Starting phenix.real_space_refine on Sat Feb 17 05:43:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_27095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_27095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_27095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_27095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8czd_27095/02_2024/8czd_27095.pdb" } 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 Residue "C GLU 53": "OE1" <-> "OE2" Residue "Q GLU 53": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.07, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.56 Conformation dependent library (CDL) restraints added in 3.3 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: 1.63 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: 4.75 Time building geometry restraints manager: 8.04 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: 102.62 - 108.36: 374 108.36 - 114.10: 10946 114.10 - 119.84: 4946 119.84 - 125.58: 7414 125.58 - 131.32: 80 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 2.520 nonbonded pdb=" OE2 GLU F 54 " pdb=" NH2 ARG J 36 " model vdw 2.172 2.520 nonbonded pdb=" OE2 GLU H 54 " pdb=" NH2 ARG L 36 " model vdw 2.182 2.520 nonbonded pdb=" OE2 GLU D 54 " pdb=" NH2 ARG H 36 " model vdw 2.238 2.520 nonbonded pdb=" OE2 GLU C 54 " pdb=" NH2 ARG G 36 " model vdw 2.256 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.270 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 46.600 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.850 ------------------------------------------------------------------------------- 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= 0.311 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.113 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: 0.2472 time to fit residues: 16.0005 Evaluate side-chains 36 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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: 0.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 0.3980 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17780 Z= 0.241 Angle : 0.797 5.194 23760 Z= 0.429 Chirality : 0.046 0.129 2760 Planarity : 0.005 0.034 3040 Dihedral : 9.191 68.260 2340 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 28.72 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: -1.47 (0.18), residues: 2080 helix: -0.96 (0.12), residues: 1540 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 37 PHE 0.015 0.003 PHE K 94 TYR 0.002 0.001 TYR T 71 ARG 0.003 0.001 ARG R 107 *********************** 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 45 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7171 (m-30) cc_final: 0.6850 (m-30) REVERT: A 17 LYS cc_start: 0.7983 (mttp) cc_final: 0.7721 (mttt) REVERT: A 24 LEU cc_start: 0.8773 (mp) cc_final: 0.8503 (mp) REVERT: A 25 ARG cc_start: 0.7468 (ttt180) cc_final: 0.6686 (ppt170) REVERT: A 32 ILE cc_start: 0.7968 (mm) cc_final: 0.7421 (mm) REVERT: A 63 LYS cc_start: 0.7643 (mtmt) cc_final: 0.6673 (tptt) REVERT: A 92 GLN cc_start: 0.5762 (pt0) cc_final: 0.5549 (tp-100) REVERT: A 95 LEU cc_start: 0.8018 (mt) cc_final: 0.7797 (mt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2623 time to fit residues: 12.3414 Evaluate side-chains 31 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17780 Z= 0.282 Angle : 0.812 6.362 23760 Z= 0.428 Chirality : 0.046 0.146 2760 Planarity : 0.004 0.018 3040 Dihedral : 9.046 66.960 2340 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -1.86 (0.17), residues: 2080 helix: -1.20 (0.12), residues: 1580 sheet: None (None), residues: 0 loop : -0.62 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 37 PHE 0.010 0.002 PHE J 94 TYR 0.003 0.001 TYR C 27 ARG 0.003 0.001 ARG H 87 *********************** 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 42 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7217 (m-30) cc_final: 0.6894 (m-30) REVERT: A 17 LYS cc_start: 0.7496 (mttp) cc_final: 0.7149 (tptp) REVERT: A 25 ARG cc_start: 0.7891 (ttt180) cc_final: 0.6825 (ptt90) REVERT: A 32 ILE cc_start: 0.8196 (mm) cc_final: 0.7717 (mm) REVERT: A 63 LYS cc_start: 0.7794 (mtmt) cc_final: 0.6967 (tptt) REVERT: A 75 ASN cc_start: 0.7550 (t0) cc_final: 0.7150 (t0) REVERT: A 82 LEU cc_start: 0.8859 (mm) cc_final: 0.8300 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2897 time to fit residues: 12.6611 Evaluate side-chains 32 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 0.0670 chunk 193 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 overall best weight: 1.