Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 20:59:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scn_10143/04_2023/6scn_10143.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 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 129 5.16 5 C 37032 2.51 5 N 11190 2.21 5 O 12231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ARG 228": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ASP 381": "OD1" <-> "OD2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ASP 229": "OD1" <-> "OD2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ASP 424": "OD1" <-> "OD2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G ASP 229": "OD1" <-> "OD2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ASP 381": "OD1" <-> "OD2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ASP 424": "OD1" <-> "OD2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H ARG 154": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ASP 381": "OD1" <-> "OD2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I ASP 187": "OD1" <-> "OD2" Residue "I ASP 229": "OD1" <-> "OD2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I ASP 381": "OD1" <-> "OD2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ASP 407": "OD1" <-> "OD2" Residue "J ARG 134": "NH1" <-> "NH2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J ARG 228": "NH1" <-> "NH2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J ASP 271": "OD1" <-> "OD2" Residue "J ASP 381": "OD1" <-> "OD2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "J ASP 407": "OD1" <-> "OD2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ASP 424": "OD1" <-> "OD2" Residue "L ARG 134": "NH1" <-> "NH2" Residue "L ARG 154": "NH1" <-> "NH2" Residue "L ARG 228": "NH1" <-> "NH2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 154": "NH1" <-> "NH2" Residue "M ASP 187": "OD1" <-> "OD2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M ASP 229": "OD1" <-> "OD2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M GLU 250": "OE1" <-> "OE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "M ASP 407": "OD1" <-> "OD2" Residue "M ASP 424": "OD1" <-> "OD2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 154": "NH1" <-> "NH2" Residue "N ASP 232": "OD1" <-> "OD2" Residue "N ASP 240": "OD1" <-> "OD2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "N ASP 407": "OD1" <-> "OD2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "P ARG 154": "NH1" <-> "NH2" Residue "P ASP 214": "OD1" <-> "OD2" Residue "P ASP 229": "OD1" <-> "OD2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P ASP 381": "OD1" <-> "OD2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "P ASP 407": "OD1" <-> "OD2" Residue "Q ARG 134": "NH1" <-> "NH2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "Q ASP 187": "OD1" <-> "OD2" Residue "Q ASP 214": "OD1" <-> "OD2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ASP 381": "OD1" <-> "OD2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 154": "NH1" <-> "NH2" Residue "R ARG 228": "NH1" <-> "NH2" Residue "R ASP 229": "OD1" <-> "OD2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R ASP 381": "OD1" <-> "OD2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "S ARG 134": "NH1" <-> "NH2" Residue "S ARG 154": "NH1" <-> "NH2" Residue "S ASP 229": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 383": "OE1" <-> "OE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "T ARG 134": "NH1" <-> "NH2" Residue "T ARG 154": "NH1" <-> "NH2" Residue "T ASP 187": "OD1" <-> "OD2" Residue "T ASP 229": "OD1" <-> "OD2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T ASP 381": "OD1" <-> "OD2" Residue "T GLU 383": "OE1" <-> "OE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "U ARG 134": "NH1" <-> "NH2" Residue "U GLU 139": "OE1" <-> "OE2" Residue "U ARG 154": "NH1" <-> "NH2" Residue "U ARG 228": "NH1" <-> "NH2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V GLU 383": "OE1" <-> "OE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "V ASP 424": "OD1" <-> "OD2" Residue "W ARG 134": "NH1" <-> "NH2" Residue "W ARG 154": "NH1" <-> "NH2" Residue "W ARG 228": "NH1" <-> "NH2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W ASP 381": "OD1" <-> "OD2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 154": "NH1" <-> "NH2" Residue "X ASP 187": "OD1" <-> "OD2" Residue "X ASP 240": "OD1" <-> "OD2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X GLU 250": "OE1" <-> "OE2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "X ASP 424": "OD1" <-> "OD2" Residue "Y ARG 134": "NH1" <-> "NH2" Residue "Y ARG 154": "NH1" <-> "NH2" Residue "Y ASP 214": "OD1" <-> "OD2" Residue "Y ASP 232": "OD1" <-> "OD2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y ASP 381": "OD1" <-> "OD2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Y ASP 407": "OD1" <-> "OD2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "Z ARG 154": "NH1" <-> "NH2" Residue "Z ASP 214": "OD1" <-> "OD2" Residue "Z ARG 228": "NH1" <-> "NH2" Residue "Z ASP 229": "OD1" <-> "OD2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z ASP 381": "OD1" <-> "OD2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "a ARG 134": "NH1" <-> "NH2" Residue "a ARG 154": "NH1" <-> "NH2" Residue "a ASP 187": "OD1" <-> "OD2" Residue "a ASP 214": "OD1" <-> "OD2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a GLU 383": "OE1" <-> "OE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "a ASP 407": "OD1" <-> "OD2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ASP 240": "OD1" <-> "OD2" Residue "b ARG 244": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ASP 407": "OD1" <-> "OD2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "c ARG 154": "NH1" <-> "NH2" Residue "c GLU 188": "OE1" <-> "OE2" Residue "c ASP 214": "OD1" <-> "OD2" Residue "c ARG 228": "NH1" <-> "NH2" Residue "c ARG 244": "NH1" <-> "NH2" Residue "c ASP 381": "OD1" <-> "OD2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "c ASP 424": "OD1" <-> "OD2" Residue "d ARG 134": "NH1" <-> "NH2" Residue "d ARG 154": "NH1" <-> "NH2" Residue "d ARG 244": "NH1" <-> "NH2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "e ARG 134": "NH1" <-> "NH2" Residue "e ARG 154": "NH1" <-> "NH2" Residue "e ARG 244": "NH1" <-> "NH2" Residue "e GLU 383": "OE1" <-> "OE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "e ASP 407": "OD1" <-> "OD2" Residue "f ARG 134": "NH1" <-> "NH2" Residue "f ARG 154": "NH1" <-> "NH2" Residue "f ARG 228": "NH1" <-> "NH2" Residue "f ARG 244": "NH1" <-> "NH2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "f ASP 407": "OD1" <-> "OD2" Residue "g ARG 244": "NH1" <-> "NH2" Residue "g GLU 383": "OE1" <-> "OE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "g ASP 424": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 60582 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "B" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "E" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "G" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "H" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "I" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "J" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "K" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1224 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 2 Chain: "L" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "M" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "N" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "O" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "P" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Q" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "R" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "S" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "T" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "U" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "V" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1224 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 2 Chain: "W" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "X" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Y" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "Z" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "a" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "b" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "c" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "d" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "e" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "f" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1897 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 11, 'TRANS': 235} Chain breaks: 3 Chain: "g" Number of atoms: 1224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1224 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain breaks: 2 Time building chain proxies: 23.07, per 1000 atoms: 0.38 Number of scatterers: 60582 At special positions: 0 Unit cell: (243.312, 242.49, 124.944, 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 129 16.00 O 12231 8.00 N 11190 7.00 C 37032 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: 18.89 Conformation dependent library (CDL) restraints added in 6.8 seconds 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14868 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 0 sheets defined 33.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.711A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.754A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.663A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 146 Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.541A pdb=" N ILE B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.541A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.614A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.790A pdb=" N GLY C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 removed outlier: 3.563A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 221 through 225 removed outlier: 4.192A pdb=" N ASN C 224 " --> pdb=" O THR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.699A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.625A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.632A pdb=" N GLY D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.614A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 232 through 258 removed outlier: 3.651A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.626A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 146 removed outlier: 3.547A pdb=" N GLY E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 removed outlier: 3.878A pdb=" N SER E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL E 194 " --> pdb=" O GLN E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 228 through 258 removed outlier: 4.333A pdb=" N GLN E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.601A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 146 removed outlier: 3.668A pdb=" N GLY F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 removed outlier: 3.565A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'F' and resid 232 