Starting phenix.real_space_refine on Sat Jul 4 00:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.map" model { file = "/net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czd_27095/07_2026/8czd_27095.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 11000 2.51 5 N 3200 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17640 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "Q" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "R" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "S" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "T" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "A" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "I" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "J" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "K" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "L" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "M" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "N" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "O" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "P" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 882 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 4.00, per 1000 atoms: 0.23 Number of scatterers: 17640 At special positions: 0 Unit cell: (105.27, 105.27, 141.81, 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 40 16.00 O 3400 8.00 N 3200 7.00 C 11000 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: 1.81 Conformation dependent library (CDL) restraints added in 955.9 milliseconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4160 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.735A pdb=" N GLU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.762A pdb=" N ARG C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN C 97 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 24 removed outlier: 3.538A pdb=" N LYS Q 18 " --> pdb=" O THR Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS Q 31 " --> pdb=" O TYR Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 39 Processing helix chain 'Q' and resid 42 through 46 Processing helix chain 'Q' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 75 removed outlier: 3.928A pdb=" N GLU Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN Q 75 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG Q 87 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 115 removed outlier: 4.293A pdb=" N GLN Q 97 " --> pdb=" O ASN Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS R 18 " --> pdb=" O THR R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS R 31 " --> pdb=" O TYR R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 39 Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU R 53 " --> pdb=" O ARG R 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN R 58 " --> pdb=" O GLU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 75 removed outlier: 3.930A pdb=" N GLU R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN R 75 " --> pdb=" O TYR R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 87 removed outlier: 3.762A pdb=" N ARG R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN R 97 " --> pdb=" O ASN R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS S 18 " --> pdb=" O THR S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS S 31 " --> pdb=" O TYR S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 39 Processing helix chain 'S' and resid 42 through 46 Processing helix chain 'S' and resid 48 through 58 removed outlier: 3.737A pdb=" N GLU S 53 " --> pdb=" O ARG S 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN S 58 " --> pdb=" O GLU S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU S 74 " --> pdb=" O ASP S 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN S 75 " --> pdb=" O TYR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG S 87 " --> pdb=" O VAL S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 115 removed outlier: 4.293A pdb=" N GLN S 97 " --> pdb=" O ASN S 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS T 18 " --> pdb=" O THR T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS T 31 " --> pdb=" O TYR T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 39 Processing helix chain 'T' and resid 42 through 46 Processing helix chain 'T' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN T 58 " --> pdb=" O GLU T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 75 removed outlier: 3.928A pdb=" N GLU T 74 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN T 75 " --> pdb=" O TYR T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG T 87 " --> pdb=" O VAL T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 115 removed outlier: 4.293A pdb=" N GLN T 97 " --> pdb=" O ASN T 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.735A