (mtm) REVERT: G 45 GLN cc_start: 0.8794 (mp10) cc_final: 0.8437 (mp10) REVERT: G 62 ASN cc_start: 0.9061 (m-40) cc_final: 0.8839 (m110) REVERT: G 65 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7915 (mm-30) REVERT: I 1 MET cc_start: 0.8038 (tpt) cc_final: 0.7704 (tpp) REVERT: K 1 MET cc_start: 0.6878 (tmm) cc_final: 0.5864 (pmm) REVERT: K 3 MET cc_start: 0.6915 (ppp) cc_final: 0.6001 (ppp) REVERT: L 8 CYS cc_start: 0.8743 (m) cc_final: 0.8523 (m) REVERT: M 13 TYR cc_start: 0.8830 (m-10) cc_final: 0.8229 (m-80) REVERT: M 30 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8028 (mt-10) REVERT: O 62 ASN cc_start: 0.8897 (m-40) cc_final: 0.8544 (m110) REVERT: O 79 ASN cc_start: 0.7603 (m-40) cc_final: 0.7399 (m110) REVERT: R 1 MET cc_start: 0.7310 (tmm) cc_final: 0.6647 (tpp) REVERT: R 66 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8381 (mttm) REVERT: S 45 GLN cc_start: 0.8519 (mp10) cc_final: 0.8305 (mp10) REVERT: S 64 GLU cc_start: 0.8136 (mp0) cc_final: 0.7843 (mt-10) REVERT: S 66 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8198 (mmtt) REVERT: U 1 MET cc_start: 0.7637 (tpp) cc_final: 0.6932 (ppp) REVERT: U 58 MET cc_start: 0.8731 (mtp) cc_final: 0.8422 (ttm) REVERT: W 30 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7321 (mp0) REVERT: X 27 MET cc_start: 0.8887 (ttp) cc_final: 0.8509 (ttm) outliers start: 19 outliers final: 15 residues processed: 543 average time/residue: 0.3638 time to fit residues: 267.9588 Evaluate side-chains 545 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 529 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU 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 90 ASP Chi-restraints excluded: chain I residue 15 GLU 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 V 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 110 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130627 restraints weight = 19379.117| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.11 r_work: 0.3436 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2152 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= 0.137 Angle : 0.619 8.887 22491 Z= 0.328 Chirality : 0.040 0.244 2310 Planarity : 0.005 0.054 2877 Dihedral : 3.736 17.370 2163 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.12 % Allowed : 16.40 % Favored : 82.48 % 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: 0.71 (0.18), residues: 1953 helix: 1.22 (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 0.014 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 939) hydrogen bonds : angle 4.45355 ( 2817) covalent geometry : bond 0.00312 (16737) covalent geometry : angle 0.61906 (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 555 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 536 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7427 (tpt) cc_final: 0.7095 (tmm) REVERT: D 1 MET cc_start: 0.7981 (tmm) cc_final: 0.7542 (tpp) REVERT: D 62 ASN cc_start: 0.8694 (m110) cc_final: 0.8410 (m110) REVERT: E 3 MET cc_start: 0.6035 (OUTLIER) cc_final: 0.5625 (tmm) REVERT: E 13 TYR cc_start: 0.8703 (m-10) cc_final: 0.8021 (m-80) REVERT: G 62 ASN cc_start: 0.8990 (m-40) cc_final: 0.8743 (m110) REVERT: G 65 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7756 (mm-30) REVERT: I 1 MET cc_start: 0.7947 (tpt) cc_final: 0.7598 (tpp) REVERT: K 1 MET cc_start: 0.6845 (tmm) cc_final: 0.5915 (pmm) REVERT: K 3 MET cc_start: 0.6747 (ppp) cc_final: 0.5832 (ppp) REVERT: O 62 ASN cc_start: 0.8781 (m-40) cc_final: 0.8573 (m110) REVERT: O 65 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8024 (mm-30) REVERT: O 79 ASN cc_start: 0.7631 (m-40) cc_final: 0.7426 (m110) REVERT: R 66 LYS cc_start: 0.8491 (mmtp) cc_final: 0.8095 (mttm) REVERT: S 45 GLN cc_start: 0.8459 (mp10) cc_final: 0.8251 (mp10) REVERT: S 64 GLU cc_start: 0.8012 (mp0) cc_final: 0.7763 (mt-10) REVERT: S 65 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8090 (mm-30) REVERT: S 66 LYS cc_start: 0.8353 (mmtp) cc_final: 0.8110 (mmtt) REVERT: U 1 MET cc_start: 0.7611 (tpp) cc_final: 0.6944 (ppp) REVERT: U 58 MET cc_start: 0.8679 (mtp) cc_final: 0.8382 (ttm) REVERT: W 30 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7106 (mp0) REVERT: X 27 MET cc_start: 0.8885 (ttp) cc_final: 0.8527 (ttm) REVERT: X 43 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8393 (tpp-160) REVERT: X 66 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7558 (mmmt) outliers