Starting phenix.real_space_refine on Sun Jun 15 10:16:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czd_27095/06_2025/8czd_27095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czd_27095/06_2025/8czd_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_27095/06_2025/8czd_27095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czd_27095/06_2025/8czd_27095.map" model { file = "/net/cci-nas-00/data/ceres_data/8czd_27095/06_2025/8czd_27095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czd_27095/06_2025/8czd_27095.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.76, per 1000 atoms: 0.55 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: 4.55 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.82 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: 4.69 Time building geometry restraints manager: 5.32 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 37.970 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 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 : 23.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (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 HIS 0.003 0.001 HIS L 37 PHE 0.013 0.004 PHE M 94 TYR 0.003 0.001 TYR A 27 ARG 0.005 0.001 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.14195 ( 1000) hydrogen bonds : angle 6.85141 ( 2880) covalent geometry : bond 0.00483 (17780) covalent geometry : angle 0.90304 (23760) *********************** 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 62 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7201 (m-30) cc_final: 0.6976 (m-30) REVERT: A 17 LYS cc_start: 0.8246 (mttp) cc_final: 0.7930 (mttt) REVERT: A 23 ASN cc_start: 0.8753 (m-40) cc_final: 0.8453 (m-40) REVERT: A 25 ARG cc_start: 0.7621 (ttt180) cc_final: 0.6815 (ppt170) REVERT: A 32 ILE cc_start: 0.8413 (mm) cc_final: 0.7997 (mm) REVERT: A 51 ASP cc_start: 0.8607 (m-30) cc_final: 0.8114 (m-30) REVERT: A 75 ASN cc_start: 0.7895 (t0) cc_final: 0.7566 (t0) REVERT: A 105 LYS cc_start: 0.7208 (mmmt) cc_final: 0.6690 (mmmt) REVERT: A 106 LEU cc_start: 0.8073 (tp) cc_final: 0.7696 (tp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2505 time to fit residues: 16.1961 Evaluate side-chains 36 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 0.0060 chunk 51 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 181 optimal weight: 9.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.138855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119359 restraints weight = 2149.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122226 restraints weight = 1511.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124239 restraints weight = 1157.717| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 17780 Z= 0.178 Angle : 0.823 5.230 23760 Z= 0.445 Chirality : 0.047 0.137 2760 Planarity : 0.005 0.034 3040 Dihedral : 9.221 68.592 2340 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2080 helix: -1.00 (0.12), residues: 1540 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 37 PHE 0.017 0.004 PHE K 94 TYR 0.003 0.001 TYR J 71 ARG 0.003 0.001 ARG G 107 Details of bonding type rmsd hydrogen bonds : bond 0.05563 ( 1000) hydrogen bonds : angle 5.68040 ( 2880) covalent geometry : bond 0.00370 (17780) covalent geometry : angle 0.82289 (23760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 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 : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7197 (m-30) cc_final: 0.6847 (m-30) REVERT: A 17 LYS cc_start: 0.8054 (mttp) cc_final: 0.7776 (mttt) REVERT: A 24 LEU cc_start: 0.8820 (mp) cc_final: 0.8486 (mp) REVERT: A 25 ARG cc_start: 0.7488 (ttt180) cc_final: 0.6679 (ppt170) REVERT: A 27 TYR cc_start: 0.7487 (m-80) cc_final: 0.7268 (m-80) REVERT: A 32 ILE cc_start: 0.8059 (mm) cc_final: 0.7798 (mm) REVERT: A 63 LYS cc_start: 0.7626 (mtmt) cc_final: 0.6779 (tptt) REVERT: A 95 LEU cc_start: 0.7992 (mt) cc_final: 0.7770 (mt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2548 time to fit residues: 12.2338 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 197 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.115315 restraints weight = 2271.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118809 restraints weight = 1578.