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.7233 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= 0.196 Angle : 0.733 5.764 23760 Z= 0.380 Chirality : 0.045 0.164 2760 Planarity : 0.003 0.016 3040 Dihedral : 8.756 63.818 2340 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -1.30 (0.18), residues: 2080 helix: -0.79 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : -0.44 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 37 PHE 0.005 0.002 PHE Q 38 TYR 0.007 0.001 TYR E 27 ARG 0.003 0.001 ARG B 87 *********************** 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 34 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7156 (m-30) cc_final: 0.6883 (m-30) REVERT: A 17 LYS cc_start: 0.7274 (mttp) cc_final: 0.6883 (tptp) REVERT: A 23 ASN cc_start: 0.8989 (t0) cc_final: 0.8706 (t0) REVERT: A 25 ARG cc_start: 0.7849 (ttt180) cc_final: 0.6739 (ptt90) REVERT: A 63 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7048 (tptt) REVERT: A 67 LYS cc_start: 0.7437 (ttmm) cc_final: 0.7212 (ttmm) REVERT: A 75 ASN cc_start: 0.7257 (t0) cc_final: 0.6937 (t0) REVERT: A 109 ILE cc_start: 0.8764 (tp) cc_final: 0.8555 (tp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.3046 time to fit residues: 10.8081 Evaluate side-chains 29 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 0.0010 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 0.0470 chunk 173 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.3088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.7462 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= 0.172 Angle : 0.766 7.550 23760 Z= 0.390 Chirality : 0.046 0.189 2760 Planarity : 0.003 0.013 3040 Dihedral : 8.442 63.090 2340 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.20), residues: 2080 helix: -0.74 (0.13), residues: 1560 sheet: None (None), residues: 0 loop : 0.52 (0.35), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 37 PHE 0.005 0.002 PHE C 94 TYR 0.003 0.001 TYR M 27 ARG 0.003 0.001 ARG G 87 *********************** 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 39 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7066 (m-30) cc_final: 0.6855 (m-30) REVERT: A 17 LYS cc_start: 0.7294 (mttp) cc_final: 0.6799 (tptp) REVERT: A 23 ASN cc_start: 0.9075 (t0) cc_final: 0.8790 (t0) REVERT: A 25 ARG cc_start: 0.7878 (ttt180) cc_final: 0.6888 (ptt90) REVERT: A 63 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7170 (tptt) REVERT: A 67 LYS cc_start: 0.7435 (ttmm) cc_final: 0.7184 (ttmm) REVERT: A 71 TYR cc_start: 0.8485 (m-10) cc_final: 0.8084 (m-10) REVERT: A 73 GLN cc_start: 0.7787 (tt0) cc_final: 0.6884 (tt0) REVERT: A 75 ASN cc_start: 0.7612 (t0) cc_final: 0.6956 (t0) REVERT: A 81 THR cc_start: 0.8561 (m) cc_final: 0.8243 (m) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2675 time to fit residues: 10.9062 Evaluate side-chains 32 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.0370 chunk 174 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 0.3980 chunk 193 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17780 Z= 0.201 Angle : 0.745 7.394 23760 Z= 0.384 Chirality : 0.046 0.219 2760 Planarity : 0.004 0.013 3040 Dihedral : 8.597 62.873 2340 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % 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: -0.37 (0.21), residues: 2080 helix: -0.42 (0.14), residues: 1480 sheet: None (None), residues: 0 loop : 0.78 (0.36), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS R 40 PHE 0.005 0.002 PHE I 94 TYR 0.003 0.001 TYR M 27 ARG 0.004 0.001 ARG B 88 *********************** 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 56 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7830 (ttt-90) REVERT: C 52 THR cc_start: 0.9159 (p) cc_final: 0.8928 (p) REVERT: C 55 ILE cc_start: 0.8348 (mm) cc_final: 0.8094 (mm) REVERT: C 67 LYS cc_start: 0.7362 (ttmm) cc_final: 0.6806 (tttt) REVERT: C 71 TYR cc_start: 0.8388 (m-10) cc_final: 0.8144 (m-80) REVERT: C 79 LEU cc_start: 0.8725 (pt) cc_final: 0.8269 (pp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2738 time to fit residues: 15.9799 Evaluate side-chains 31 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 120 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.9187 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= 0.254 Angle : 0.871 7.408 23760 Z= 0.458 Chirality : 0.048 0.221 2760 Planarity : 0.008 0.075 3040 Dihedral : 8.292 51.814 2340 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -1.51 (0.19), residues: 2080 helix: -1.11 (0.13), residues: 1640 sheet: None (None), residues: 0 loop : 0.33 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 40 PHE 0.007 0.003 PHE L 38 TYR 0.005 0.001 TYR D 71 ARG 0.007 0.001 ARG R 107 *********************** 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 46 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: C 12 ASP cc_start: 0.7405 (t0) cc_final: 0.6454 (t0) REVERT: C 30 GLU cc_start: 0.7718 (mt-10) cc_final: 0.5705 (tp30) REVERT: C 36 ARG cc_start: 0.8396 (ptm160) cc_final: 0.8079 (tmt170) REVERT: C 52 THR cc_start: 0.9101 (p) cc_final: 0.8878 (p) REVERT: C 54 GLU cc_start: 0.6404 (pt0) cc_final: 0.4422 (tp30) REVERT: C 67 LYS cc_start: 0.7206 (ttmm) cc_final: 0.6858 (tptt) REVERT: C 79 LEU cc_start: 0.8609 (pt) cc_final: 0.8209 (pp) REVERT: C 107 ARG cc_start: 0.8914 (mtp-110) cc_final: 0.8211 (tpt170) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2145 