start: 19 outliers final: 13 residues processed: 539 average time/residue: 0.3629 time to fit residues: 265.3868 Evaluate side-chains 541 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 527 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 C residue 59 ILE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain I residue 15 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 180 optimal weight: 10.0000 chunk 175 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ** K 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** R 62 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 = 0.3869 r_free = 0.3869 target = 0.154900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127429 restraints weight = 19578.039| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.12 r_work: 0.3396 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16737 Z= 0.179 Angle : 0.663 10.432 22491 Z= 0.350 Chirality : 0.042 0.262 2310 Planarity : 0.005 0.056 2877 Dihedral : 3.841 16.741 2163 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.06 % Allowed : 17.11 % Favored : 81.83 % 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: 0.62 (0.18), residues: 1953 helix: 1.05 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 94 HIS 0.017 0.002 HIS L 51 PHE 0.009 0.001 PHE N 25 TYR 0.017 0.001 TYR K 32 ARG 0.015 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 939) hydrogen bonds : angle 4.57317 ( 2817) covalent geometry : bond 0.00422 (16737) covalent geometry : angle 0.66313 (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 555 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 537 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7488 (tpt) cc_final: 0.7024 (tmm) REVERT: D 1 MET cc_start: 0.7981 (tmm) cc_final: 0.7448 (tpp) REVERT: D 66 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7780 (mmmt) REVERT: E 3 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5520 (tmm) REVERT: E 13 TYR cc_start: 0.8833 (m-10) cc_final: 0.8264 (m-80) REVERT: F 1 MET cc_start: 0.7249 (tmm) cc_final: 0.6546 (mtm) REVERT: F 13 TYR cc_start: 0.9225 (m-10) cc_final: 0.8993 (m-10) REVERT: G 45 GLN cc_start: 0.8606 (mp10) cc_final: 0.8395 (mp10) REVERT: G 62 ASN cc_start: 0.9051 (m-40) cc_final: 0.8806 (m110) REVERT: G 65 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8006 (mm-30) REVERT: I 1 MET cc_start: 0.7999 (tpt) cc_final: 0.7604 (tpp) REVERT: K 1 MET cc_start: 0.6832 (tmm) cc_final: 0.5924 (pmm) REVERT: K 3 MET cc_start: 0.6812 (ppp) cc_final: 0.5885 (ppp) REVERT: L 8 CYS cc_start: 0.8736 (m) cc_final: 0.8524 (m) REVERT: M 13 TYR cc_start: 0.8852 (m-10) cc_final: 0.8414 (m-10) REVERT: O 62 ASN cc_start: 0.8838 (m-40) cc_final: 0.8583 (m110) REVERT: O 64 GLU cc_start: 0.8131 (mp0) cc_final: 0.7841 (mt-10) REVERT: O 65 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8206 (mm-30) REVERT: O 79 ASN cc_start: 0.7909 (m-40) cc_final: 0.7670 (m110) REVERT: R 1 MET cc_start: 0.7351 (tmm) cc_final: 0.6911 (tmm) REVERT: R 45 GLN cc_start: 0.8490 (mp10) cc_final: 0.8206 (mp10) REVERT: R 66 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8471 (mttm) REVERT: S 64 GLU cc_start: 0.8254 (mp0) cc_final: 0.7918 (mt-10) REVERT: S 65 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8279 (mm-30) REVERT: S 66 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8261 (mmtt) REVERT: U 1 MET cc_start: 0.7780 (tpp) cc_final: 0.6945 (ppp) REVERT: U 58 MET cc_start: 0.8795 (mtp) cc_final: 0.8442 (ttm) REVERT: W 30 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7186 (mp0) REVERT: X 27 MET cc_start: 0.8955 (ttp) cc_final: 0.8606 (ttm) REVERT: X 43 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8605 (tpp-160) REVERT: X 66 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7604 (mmmt) outliers start: 18 outliers final: 15 residues processed: 539 average time/residue: 0.3646 time to fit residues: 266.6240 Evaluate side-chains 546 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 530 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 C residue 59 ILE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain I residue 15 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** K 62 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN U 51 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.157722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130605 restraints weight = 19435.089| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.10 