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121205 restraints weight = 1182.338| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.6937 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= 0.158 Angle : 0.825 6.739 23760 Z= 0.426 Chirality : 0.046 0.156 2760 Planarity : 0.004 0.022 3040 Dihedral : 8.883 64.697 2340 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.19), residues: 2080 helix: -1.00 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 37 PHE 0.002 0.001 PHE F 94 TYR 0.002 0.000 TYR L 27 ARG 0.006 0.001 ARG R 87 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 1000) hydrogen bonds : angle 5.08896 ( 2880) covalent geometry : bond 0.00351 (17780) covalent geometry : angle 0.82457 (23760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.106 Fit side-chains REVERT: A 12 ASP cc_start: 0.7283 (m-30) cc_final: 0.6929 (m-30) REVERT: A 25 ARG cc_start: 0.7678 (ttt180) cc_final: 0.6769 (ptt90) REVERT: A 32 ILE cc_start: 0.7855 (mm) cc_final: 0.7346 (mm) REVERT: A 63 LYS cc_start: 0.7655 (mtmt) cc_final: 0.6813 (tptt) REVERT: A 67 LYS cc_start: 0.7497 (ttmm) cc_final: 0.7246 (ttmm) REVERT: A 81 THR cc_start: 0.8489 (m) cc_final: 0.8141 (m) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2475 time to fit residues: 9.0962 Evaluate side-chains 30 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 55 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 58 optimal weight: 0.0770 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115002 restraints weight = 2345.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117864 restraints weight = 1582.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120020 restraints weight = 1173.802| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17780 Z= 0.211 Angle : 0.797 5.283 23760 Z= 0.429 Chirality : 0.045 0.126 2760 Planarity : 0.004 0.019 3040 Dihedral : 9.017 66.653 2340 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.19), residues: 2080 helix: -1.00 (0.12), residues: 1540 sheet: None (None), residues: 0 loop : 1.04 (0.36), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 40 PHE 0.012 0.002 PHE T 94 TYR 0.011 0.002 TYR E 27 ARG 0.003 0.001 ARG S 88 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1000) hydrogen bonds : angle 4.91663 ( 2880) covalent geometry : bond 0.00472 (17780) covalent geometry : angle 0.79729 (23760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 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 : 0.122 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7249 (m-30) cc_final: 0.6846 (m-30) REVERT: A 17 LYS cc_start: 0.7624 (mtmm) cc_final: 0.6743 (tmtt) REVERT: A 21 LEU cc_start: 0.8676 (pp) cc_final: 0.8349 (pp) REVERT: A 25 ARG cc_start: 0.7735 (ttt180) cc_final: 0.6754 (ptt90) REVERT: A 32 ILE cc_start: 0.8171 (mm) cc_final: 0.7873 (mm) REVERT: A 51 ASP cc_start: 0.8154 (m-30) cc_final: 0.7951 (m-30) REVERT: A 63 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7056 (tptt) REVERT: A 75 ASN cc_start: 0.7508 (t0) cc_final: 0.7230 (t0) REVERT: A 109 ILE cc_start: 0.8807 (tp) cc_final: 0.8567 (tp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.3095 time to fit residues: 12.9138 Evaluate side-chains 30 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 6 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.121570 restraints weight = 2257.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124326 restraints weight = 1512.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126625 restraints weight = 1104.487| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17780 Z= 0.158 Angle : 0.809 7.587 23760 Z= 0.424 Chirality : 0.050 0.212 2760 Planarity : 0.004 0.019 3040 Dihedral : 8.563 64.022 2340 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 2080 helix: -1.22 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : 1.37 (0.42), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 40 PHE 0.007 0.002 PHE J 94 TYR 0.006 0.001 TYR C 27 ARG 0.006 0.001 ARG J 87 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1000) hydrogen bonds : angle 5.07082 ( 2880) covalent geometry : bond 0.00347 (17780) covalent geometry : angle 0.80860 (23760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7025 (m-30) cc_final: 0.6792 (m-30) REVERT: A 17 LYS cc_start: 0.7538 (mtmm) cc_final: 0.6827 (tmtt) REVERT: A 21 LEU cc_start: 0.8842 (pp) cc_final: 0.8610 (pp) REVERT: A 25 ARG cc_start: 0.7736 (ttt180) cc_final: 0.6869 (ptt90) REVERT: A 32 ILE cc_start: 0.7940 (mm) cc_final: 0.7719 (mm) REVERT: A 63 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7015 (tptt) REVERT: A 67 LYS cc_start: 0.7295 (ttmm) cc_final: 0.6964 (ttmm) REVERT: A 73 GLN cc_start: 0.7376 (tt0) cc_final: 0.6842 (tt0) REVERT: A 75 ASN cc_start: 0.7846 (t0) cc_final: 0.7430 (t0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2579 time to fit residues: 9.4771 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 : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.122721 restraints weight = 2300.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125889 restraints weight = 1507.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128420 restraints weight = 1085.555| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.8708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17780 Z= 0.143 Angle : 0.805 6.301 23760 Z= 0.415 Chirality : 0.049 0.187 2760 Planarity : 0.005 0.028 3040 Dihedral : 8.453 62.895 2340 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 21.