pdb=" N GLU B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 75 removed outlier: 3.928A pdb=" N GLU B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.762A pdb=" N ARG D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN D 97 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN E 75 " --> pdb=" O TYR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN E 97 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS F 31 " --> pdb=" O TYR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 75 removed outlier: 3.928A pdb=" N GLU F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN F 75 " --> pdb=" O TYR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 48 through 58 removed outlier: 3.737A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 75 removed outlier: 3.930A pdb=" N GLU G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN G 75 " --> pdb=" O TYR G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG G 87 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN G 97 " --> pdb=" O ASN G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS H 31 " --> pdb=" O TYR H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'H' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN H 75 " --> pdb=" O TYR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG H 87 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN H 97 " --> pdb=" O ASN H 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS I 18 " --> pdb=" O THR I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 32 removed outlier: 3.808A pdb=" N LYS I 31 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU I 53 " --> pdb=" O ARG I 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN I 58 " --> pdb=" O GLU I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN I 75 " --> pdb=" O TYR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 87 removed outlier: 3.762A pdb=" N ARG I 87 " --> pdb=" O VAL I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN I 97 " --> pdb=" O ASN I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS J 18 " --> pdb=" O THR J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 32 removed outlier: 3.808A pdb=" N LYS J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 42 through 46 Processing helix chain 'J' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU J 53 " --> pdb=" O ARG J 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN J 75 " --> pdb=" O TYR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG J 87 " --> pdb=" O VAL J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN J 97 " --> pdb=" O ASN J 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS K 18 " --> pdb=" O THR K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS K 31 " --> pdb=" O TYR K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 42 through 46 Processing helix chain 'K' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU K 53 " --> pdb=" O ARG K 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN K 75 " --> pdb=" O TYR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG K 87 " --> pdb=" O VAL K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN K 97 " --> pdb=" O ASN K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS L 18 " --> pdb=" O THR L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS L 31 " --> pdb=" O TYR L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 42 through 46 Processing helix chain 'L' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU L 53 " --> pdb=" O ARG L 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN L 58 " --> pdb=" O GLU L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN L 75 " --> pdb=" O TYR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 87 removed outlier: 3.762A pdb=" N ARG L 87 " --> pdb=" O VAL L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS M 18 " --> pdb=" O THR M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 32 removed outlier: 3.808A pdb=" N LYS M 31 " --> pdb=" O TYR M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 39 Processing helix chain 'M' and resid 42 through 46 Processing helix chain 'M' and resid 48 through 58 removed outlier: 3.737A pdb=" N GLU M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN M 75 " --> pdb=" O TYR M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG M 87 " --> pdb=" O VAL M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN M 97 " --> pdb=" O ASN M 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS N 18 " --> pdb=" O THR N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS N 31 " --> pdb=" O TYR N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 42 through 46 Processing helix chain 'N' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU N 53 " --> pdb=" O ARG N 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN N 75 " --> pdb=" O TYR N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG N 87 " --> pdb=" O VAL N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN N 97 " --> pdb=" O ASN N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 24 removed outlier: 3.537A pdb=" N LYS O 18 " --> pdb=" O THR O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 32 removed outlier: 3.809A pdb=" N LYS O 31 " --> pdb=" O TYR O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 39 Processing helix chain 'O' and resid 42 through 46 Processing helix chain 'O' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU O 53 " --> pdb=" O ARG O 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN O 75 " --> pdb=" O TYR O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG O 87 " --> pdb=" O VAL O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN O 97 " --> pdb=" O ASN O 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 24 removed outlier: 3.536A pdb=" N LYS P 18 " --> pdb=" O THR P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 32 removed outlier: 3.810A pdb=" N LYS P 31 " --> pdb=" O TYR P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 39 Processing helix chain 'P' and resid 42 through 46 Processing helix chain 'P' and resid 48 through 58 removed outlier: 3.736A pdb=" N GLU P 53 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN P 58 " --> pdb=" O GLU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 75 removed outlier: 3.929A pdb=" N GLU P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN P 75 " --> pdb=" O TYR P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 87 removed outlier: 3.761A pdb=" N ARG P 87 " --> pdb=" O VAL P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 115 removed outlier: 4.292A pdb=" N GLN P 97 " --> pdb=" O ASN P 93 " (cutoff:3.500A) 1000 hydrogen bonds defined for protein. 2880 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: 3.11 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6060 1.34 - 1.46: 2374 1.46 - 1.57: 9306 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 17780 Sorted by residual: bond pdb=" CA ARG A 42 " pdb=" C ARG A 42 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.02e-02 9.61e+03 1.68e+00 bond pdb=" CA ARG G 42 " pdb=" C ARG G 42 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.02e-02 9.61e+03 1.64e+00 bond pdb=" CA ARG T 42 " pdb=" C ARG T 42 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.02e-02 9.61e+03 1.64e+00 bond pdb=" CA ARG F 42 " pdb=" C ARG F 42 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.02e-02 9.61e+03 1.60e+00 bond pdb=" CA ARG R 42 " pdb=" C ARG R 42 " ideal model delta sigma weight residual 1.525 1.512 0.013 1.02e-02 9.61e+03 1.59e+00 ... (remaining 17775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 21236 1.30 - 2.59: 1904 2.59 - 3.89: 460 3.89 - 5.18: 114 5.18 - 6.48: 46 Bond angle restraints: 23760 Sorted by residual: angle pdb=" N ILE T 32 " pdb=" CA ILE T 32 " pdb=" C ILE T 32 " ideal model delta sigma weight residual 112.17 107.12 5.05 9.50e-01 1.11e+00 2.83e+01 angle pdb=" N ILE I 32 " pdb=" CA ILE I 32 " pdb=" C ILE I 32 " ideal model delta sigma weight residual 112.17 107.13 5.04 9.50e-01 1.11e+00 2.82e+01 angle pdb=" N ILE G 32 " pdb=" CA ILE G 32 " pdb=" C ILE G 32 " ideal model delta sigma weight residual 112.17 107.13 5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" N ILE K 32 " pdb=" CA ILE K 32 " pdb=" C ILE K 32 " ideal model delta sigma weight residual 112.17 107.13 5.04 9.50e-01 1.11e+00 2.81e+01 angle pdb=" N ILE C 32 " pdb=" CA ILE C 32 " pdb=" C ILE C 32 " ideal model delta sigma weight residual 112.17 107.14 5.03 9.50e-01 1.11e+00 2.81e+01 ... (remaining 23755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9780 17.96 - 35.92: 1320 35.92 - 53.88: 260 53.88 - 71.84: 20 71.84 - 89.80: 40 Dihedral angle restraints: 11420 sinusoidal: 5120 harmonic: 6300 Sorted by residual: dihedral pdb=" CA SER P 56 " pdb=" C SER P 56 " pdb=" N CYS P 57 " pdb=" CA CYS P 57 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA SER L 56 " pdb=" C SER L 56 " pdb=" N CYS L 57 " pdb=" CA CYS L 57 " ideal model delta harmonic sigma weight residual -180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA SER S 56 " pdb=" C SER S 56 " pdb=" N CYS S 57 " pdb=" CA CYS S 57 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2361 0.066 - 0.131: 379 0.131 - 0.197: 0 0.197 - 0.263: 0 0.263 - 0.329: 20 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CG LEU H 95 " pdb=" CB LEU H 95 " pdb=" CD1 LEU H 95 " pdb=" CD2 LEU H 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CG LEU O 95 " pdb=" CB LEU O 95 " pdb=" CD1 LEU O 95 " pdb=" CD2 LEU O 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CG LEU S 95 " pdb=" CB LEU S 95 " pdb=" CD1 LEU S 95 " pdb=" CD2 LEU S 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 2757 not shown) Planarity restraints: 3040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN P 75 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO P 76 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO P 76 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 76 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 75 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.55e+00 pdb=" N PRO D 76 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 76 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 76 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Q 75 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO Q 76 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO Q 76 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO Q 76 " -0.022 5.00e-02 4.00e+02 ... (remaining 3037 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 371 2.68 - 3.23: 20161 3.23 - 3.79: 27416 3.79 - 4.34: 39569 4.34 - 4.90: 59522 Nonbonded interactions: 147039 Sorted by model distance: nonbonded pdb=" OD2 ASP D 70 " pdb=" NH1 ARG G 49 " model vdw 2.121 3.120 nonbonded pdb=" OE2 GLU F 54 " pdb=" NH2 ARG J 36 " model vdw 2.172 3.120 nonbonded pdb=" OE2 GLU H 54 " pdb=" NH2 ARG L 36 " model vdw 2.182 3.120 nonbonded pdb=" OE2 GLU D 54 " pdb=" NH2 ARG H 36 " model vdw 2.238 3.120 nonbonded pdb=" OE2 GLU C 54 " pdb=" NH2 ARG G 36 " model vdw 2.256 3.120 ... (remaining 147034 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.720 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 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 : 0.005 0.025 17780 Z= 0.258 Angle : 0.903 6.478 23760 Z= 0.557 Chirality : 0.052 0.329 2760 Planarity : 0.004 0.040 3040 Dihedral : 16.557 89.799 7260 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 2080 helix: -0.15 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 62 TYR 0.003 0.001 TYR A 27 PHE 0.013 0.004 PHE M 94 HIS 0.003 0.001 HIS L 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.26 (17780) covalent geometry : angle 0.90304 / 0.56 (23760) hydrogen bonds : bond 0.14195 / 9.41 ( 1000) hydrogen bonds : angle 6.85141 / 4.87 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8421 (ptt90) cc_final: 0.7985 (ttt180) REVERT: C 63 LYS cc_start: 0.8826 (tttt) cc_final: 0.8505 (tttm) REVERT: C 67 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7312 (tptt) REVERT: C 69 LEU cc_start: 0.9143 (mp) cc_final: 0.8811 (mt) REVERT: C 71 TYR cc_start: 0.8033 (m-80) cc_final: 0.7531 (m-80) REVERT: C 75 ASN cc_start: 0.6538 (t0) cc_final: 0.5389 (t0) REVERT: C 114 LEU cc_start: 0.7186 (mm) cc_final: 0.6935 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1064 time to fit residues: 6.2212 Evaluate side-chains 34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.0570 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133215 restraints weight = 2344.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136747 restraints weight = 1597.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139372 restraints weight = 1149.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141379 restraints weight = 856.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142873 restraints weight = 652.328| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17780 Z= 0.177 Angle : 0.827 8.189 23760 Z= 0.416 Chirality : 0.047 0.152 2760 Planarity : 0.007 0.050 3040 Dihedral : 7.704 46.000 2340 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.00 % Allowed : 11.00 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 2080 helix: -0.14 (0.14), residues: 1620 sheet: None (None), residues: 0 loop : -0.71 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 88 TYR 0.006 0.002 TYR R 71 PHE 0.018 0.004 PHE L 94 HIS 0.001 0.000 HIS L 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (17780) covalent geometry : angle 0.82672 / 0.42 (23760) hydrogen bonds : bond 0.05148 / 3.35 ( 1000) hydrogen bonds : angle 5.28180 / 3.73 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: C 12 ASP cc_start: 0.7629 (t0) cc_final: 0.7346 (t70) REVERT: C 33 ILE cc_start: 0.7028 (mm) cc_final: 0.6803 (mm) REVERT: C 36 ARG cc_start: 0.8458 (ptt90) cc_final: 0.7758 (ttt180) REVERT: C 54 GLU cc_start: 0.7201 (pt0) cc_final: 0.6938 (pt0) REVERT: C 67 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7336 (ttmt) REVERT: C 69 LEU cc_start: 0.8881 (mp) cc_final: 0.8581 (mt) REVERT: C 75 ASN cc_start: 0.5605 (t0) cc_final: 0.4712 (t0) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.0961 time to fit residues: 5.0588 Evaluate side-chains 35 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 181 optimal weight: 0.0270 chunk 113 optimal weight: 20.0000 chunk 26 optimal weight: 0.0000 chunk 191 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.148452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129816 restraints weight = 2383.