through 258 removed outlier: 3.535A pdb=" N SER F 254 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.603A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 146 Processing helix chain 'G' and resid 187 through 200 removed outlier: 3.607A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 232 through 258 removed outlier: 3.716A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 254 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.606A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 146 Processing helix chain 'H' and resid 187 through 200 removed outlier: 3.633A pdb=" N ILE H 191 " --> pdb=" O ASP H 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 232 through 258 removed outlier: 3.639A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 254 " --> pdb=" O GLU H 250 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.630A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 146 removed outlier: 3.539A pdb=" N GLY I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.584A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 229 through 231 No H-bonds generated for 'chain 'I' and resid 229 through 231' Processing helix chain 'I' and resid 232 through 258 removed outlier: 3.547A pdb=" N SER I 254 " --> pdb=" O GLU I 250 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.576A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 146 removed outlier: 3.720A pdb=" N GLY J 138 " --> pdb=" O ARG J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 200 removed outlier: 4.056A pdb=" N VAL J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.616A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.525A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER K 254 " --> pdb=" O GLU K 250 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.619A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 146 Processing helix chain 'L' and resid 187 through 200 removed outlier: 3.773A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.700A pdb=" N LYS L 236 " --> pdb=" O ASP L 232 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.638A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 146 removed outlier: 3.515A pdb=" N GLY M 138 " --> pdb=" O ARG M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 4.202A pdb=" N SER M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL M 194 " --> pdb=" O GLN M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'M' and resid 232 through 258 removed outlier: 3.658A pdb=" N LYS M 236 " --> pdb=" O ASP M 232 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.589A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 146 removed outlier: 3.802A pdb=" N GLY N 138 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR N 146 " --> pdb=" O ARG N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 200 removed outlier: 3.574A pdb=" N SER N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA N 193 " --> pdb=" O GLY N 189 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL N 194 " --> pdb=" O GLN N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'N' and resid 229 through 231 No H-bonds generated for 'chain 'N' and resid 229 through 231' Processing helix chain 'N' and resid 232 through 258 removed outlier: 3.746A pdb=" N LYS N 236 " --> pdb=" O ASP N 232 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.649A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 146 removed outlier: 3.659A pdb=" N GLY O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 200 removed outlier: 3.651A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL O 194 " --> pdb=" O GLN O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'O' and resid 221 through 225 removed outlier: 3.677A pdb=" N ASN O 224 " --> pdb=" O THR O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 258 removed outlier: 3.843A pdb=" N LYS O 236 " --> pdb=" O ASP O 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER O 254 " --> pdb=" O GLU O 250 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.620A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 146 removed outlier: 3.517A pdb=" N GLY P 138 " --> pdb=" O ARG P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 200 removed outlier: 3.500A pdb=" N ILE P 191 " --> pdb=" O ASP P 187 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL P 194 " --> pdb=" O GLN P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'P' and resid 232 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.632A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 146 removed outlier: 3.652A pdb=" N GLY Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 200 removed outlier: 3.530A pdb=" N SER Q 192 " --> pdb=" O GLU Q 188 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Q 193 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL Q 194 " --> pdb=" O GLN Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'Q' and resid 228 through 231 Processing helix chain 'Q' and resid 232 through 258 removed outlier: 3.542A pdb=" N SER Q 254 " --> pdb=" O GLU Q 250 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.593A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 146 removed outlier: 3.512A pdb=" N GLY R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.635A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.720A pdb=" N LYS R 236 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER R 254 " --> pdb=" O GLU R 250 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.602A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 146 removed outlier: 