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 2080 helix: -1.35 (0.12), residues: 1620 sheet: None (None), residues: 0 loop : 0.44 (0.38), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 37 PHE 0.006 0.002 PHE J 94 TYR 0.005 0.001 TYR R 27 ARG 0.004 0.001 ARG R 87 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1000) hydrogen bonds : angle 4.96942 ( 2880) covalent geometry : bond 0.00318 (17780) covalent geometry : angle 0.80466 (23760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 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 : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6820 (m-30) cc_final: 0.6596 (m-30) REVERT: A 17 LYS cc_start: 0.7403 (mtmm) cc_final: 0.6590 (tptp) REVERT: A 25 ARG cc_start: 0.7639 (ttt180) cc_final: 0.6891 (ptt180) REVERT: A 32 ILE cc_start: 0.8006 (mm) cc_final: 0.7805 (mm) REVERT: A 50 GLU cc_start: 0.6316 (pp20) cc_final: 0.5867 (pp20) REVERT: A 63 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7088 (tptt) REVERT: A 67 LYS cc_start: 0.7314 (ttmm) cc_final: 0.7031 (ttmm) REVERT: A 71 TYR cc_start: 0.8392 (m-10) cc_final: 0.7973 (m-10) REVERT: A 73 GLN cc_start: 0.7427 (tt0) cc_final: 0.6954 (tt0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.3288 time to fit residues: 13.3019 Evaluate side-chains 32 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 11.9990 chunk 41 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 138 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 83 optimal weight: 0.0770 chunk 174 optimal weight: 9.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 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 = 0.3878 r_free = 0.3878 target = 0.141237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122782 restraints weight = 2161.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125861 restraints weight = 1437.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128187 restraints weight = 1056.903| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17780 Z= 0.149 Angle : 0.785 5.727 23760 Z= 0.409 Chirality : 0.047 0.174 2760 Planarity : 0.010 0.111 3040 Dihedral : 8.381 61.997 2340 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 2080 helix: -0.91 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : 0.03 (0.35), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS R 40 PHE 0.005 0.002 PHE C 94 TYR 0.006 0.001 TYR I 27 ARG 0.006 0.001 ARG M 49 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1000) hydrogen bonds : angle 4.79876 ( 2880) covalent geometry : bond 0.00327 (17780) covalent geometry : angle 0.78518 (23760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.120 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7074 (m-30) cc_final: 0.6684 (m-30) REVERT: A 25 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7403 (ptt180) REVERT: A 63 LYS cc_start: 0.7877 (mtmt) cc_final: 0.7135 (tptt) REVERT: A 67 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7105 (ttmm) REVERT: A 71 TYR cc_start: 0.8400 (m-10) cc_final: 0.7905 (m-10) REVERT: A 73 GLN cc_start: 0.7356 (tt0) cc_final: 0.6999 (tt0) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2646 time to fit residues: 9.4493 Evaluate side-chains 33 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 197 optimal weight: 0.0010 chunk 144 optimal weight: 0.4980 chunk 163 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122551 restraints weight = 2238.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125967 restraints weight = 1416.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128353 restraints weight = 990.874| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.9705 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= 0.186 Angle : 0.893 8.174 23760 Z= 0.466 Chirality : 0.056 0.236 2760 Planarity : 0.007 0.044 3040 Dihedral : 8.218 61.910 2340 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.19), residues: 2080 helix: -0.87 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.17 (0.32), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 37 PHE 0.008 0.003 PHE N 38 TYR 0.003 0.001 TYR G 27 ARG 0.003 0.001 ARG B 88 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1000) hydrogen bonds : angle 5.09069 ( 2880) covalent geometry : bond 0.00410 (17780) covalent geometry : angle 0.89292 (23760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.099 Fit side-chains REVERT: A 12 ASP cc_start: 0.7388 (m-30) cc_final: 0.6949 (m-30) REVERT: A 46 ILE cc_start: 0.5588 (tt) cc_final: 0.5380 (tt) REVERT: A 63 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7070 (tptt) REVERT: A 67 LYS cc_start: 0.7502 (ttmm) cc_final: 0.6998 (ttpt) REVERT: A 73 GLN cc_start: 0.7467 (tt0) cc_final: 0.7058 (tt0) REVERT: A 75 ASN cc_start: 0.8354 (t0) cc_final: 0.7880 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2926 time to fit residues: 11.2634 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 47 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 195 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122257 restraints weight = 2348.