r_work: 0.3449 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16737 Z= 0.142 Angle : 0.664 10.046 22491 Z= 0.351 Chirality : 0.041 0.264 2310 Planarity : 0.005 0.059 2877 Dihedral : 3.830 17.327 2163 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.88 % Allowed : 17.40 % 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: 0.57 (0.18), residues: 1953 helix: 1.01 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 94 HIS 0.015 0.002 HIS X 51 PHE 0.008 0.001 PHE N 25 TYR 0.015 0.001 TYR K 32 ARG 0.016 0.001 ARG F 43 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 939) hydrogen bonds : angle 4.52129 ( 2817) covalent geometry : bond 0.00321 (16737) covalent geometry : angle 0.66352 (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 547 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 532 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7519 (tpt) cc_final: 0.7105 (tmm) REVERT: C 30 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7040 (mp0) REVERT: D 1 MET cc_start: 0.7970 (tmm) cc_final: 0.7472 (tpp) REVERT: D 14 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 70 MET cc_start: 0.8885 (mtp) cc_final: 0.8539 (mtp) REVERT: E 3 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.5487 (tmm) REVERT: F 1 MET cc_start: 0.7215 (tmm) cc_final: 0.6519 (mtm) REVERT: F 13 TYR cc_start: 0.9193 (m-10) cc_final: 0.8938 (m-10) REVERT: F 46 THR cc_start: 0.8550 (p) cc_final: 0.8337 (p) REVERT: G 45 GLN cc_start: 0.8611 (mp10) cc_final: 0.8382 (mp10) REVERT: G 62 ASN cc_start: 0.9017 (m-40) cc_final: 0.8756 (m110) REVERT: G 65 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7964 (mm-30) REVERT: I 1 MET cc_start: 0.7988 (tpt) cc_final: 0.7641 (tpp) REVERT: K 1 MET cc_start: 0.6752 (tmm) cc_final: 0.5894 (pmm) REVERT: K 3 MET cc_start: 0.6889 (ppp) cc_final: 0.5922 (ppp) REVERT: M 13 TYR cc_start: 0.8868 (m-10) cc_final: 0.8385 (m-10) REVERT: M 30 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8056 (mt-10) REVERT: O 62 ASN cc_start: 0.8786 (m-40) cc_final: 0.8540 (m110) REVERT: O 64 GLU cc_start: 0.8156 (mp0) cc_final: 0.7846 (mt-10) REVERT: O 65 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8215 (mm-30) REVERT: R 1 MET cc_start: 0.7339 (tmm) cc_final: 0.6951 (tmm) REVERT: R 66 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8366 (mttm) REVERT: S 64 GLU cc_start: 0.8195 (mp0) cc_final: 0.7863 (mt-10) REVERT: S 65 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8195 (mm-30) REVERT: S 66 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8221 (mmtt) REVERT: U 1 MET cc_start: 0.7715 (tpp) cc_final: 0.7003 (ppp) REVERT: U 58 MET cc_start: 0.8771 (mtp) cc_final: 0.8429 (ttm) REVERT: W 30 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7179 (mp0) REVERT: X 27 MET cc_start: 0.8937 (ttp) cc_final: 0.8614 (ttm) REVERT: X 43 ARG cc_start: 0.8833 (tpp80) cc_final: 0.8559 (tpp-160) REVERT: X 66 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7574 (mmmt) outliers start: 15 outliers final: 11 residues processed: 534 average time/residue: 0.3628 time to fit residues: 262.8232 Evaluate side-chains 538 residues out of total 1701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 525 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 D residue 14 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain I residue 15 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 117 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130683 restraints weight = 19535.306| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.09 r_work: 0.3426 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16737 Z= 0.143 Angle : 0.657 9.741 22491 Z= 0.347 Chirality : 0.041 0.261 2310 Planarity : 0.005 0.059 2877 Dihedral : 3.784 17.768 2163 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.76 % Allowed : 18.05 % Favored : 81.19 % 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: 0.62 (0.18), residues: 1953 helix: 1.04 (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 0.007 0.001 TRP V 94 HIS 0.017 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.015 0.001 TYR K 32 ARG 0.015 0.001 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 939) hydrogen bonds : angle 4.51562 ( 2817) covalent geometry : bond 0.00327 (16737) covalent geometry : angle 0.65655 (22491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8489.80 seconds wall clock time: 147 minutes 39.80 seconds (8859.80 seconds total)