3.621A pdb=" N GLY S 138 " --> pdb=" O ARG S 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR S 146 " --> pdb=" O ARG S 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 187 through 200 removed outlier: 3.593A pdb=" N ILE S 191 " --> pdb=" O ASP S 187 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER S 192 " --> pdb=" O GLU S 188 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA S 193 " --> pdb=" O GLY S 189 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL S 194 " --> pdb=" O GLN S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'S' and resid 232 through 258 removed outlier: 3.784A pdb=" N LYS S 236 " --> pdb=" O ASP S 232 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER S 254 " --> pdb=" O GLU S 250 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.640A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 146 removed outlier: 3.535A pdb=" N GLY T 138 " --> pdb=" O ARG T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 200 removed outlier: 3.569A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'T' and resid 229 through 231 No H-bonds generated for 'chain 'T' and resid 229 through 231' Processing helix chain 'T' and resid 232 through 258 removed outlier: 3.533A pdb=" N SER T 254 " --> pdb=" O GLU T 250 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.610A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 146 removed outlier: 3.753A pdb=" N GLY U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 200 removed outlier: 3.740A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA U 193 " --> pdb=" O GLY U 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.633A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.566A pdb=" N LYS V 236 " --> pdb=" O ASP V 232 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER V 254 " --> pdb=" O GLU V 250 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.645A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 126 through 146 removed outlier: 3.513A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 200 removed outlier: 3.755A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing helix chain 'W' and resid 232 through 258 removed outlier: 3.661A pdb=" N LYS W 236 " --> pdb=" O ASP W 232 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.661A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 126 through 146 removed outlier: 3.546A pdb=" N GLY X 138 " --> pdb=" O ARG X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 200 removed outlier: 4.221A pdb=" N SER X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA X 193 " --> pdb=" O GLY X 189 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL X 194 " --> pdb=" O GLN X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 206 through 208 No H-bonds generated for 'chain 'X' and resid 206 through 208' Processing helix chain 'X' and resid 232 through 258 removed outlier: 3.567A pdb=" N LYS X 236 " --> pdb=" O ASP X 232 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER X 254 " --> pdb=" O GLU X 250 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.618A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.770A pdb=" N GLY Y 138 " --> pdb=" O ARG Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 200 removed outlier: 3.537A pdb=" N SER Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA Y 193 " --> pdb=" O GLY Y 189 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL Y 194 " --> pdb=" O GLN Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 221 through 225 removed outlier: 4.013A pdb=" N ASN Y 224 " --> pdb=" O THR Y 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 231 No H-bonds generated for 'chain 'Y' and resid 229 through 231' Processing helix chain 'Y' and resid 232 through 258 removed outlier: 3.670A pdb=" N LYS Y 236 " --> pdb=" O ASP Y 232 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.632A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 126 through 146 removed outlier: 3.645A pdb=" N GLY Z 138 " --> pdb=" O ARG Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 200 removed outlier: 3.617A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 208 No H-bonds generated for 'chain 'Z' and resid 206 through 208' Processing helix chain 'Z' and resid 232 through 258 removed outlier: 3.648A pdb=" N LYS Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER Z 254 " --> pdb=" O GLU Z 250 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.623A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 146 removed outlier: 3.534A pdb=" N GLY a 138 " --> pdb=" O ARG a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 187 through 200 removed outlier: 3.873A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL a 194 " --> pdb=" O GLN a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 208 No H-bonds generated for 'chain 'a' and resid 206 through 208' Processing helix chain 'a' and resid 232 through 258 removed outlier: 3.508A pdb=" N SER a 254 " --> pdb=" O GLU a 250 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.601A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 146 removed outlier: 3.698A pdb=" N GLY b 138 " --> pdb=" O ARG b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 200 removed outlier: 3.577A pdb=" N ALA b 193 " --> pdb=" O GLY b 189 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL b 194 " --> pdb=" O GLN b 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 208 No H-bonds generated for 'chain 'b' and resid 206 through 208' Processing helix chain 'b' and resid 228 through 231 Processing