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132901 restraints weight = 1757.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135311 restraints weight = 1357.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137272 restraints weight = 1080.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138907 restraints weight = 880.621| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17780 Z= 0.170 Angle : 0.808 6.404 23760 Z= 0.427 Chirality : 0.050 0.170 2760 Planarity : 0.009 0.080 3040 Dihedral : 7.830 45.951 2340 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.00 % Allowed : 8.00 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 2080 helix: -0.33 (0.14), residues: 1640 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 42 TYR 0.003 0.001 TYR L 27 PHE 0.029 0.005 PHE B 94 HIS 0.004 0.001 HIS S 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (17780) covalent geometry : angle 0.80838 / 0.43 (23760) hydrogen bonds : bond 0.04515 / 2.93 ( 1000) hydrogen bonds : angle 5.14820 / 3.63 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: C 12 ASP cc_start: 0.7582 (t0) cc_final: 0.7370 (t70) REVERT: C 16 VAL cc_start: 0.9276 (m) cc_final: 0.9073 (p) REVERT: C 18 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8362 (ttpt) REVERT: C 69 LEU cc_start: 0.8916 (mp) cc_final: 0.8677 (mt) REVERT: C 75 ASN cc_start: 0.5842 (t0) cc_final: 0.5275 (t0) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0905 time to fit residues: 3.6670 Evaluate side-chains 28 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130583 restraints weight = 2347.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133693 restraints weight = 1706.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136160 restraints weight = 1311.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.137937 restraints weight = 1047.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139599 restraints weight = 865.156| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17780 Z= 0.145 Angle : 0.763 7.109 23760 Z= 0.391 Chirality : 0.047 0.195 2760 Planarity : 0.006 0.047 3040 Dihedral : 7.439 45.405 2340 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 2080 helix: -0.18 (0.14), residues: 1640 sheet: None (None), residues: 0 loop : -1.04 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 42 TYR 0.003 0.001 TYR K 27 PHE 0.022 0.004 PHE T 94 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (17780) covalent geometry : angle 0.76285 / 0.39 (23760) hydrogen bonds : bond 0.04074 / 2.65 ( 1000) hydrogen bonds : angle 5.02766 / 3.53 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: C 12 ASP cc_start: 0.7639 (t0) cc_final: 0.7403 (t0) REVERT: C 75 ASN cc_start: 0.5686 (t0) cc_final: 0.5179 (t0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0769 time to fit residues: 3.1284 Evaluate side-chains 31 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 55 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128838 restraints weight = 2415.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131944 restraints weight = 1817.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134518 restraints weight = 1417.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136918 restraints weight = 1115.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138638 restraints weight = 871.887| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17780 Z= 0.171 Angle : 0.874 8.579 23760 Z= 0.427 Chirality : 0.051 0.200 2760 Planarity : 0.009 0.079 3040 Dihedral : 7.115 44.135 2340 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 2080 helix: -0.22 (0.14), residues: 1640 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 42 TYR 0.004 0.001 TYR N 27 PHE 0.019 0.004 PHE T 94 HIS 0.006 0.001 HIS T 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (17780) covalent geometry : angle 0.87373 / 0.43 (23760) hydrogen bonds : bond 0.03952 / 2.58 ( 1000) hydrogen bonds : angle 5.11056 / 3.57 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.039 Fit side-chains REVERT: C 12 ASP cc_start: 0.7303 (t0) cc_final: 0.6864 (t0) REVERT: C 36 ARG cc_start: 0.8577 (ptt90) cc_final: 0.8040 (ttt-90) REVERT: C 75 ASN cc_start: 0.5642 (t0) cc_final: 0.5241 (t0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0827 time to fit residues: 3.5974 Evaluate side-chains 26 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 131 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125182 restraints weight = 2270.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127998 restraints weight = 1663.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130055 restraints weight = 1295.