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125688 restraints weight = 1555.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128422 restraints weight = 1111.140| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 1.0144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17780 Z= 0.184 Angle : 0.978 7.972 23760 Z= 0.503 Chirality : 0.052 0.200 2760 Planarity : 0.005 0.032 3040 Dihedral : 8.526 62.835 2340 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 23.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 2080 helix: -0.88 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 40 PHE 0.007 0.003 PHE T 94 TYR 0.006 0.001 TYR L 27 ARG 0.025 0.002 ARG R 25 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1000) hydrogen bonds : angle 4.92096 ( 2880) covalent geometry : bond 0.00427 (17780) covalent geometry : angle 0.97815 (23760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.112 Fit side-chains REVERT: A 12 ASP cc_start: 0.7506 (m-30) cc_final: 0.7123 (m-30) REVERT: A 49 ARG cc_start: 0.7406 (tmm-80) cc_final: 0.7133 (tmt170) REVERT: A 50 GLU cc_start: 0.6203 (pp20) cc_final: 0.5717 (pp20) REVERT: A 63 LYS cc_start: 0.7910 (mtmt) cc_final: 0.6883 (tptt) REVERT: A 64 ARG cc_start: 0.7589 (ptt180) cc_final: 0.6660 (ptp90) REVERT: A 67 LYS cc_start: 0.7632 (ttmm) cc_final: 0.7026 (ttpt) REVERT: A 71 TYR cc_start: 0.8437 (m-10) cc_final: 0.8044 (m-10) REVERT: A 75 ASN cc_start: 0.8416 (t0) cc_final: 0.8133 (t0) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2999 time to fit residues: 10.3723 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 : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.143110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125538 restraints weight = 2338.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130102 restraints weight = 1548.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.133175 restraints weight = 1062.577| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 1.0311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17780 Z= 0.200 Angle : 1.022 12.424 23760 Z= 0.514 Chirality : 0.052 0.206 2760 Planarity : 0.013 0.139 3040 Dihedral : 8.696 61.963 2340 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 2080 helix: -0.69 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -1.40 (0.32), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 37 PHE 0.004 0.002 PHE F 94 TYR 0.004 0.001 TYR G 27 ARG 0.005 0.001 ARG I 42 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 1000) hydrogen bonds : angle 5.05519 ( 2880) covalent geometry : bond 0.00473 (17780) covalent geometry : angle 1.02230 (23760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.120 Fit side-chains REVERT: A 12 ASP cc_start: 0.7253 (m-30) cc_final: 0.6903 (m-30) REVERT: A 24 LEU cc_start: 0.8959 (pp) cc_final: 0.8722 (pp) REVERT: A 49 ARG cc_start: 0.7161 (tmm-80) cc_final: 0.6509 (tpp80) REVERT: A 50 GLU cc_start: 0.6181 (pp20) cc_final: 0.5611 (pp20) REVERT: A 63 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7196 (tptt) REVERT: A 67 LYS cc_start: 0.7715 (ttmm) cc_final: 0.7315 (ttpt) REVERT: A 71 TYR cc_start: 0.8381 (m-10) cc_final: 0.7992 (m-10) REVERT: A 75 ASN cc_start: 0.8564 (t0) cc_final: 0.8337 (t0) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2334 time to fit residues: 7.9048 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 : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 75 optimal weight: 0.0770 chunk 111 optimal weight: 0.0020 chunk 171 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 191 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.6750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.145406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129475 restraints weight = 2504.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133070 restraints weight = 1644.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.135537 restraints weight = 1150.558| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 1.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17780 Z= 0.170 Angle : 0.912 7.046 23760 Z= 0.474 Chirality : 0.053 0.240 2760 Planarity : 0.008 0.061 3040 Dihedral : 8.374 61.608 2340 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 2080 helix: -0.78 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : -1.27 (0.32), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 37 PHE 0.004 0.001 PHE F 94 TYR 0.006 0.001 TYR M 27 ARG 0.009 0.001 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 1000) hydrogen bonds : angle 5.41648 ( 2880) covalent geometry : bond 0.00375 (17780) covalent geometry : angle 0.91176 (23760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.29 seconds wall clock time: 61 minutes 38.12 seconds (3698.12 seconds total)