helix chain 'b' and resid 232 through 258 removed outlier: 3.552A pdb=" N SER b 254 " --> pdb=" O GLU b 250 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.606A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 126 through 146 removed outlier: 3.549A pdb=" N GLY c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 200 removed outlier: 3.604A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 206 through 208 No H-bonds generated for 'chain 'c' and resid 206 through 208' Processing helix chain 'c' and resid 232 through 258 removed outlier: 3.518A pdb=" N LYS c 236 " --> pdb=" O ASP c 232 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER c 254 " --> pdb=" O GLU c 250 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.593A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.559A pdb=" N GLY d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 200 removed outlier: 3.568A pdb=" N ILE d 191 " --> pdb=" O ASP d 187 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 206 through 208 No H-bonds generated for 'chain 'd' and resid 206 through 208' Processing helix chain 'd' and resid 232 through 258 removed outlier: 3.652A pdb=" N LYS d 236 " --> pdb=" O ASP d 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER d 254 " --> pdb=" O GLU d 250 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.633A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 146 removed outlier: 3.545A pdb=" N GLY e 138 " --> pdb=" O ARG e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 200 removed outlier: 3.551A pdb=" N SER e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA e 193 " --> pdb=" O GLY e 189 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL e 194 " --> pdb=" O GLN e 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 229 through 231 No H-bonds generated for 'chain 'e' and resid 229 through 231' Processing helix chain 'e' and resid 232 through 258 removed outlier: 3.531A pdb=" N LYS e 236 " --> pdb=" O ASP e 232 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER e 254 " --> pdb=" O GLU e 250 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.595A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 146 removed outlier: 3.676A pdb=" N GLY f 138 " --> pdb=" O ARG f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 200 removed outlier: 3.742A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA f 193 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL f 194 " --> pdb=" O GLN f 190 " (cutoff:3.500A) Processing helix chain 'f' and resid 206 through 208 No H-bonds generated for 'chain 'f' and resid 206 through 208' Processing helix chain 'f' and resid 232 through 258 removed outlier: 3.507A pdb=" N SER f 254 " --> pdb=" O GLU f 250 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.622A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 removed outlier: 3.581A pdb=" N LYS g 236 " --> pdb=" O ASP g 232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER g 254 " --> pdb=" O GLU g 250 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.626A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) 1706 hydrogen bonds defined for protein. 5100 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: 11.79 Time building geometry restraints manager: 20.59 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: 21518 1.34 - 1.46: 9471 1.46 - 1.58: 30013 1.58 - 1.69: 18 1.69 - 1.81: 258 Bond restraints: 61278 Sorted by residual: bond pdb=" CG PRO L 172 " pdb=" CD PRO L 172 " ideal model delta sigma weight residual 1.503 1.577 -0.074 3.40e-02 8.65e+02 4.80e+00 bond pdb=" CG PRO A 172 " pdb=" CD PRO A 172 " ideal model delta sigma weight residual 1.503 1.575 -0.072 3.40e-02 8.65e+02 4.48e+00 bond pdb=" CG PRO C 172 " pdb=" CD PRO C 172 " ideal model delta sigma weight residual 1.503 1.574 -0.071 3.40e-02 8.65e+02 4.39e+00 bond pdb=" CG PRO E 172 " pdb=" CD PRO E 172 " ideal model delta sigma weight residual 1.503 1.574 -0.071 3.40e-02 8.65e+02 4.36e+00 bond pdb=" CG PRO W 172 " pdb=" CD PRO W 172 " ideal model delta sigma weight residual 1.503 1.573 -0.070 3.40e-02 8.65e+02 4.27e+00 ... (remaining 61273 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.91: 1860 106.91 - 114.02: 36367 114.02 - 121.13: 28261 121.13 - 128.24: 16209 128.24 - 135.36: 238 Bond angle restraints: 82935 Sorted by residual: angle pdb=" N LEU Z 230 " pdb=" CA LEU Z 230 " pdb=" C LEU Z 230 " ideal model delta sigma weight residual 114.56 102.91 11.65 1.27e+00 6.20e-01 8.42e+01 angle pdb=" N LEU G 230 " pdb=" CA LEU G 230 " pdb=" C LEU G 230 " ideal model delta sigma weight residual 114.56 107.55 7.01 1.27e+00 6.20e-01 3.05e+01 angle pdb=" CA LEU N 147 " pdb=" CB LEU N 147 " pdb=" CG LEU N 147 " ideal model delta sigma weight residual 116.30 135.36 -19.06 3.50e+00 8.16e-02 2.96e+01 angle pdb=" CA LEU Z 230 " pdb=" C LEU Z 230 " pdb=" N ASN Z 231 " ideal model delta sigma weight residual 119.26 113.84 5.42 1.14e+00 7.69e-01 2.26e+01 angle pdb=" N ALA a 233 " pdb=" CA ALA a 233 " pdb=" C ALA a 233 " ideal model delta sigma weight residual 112.54 107.27 5.27 1.22e+00 6.72e-01 1.87e+01 ... (remaining 82930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 36282 17.92 - 35.84: 1427 35.84 - 53.76: 280 53.76 - 71.68: 17 71.68 - 89.60: 10 Dihedral angle restraints: 38016 sinusoidal: 15273 harmonic: 22743 Sorted by residual: dihedral pdb=" CA GLY T 227 " pdb=" C GLY T 227 " pdb=" N ARG T 228 " pdb=" CA ARG T 228 " ideal model delta harmonic sigma weight residual -180.00 -148.17 -31.83 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA GLY I 227 " pdb=" C GLY I 227 " pdb=" N ARG I 228 " pdb=" CA ARG I 228 " ideal model delta harmonic sigma weight residual -180.00 -148.87 -31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA GLY L 227 " pdb=" C GLY L 227 " pdb=" N ARG L 228 " pdb=" CA ARG L 228 " ideal model delta harmonic sigma weight residual 180.00 151.38 28.62 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 38013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 7700 0.055 - 0.109: 1785 0.109 - 0.164: 242 0.164 - 0.218: 18 0.218 - 0.273: 5 Chirality restraints: 9750 Sorted by residual: chirality pdb=" CB ILE I 191 " pdb=" CA ILE I 191 " pdb=" CG1 ILE I 191 " pdb=" CG2 ILE I 191 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU N 157 " pdb=" CB LEU N 157 " pdb=" CD1 LEU N 157 " pdb=" CD2 LEU N 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE L 191 " pdb=" CA ILE L 191 " pdb=" CG1 ILE L 191 " pdb=" CG2 ILE L 191 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 9747 not shown) Planarity restraints: 11082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET c 159 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO c 160 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO c 160 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO c 160 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 159 " 0.076 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO G 160 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO G 160 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO G 160 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 159 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO R 160 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO R 160 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 160 " -0.062 5.00e-02 4.00e+02 ... (remaining 11079 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 762 2.61 - 3.18: 53575 3.18 - 3.75: 90696 3.75 - 4.33: 136336 4.33 - 4.90: 218201 Nonbonded interactions: 499570 Sorted by model distance: nonbonded pdb=" OG1 THR H 405 " pdb=" OD1 ASP H 407 " model vdw 2.037 2.440 nonbonded pdb=" O GLN D 222 " pdb=" OG1 THR D 225 " model vdw 2.079 2.440 nonbonded pdb=" OG SER Y 200 " pdb=" OG SER Z 175 " model vdw 2.105 2.440 nonbonded pdb=" OG1 THR c 221 " pdb=" ND2 ASN c 224 " model vdw 2.109 2.520 nonbonded pdb=" OG SER W 199 " pdb=" O LEU W 205 " model vdw 2.113 2.440 ... (remaining 499565 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 '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' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'K' selection = chain 'V' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.060 Extract box with map and model: 20.410 Check model and map are aligned: 0.830 Set scattering table: 0.420 Process input model: 105.380 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.007 0.092 61278 Z= 0.483 Angle : 0.836 19.056 82935 Z= 0.465 Chirality : 0.047 0.273 9750 Planarity : 0.006 0.116 11082 Dihedral : 10.499 89.603 23148 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.79 % Allowed : 4.88 % Favored : 94.33 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.90 (0.09), residues: 7617 helix: -1.65 (0.08), residues: 2351 sheet: -1.23 (0.10), residues: 2862 loop : -2.78 (0.11), residues: 2404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 809 time to evaluate : 6.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 22 residues processed: 861 average time/residue: 0.6196 time to fit residues: 865.9018 Evaluate side-chains 554 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 532 time to evaluate : 5.697 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 22 average time/residue: 0.3940 time to fit residues: 24.5300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 645 optimal weight: 4.9990 chunk 579 optimal weight: 20.0000 chunk 321 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 391 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 599 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 364 optimal weight: 3.9990 chunk 446 optimal weight: 1.9990 chunk 694 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 196 HIS A 365 ASN A 411 GLN A 434 ASN B 125 GLN B 222 GLN B 224 ASN B 231 ASN B 365 ASN B 431 ASN B 434 ASN C 125 GLN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 365 ASN C 434 ASN D 125 GLN D 133 GLN D 365 ASN D 431 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 133 GLN E 209 ASN E 365 ASN E 434 ASN F 224 ASN F 365 ASN F 431 ASN F 434 ASN G 133 GLN ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 ASN G 434 ASN H 125 GLN H 133 GLN H 431 ASN H 434 ASN I 125 GLN I 133 GLN I 231 ASN I 365 ASN I 434 ASN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN J 431 ASN J 434 ASN K 297 GLN K 365 ASN K 431 ASN K 434 ASN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN L 196 HIS ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 365 ASN L 431 ASN L 434 ASN M 125 GLN M 215 GLN M 365 ASN M 431 ASN M 434 ASN N 125 GLN N 222 GLN N 365 ASN N 434 ASN O 125 GLN O 133 GLN O 365 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 125 GLN P 133 GLN P 209 ASN P 365 ASN P 431 ASN P 434 ASN Q 133 GLN Q 224 ASN Q 365 ASN Q 431 ASN Q 434 ASN R 133 GLN R 365 ASN R 431 ASN R 434 ASN S 125 GLN S 133 GLN S 365 ASN S 411 GLN S 434 ASN T 133 GLN T 231 ASN T 365 ASN T 434 ASN U 133 GLN ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 365 ASN U 431 ASN U 434 ASN V 297 GLN V 365 ASN V 434 ASN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 GLN