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131675 restraints weight = 1040.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132928 restraints weight = 866.724| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17780 Z= 0.195 Angle : 0.842 7.811 23760 Z= 0.422 Chirality : 0.050 0.198 2760 Planarity : 0.007 0.048 3040 Dihedral : 7.226 43.028 2340 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 2080 helix: -0.10 (0.14), residues: 1660 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG N 42 TYR 0.002 0.001 TYR J 27 PHE 0.014 0.003 PHE T 94 HIS 0.003 0.001 HIS F 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17780) covalent geometry : angle 0.84242 / 0.42 (23760) hydrogen bonds : bond 0.04301 / 2.80 ( 1000) hydrogen bonds : angle 4.91097 / 3.43 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.024 Fit side-chains REVERT: C 12 ASP cc_start: 0.7312 (t0) cc_final: 0.6845 (t0) REVERT: C 35 GLU cc_start: 0.8587 (pm20) cc_final: 0.8378 (pm20) REVERT: C 36 ARG cc_start: 0.8815 (ptt90) cc_final: 0.8086 (ttt-90) REVERT: C 64 ARG cc_start: 0.6754 (ptp-170) cc_final: 0.6231 (ptp-170) REVERT: C 75 ASN cc_start: 0.6298 (t0) cc_final: 0.5614 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0901 time to fit residues: 3.8114 Evaluate side-chains 23 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 1.9990 chunk 194 optimal weight: 0.0870 chunk 104 optimal weight: 0.7980 chunk 184 optimal weight: 0.0070 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 chunk 142 optimal weight: 0.0040 chunk 21 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 chunk 182 optimal weight: 3.9990 overall best weight: 0.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126538 restraints weight = 2412.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129327 restraints weight = 1789.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131193 restraints weight = 1408.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132902 restraints weight = 1179.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134214 restraints weight = 1016.391| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17780 Z= 0.174 Angle : 0.903 7.426 23760 Z= 0.466 Chirality : 0.050 0.183 2760 Planarity : 0.005 0.031 3040 Dihedral : 7.822 52.359 2340 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 2080 helix: -0.49 (0.14), residues: 1680 sheet: None (None), residues: 0 loop : -2.22 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG N 62 TYR 0.006 0.001 TYR K 71 PHE 0.008 0.002 PHE S 94 HIS 0.004 0.001 HIS I 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17780) covalent geometry : angle 0.90304 / 0.47 (23760) hydrogen bonds : bond 0.04354 / 2.80 ( 1000) hydrogen bonds : angle 4.90837 / 3.43 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.037 Fit side-chains REVERT: C 36 ARG cc_start: 0.8781 (ptt90) cc_final: 0.8189 (ttt-90) REVERT: C 75 ASN cc_start: 0.5729 (t0) cc_final: 0.5183 (t0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0956 time to fit residues: 3.9339 Evaluate side-chains 27 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 35 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140644 restraints weight = 2021.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.143694 restraints weight = 1349.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145882 restraints weight = 984.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.147410 restraints weight = 759.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.148605 restraints weight = 612.729| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.9183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17780 Z= 0.163 Angle : 0.917 8.276 23760 Z= 0.466 Chirality : 0.050 0.246 2760 Planarity : 0.006 0.061 3040 Dihedral : 7.743 51.431 2340 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 2080 helix: -0.39 (0.14), residues: 1680 sheet: None (None), residues: 0 loop : -0.99 (0.37), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 107 TYR 0.001 0.000 TYR K 27 PHE 0.015 0.004 PHE T 94 HIS 0.003 0.001 HIS Q 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (17780) covalent geometry : angle 0.91669 / 0.47 (23760) hydrogen bonds : bond 0.04025 / 2.60 ( 1000) hydrogen bonds : angle 5.00274 / 3.49 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 17 LYS cc_start: 0.8865 (mmtm) cc_final: 0.8646 (tppt) REVERT: K 24 LEU cc_start: 0.7863 (tp) cc_final: 0.7506 (tp) REVERT: K 47 LEU cc_start: 0.8242 (tp) cc_final: 0.7945 (tp) REVERT: K 51 ASP cc_start: 0.7275 (m-30) cc_final: 0.7049 (m-30) REVERT: K 79 LEU cc_start: 0.8984 (pp) cc_final: 0.8583 (pp) REVERT: K 86 ILE cc_start: 0.7519 (mt) cc_final: 0.7126 (tp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1066 time to fit residues: 5.1380 Evaluate side-chains 35 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 99 optimal weight: 6.9990 chunk 42 optimal weight: 0.0570 chunk 33 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 125 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141433 restraints weight = 1842.