time to fit residues: 10.4120 Evaluate side-chains 31 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.0070 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.9482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17780 Z= 0.246 Angle : 0.900 7.563 23760 Z= 0.446 Chirality : 0.049 0.232 2760 Planarity : 0.007 0.066 3040 Dihedral : 8.390 53.484 2340 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -1.10 (0.13), residues: 1620 sheet: None (None), residues: 0 loop : 1.25 (0.40), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 40 PHE 0.006 0.003 PHE A 94 TYR 0.009 0.001 TYR S 27 ARG 0.006 0.001 ARG D 107 *********************** 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 43 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: C 12 ASP cc_start: 0.7407 (t0) cc_final: 0.6666 (t0) REVERT: C 36 ARG cc_start: 0.8356 (ptm160) cc_final: 0.7830 (ttt-90) REVERT: C 67 LYS cc_start: 0.7359 (ttmm) cc_final: 0.7008 (tptt) REVERT: C 98 LYS cc_start: 0.7384 (mtpp) cc_final: 0.6673 (mmmt) REVERT: C 107 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8072 (tpt170) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2430 time to fit residues: 10.9810 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 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 184 optimal weight: 0.9980 chunk 168 optimal weight: 0.0170 chunk 179 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 162 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 0.0980 chunk 189 optimal weight: 6.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 1.0526 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= 0.269 Angle : 0.934 8.114 23760 Z= 0.476 Chirality : 0.052 0.241 2760 Planarity : 0.007 0.058 3040 Dihedral : 8.278 52.576 2340 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 28.63 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: -1.42 (0.20), residues: 2080 helix: -1.26 (0.12), residues: 1580 sheet: None (None), residues: 0 loop : 0.98 (0.39), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS O 37 PHE 0.007 0.003 PHE L 38 TYR 0.004 0.001 TYR M 27 ARG 0.007 0.001 ARG S 88 *********************** 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 41 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8553 (ptm160) cc_final: 0.7906 (ttt-90) REVERT: C 67 LYS cc_start: 0.7239 (ttmm) cc_final: 0.6899 (tttt) REVERT: C 107 ARG cc_start: 0.8863 (mtp-110) cc_final: 0.8147 (tpm170) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2393 time to fit residues: 10.3232 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 183 optimal weight: 0.0970 chunk 158 optimal weight: 0.0470 chunk 16 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 1.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17780 Z= 0.228 Angle : 0.912 7.595 23760 Z= 0.463 Chirality : 0.049 0.221 2760 Planarity : 0.005 0.024 3040 Dihedral : 8.220 52.211 2340 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 29.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.00 % Allowed : 1.00 % Favored : 98.00 % 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: -2.24 (0.18), residues: 2080 helix: -1.46 (0.12), residues: 1700 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 37 PHE 0.005 0.002 PHE G 38 TYR 0.008 0.002 TYR S 27 ARG 0.005 0.001 ARG R 62 ********************** 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 36 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.116 Fit side-chains REVERT: C 36 ARG cc_start: 0.8472 (ptm160) cc_final: 0.7828 (ttt-90) REVERT: C 67 LYS cc_start: 0.7480 (ttmm) cc_final: 0.7167 (tttt) REVERT: C 106 LEU cc_start: 0.7556 (tp) cc_final: 0.7298 (tp) REVERT: C 107 ARG cc_start: 0.8839 (mtp-110) cc_final: 0.8132 (tpm170) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.2269 time to fit residues: 8.6498 Evaluate side-chains 26 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 44 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 139 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135954 restraints weight = 2270.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139345 restraints weight = 1513.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141677 restraints weight = 1083.497| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 1.0890 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= 0.209 Angle : 0.854 6.719 23760 Z= 0.439 Chirality : 0.048 0.195 2760 Planarity : 0.004 0.026 3040 Dihedral : 8.069 51.691 2340 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 30.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.00 % Allowed : 1.00 % Favored : 98.00 % 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: -1.99 (0.19), residues: 2080 helix: -1.34 (0.13), residues: 1700 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 37 PHE 0.005 0.001 PHE A 94 TYR 0.006 0.001 TYR P 27 ARG 0.005 0.001 ARG R 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.66 seconds wall clock time: 51 minutes 58.72 seconds (3118.72 seconds total)