W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 411 GLN W 434 ASN X 125 GLN ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 231 ASN X 365 ASN X 431 ASN X 434 ASN Y 125 GLN Y 434 ASN Z 125 GLN Z 133 GLN Z 365 ASN Z 434 ASN a 125 GLN a 133 GLN a 196 HIS a 209 ASN a 365 ASN a 434 ASN b 133 GLN b 365 ASN b 431 ASN b 434 ASN c 133 GLN ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 365 ASN c 431 ASN c 434 ASN d 125 GLN d 133 GLN d 196 HIS d 365 ASN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN e 133 GLN e 231 ASN e 365 ASN e 431 ASN e 434 ASN ** f 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 365 ASN f 431 ASN f 434 ASN g 365 ASN g 431 ASN g 434 ASN Total number of N/Q/H flips: 141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 61278 Z= 0.371 Angle : 0.635 12.033 82935 Z= 0.320 Chirality : 0.042 0.183 9750 Planarity : 0.005 0.070 11082 Dihedral : 5.062 29.217 8424 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer Outliers : 1.88 % 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: -1.55 (0.10), residues: 7617 helix: 0.45 (0.10), residues: 2340 sheet: -1.09 (0.10), residues: 2920 loop : -2.26 (0.12), residues: 2357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 565 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 52 residues processed: 667 average time/residue: 0.6170 time to fit residues: 682.3071 Evaluate side-chains 554 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 502 time to evaluate : 5.608 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.4944 time to fit residues: 54.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 386 optimal weight: 2.9990 chunk 215 optimal weight: 0.0470 chunk 578 optimal weight: 5.9990 chunk 473 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 695 optimal weight: 2.9990 chunk 751 optimal weight: 2.9990 chunk 619 optimal weight: 5.9990 chunk 690 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 558 optimal weight: 20.0000 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 133 GLN F 431 ASN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN J 431 ASN K 297 GLN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 196 HIS ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 411 GLN R 196 HIS ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 431 ASN V 297 GLN V 411 GLN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 411 GLN b 224 ASN ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 411 GLN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 431 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 61278 Z= 0.190 Angle : 0.557 13.386 82935 Z= 0.271 Chirality : 0.040 0.141 9750 Planarity : 0.003 0.048 11082 Dihedral : 4.585 27.247 8424 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 7617 helix: 1.42 (0.11), residues: 2316 sheet: -0.75 (0.10), residues: 2937 loop : -1.96 (0.12), residues: 2364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 578 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 628 average time/residue: 0.6088 time to fit residues: 636.7912 Evaluate side-chains 526 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 505 time to evaluate : 5.778 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4270 time to fit residues: 24.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 687 optimal weight: 30.0000 chunk 523 optimal weight: 5.9990 chunk 361 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 332 optimal weight: 9.9990 chunk 467 optimal weight: 5.9990 chunk 698 optimal weight: 9.9990 chunk 739 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 661 optimal weight: 40.0000 chunk 199 optimal weight: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN B 133 GLN B 411 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS F 263 HIS G 190 GLN I 263 HIS ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 259 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 HIS Q 263 HIS ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 HIS ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 411 GLN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 231 ASN ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 GLN X 263 HIS Z 431 ASN b 263 HIS ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 411 GLN ** f 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 263 HIS g 263 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.031 61278 Z= 0.393 Angle : 0.608 12.063 82935 Z= 0.303 Chirality : 0.041 0.180 9750 Planarity : 0.003 0.050 11082 Dihedral : 4.654 27.315 8424 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.35 % Rotamer Outliers : 1.16 % 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: -0.64 (0.10), residues: 7617 helix: 1.59 (0.11), residues: 2322 sheet: -0.92 (0.10), residues: 2961 loop : -1.67 (0.12), residues: 2334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 523 time to evaluate : 5.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 41 residues processed: 588 average time/residue: 0.6078 time to fit residues: 594.8234 Evaluate side-chains 543 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 502 time to evaluate : 5.797 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4439 time to fit residues: 41.7736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 615 optimal weight: 20.0000 chunk 419 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 550 optimal weight: 7.9990 chunk 305 optimal weight: 0.3980 chunk 631 optimal weight: 20.0000 chunk 511 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 377 optimal weight: 30.0000 chunk 663 optimal weight: 30.0000 chunk 186 optimal weight: 0.