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143893 restraints weight = 1202.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.145587 restraints weight = 831.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146957 restraints weight = 595.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147857 restraints weight = 433.195| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 1.0308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17780 Z= 0.196 Angle : 1.084 10.714 23760 Z= 0.541 Chirality : 0.053 0.206 2760 Planarity : 0.006 0.039 3040 Dihedral : 7.780 52.899 2340 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.19), residues: 2080 helix: -0.77 (0.12), residues: 1680 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 87 TYR 0.008 0.001 TYR G 71 PHE 0.041 0.008 PHE B 94 HIS 0.005 0.002 HIS H 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (17780) covalent geometry : angle 1.08442 / 0.54 (23760) hydrogen bonds : bond 0.04213 / 2.72 ( 1000) hydrogen bonds : angle 5.05120 / 3.55 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 ASP cc_start: 0.7104 (m-30) cc_final: 0.6832 (m-30) REVERT: K 64 ARG cc_start: 0.8267 (ptp-170) cc_final: 0.7757 (ptp90) REVERT: K 86 ILE cc_start: 0.7409 (mt) cc_final: 0.6894 (tp) REVERT: K 88 ARG cc_start: 0.6964 (ptp-110) cc_final: 0.6465 (mtt90) REVERT: K 102 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6921 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0893 time to fit residues: 3.7893 Evaluate side-chains 31 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134302 restraints weight = 2017.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137044 restraints weight = 1390.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139008 restraints weight = 1014.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139893 restraints weight = 766.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141297 restraints weight = 637.740| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 1.0098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17780 Z= 0.229 Angle : 1.079 11.733 23760 Z= 0.527 Chirality : 0.055 0.215 2760 Planarity : 0.006 0.038 3040 Dihedral : 8.120 52.755 2340 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 2080 helix: -0.93 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : 0.15 (0.40), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 87 TYR 0.010 0.002 TYR F 27 PHE 0.040 0.008 PHE B 94 HIS 0.003 0.002 HIS H 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (17780) covalent geometry : angle 1.07873 / 0.53 (23760) hydrogen bonds : bond 0.04562 / 2.96 ( 1000) hydrogen bonds : angle 5.17835 / 3.63 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: K 47 LEU cc_start: 0.7981 (tp) cc_final: 0.7735 (tp) REVERT: K 61 SER cc_start: 0.6390 (p) cc_final: 0.5906 (p) REVERT: K 79 LEU cc_start: 0.8328 (mt) cc_final: 0.7936 (tp) REVERT: K 86 ILE cc_start: 0.7549 (mt) cc_final: 0.7163 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0970 time to fit residues: 4.2980 Evaluate side-chains 34 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.0000 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 0.0170 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132858 restraints weight = 2005.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135476 restraints weight = 1386.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137408 restraints weight = 1005.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138645 restraints weight = 755.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139807 restraints weight = 593.521| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 1.0473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17780 Z= 0.209 Angle : 1.096 12.012 23760 Z= 0.543 Chirality : 0.053 0.198 2760 Planarity : 0.005 0.032 3040 Dihedral : 8.021 52.436 2340 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.18), residues: 2080 helix: -1.80 (0.11), residues: 1720 sheet: None (None), residues: 0 loop : 0.48 (0.42), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 62 TYR 0.012 0.003 TYR B 27 PHE 0.039 0.010 PHE B 94 HIS 0.006 0.002 HIS T 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (17780) covalent geometry : angle 1.09649 / 0.54 (23760) hydrogen bonds : bond 0.04048 / 2.60 ( 1000) hydrogen bonds : angle 5.55443 / 3.89 ( 2880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.29 seconds wall clock time: 28 minutes 40.31 seconds (1720.31 seconds total)