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 HIS K 297 GLN K 365 ASN ** L 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN M 263 HIS N 263 HIS O 411 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN Q 411 GLN R 263 HIS ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 231 ASN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 411 GLN Z 411 GLN Z 431 ASN b 411 GLN ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 61278 Z= 0.266 Angle : 0.561 11.708 82935 Z= 0.275 Chirality : 0.040 0.144 9750 Planarity : 0.003 0.050 11082 Dihedral : 4.475 25.218 8424 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.15 % 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: -0.24 (0.10), residues: 7617 helix: 1.86 (0.11), residues: 2322 sheet: -0.70 (0.10), residues: 3033 loop : -1.38 (0.13), residues: 2262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 518 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 27 residues processed: 585 average time/residue: 0.6019 time to fit residues: 585.5532 Evaluate side-chains 520 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 493 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5001 time to fit residues: 31.3956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 248 optimal weight: 9.9990 chunk 665 optimal weight: 1.9990 chunk 146 optimal weight: 0.0470 chunk 434 optimal weight: 0.2980 chunk 182 optimal weight: 4.9990 chunk 740 optimal weight: 10.0000 chunk 614 optimal weight: 0.0170 chunk 342 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 431 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN I 125 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 277 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 218 HIS ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 411 GLN V 297 GLN V 411 GLN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 HIS ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 218 HIS ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 411 GLN ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 133 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 61278 Z= 0.121 Angle : 0.527 11.855 82935 Z= 0.253 Chirality : 0.040 0.182 9750 Planarity : 0.002 0.054 11082 Dihedral : 4.163 25.252 8424 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer Outliers : 0.79 % 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: 0.31 (0.10), residues: 7617 helix: 2.15 (0.11), residues: 2334 sheet: -0.24 (0.10), residues: 3024 loop : -1.13 (0.13), residues: 2259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 554 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 25 residues processed: 592 average time/residue: 0.5946 time to fit residues: 589.9858 Evaluate side-chains 527 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 502 time to evaluate : 5.739 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4220 time to fit residues: 27.9209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 713 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 540 optimal weight: 5.9990 chunk 418 optimal weight: 3.9990 chunk 623 optimal weight: 4.9990 chunk 413 optimal weight: 4.9990 chunk 737 optimal weight: 6.9990 chunk 461 optimal weight: 0.9990 chunk 449 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 277 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 125 GLN ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 297 GLN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 411 GLN ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 61278 Z= 0.239 Angle : 0.550 11.994 82935 Z= 0.266 Chirality : 0.040 0.217 9750 Planarity : 0.003 0.053 11082 Dihedral : 4.203 24.882 8424 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer Outliers : 0.84 % 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: 0.40 (0.11), residues: 7617 helix: 2.20 (0.11), residues: 2334 sheet: -0.21 (0.10), residues: 3045 loop : -1.01 (0.13), residues: 2238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 506 time to evaluate : 5.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 22 residues processed: 550 average time/residue: 0.5989 time to fit residues: 550.6545 Evaluate side-chains 517 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 495 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4564 time to fit residues: 26.1089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 456 optimal weight: 0.5980 chunk 294 optimal weight: 0.0020 chunk 440 optimal weight: 10.0000 chunk 222 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 502 optimal weight: 7.9990 chunk 364 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 579 optimal weight: 0.1980 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 218 HIS ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 HIS V 297 GLN V 411 GLN ** W 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 61278 Z= 0.223 Angle : 0.545 12.385 82935 Z= 0.264 Chirality : 0.040 0.201 9750 Planarity : 0.003 0.057 11082 Dihedral : 4.184 24.330 8424 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer Outliers : 0.44 % 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: 0.55 (0.11), residues: 7617 helix: 2.28 (0.11), residues: 2343 sheet: -0.13 (0.10), residues: 3045 loop : -0.87 (0.14), residues: 2229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 512 time to evaluate : 5.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 533 average time/residue: 0.6332 time to fit residues: 567.0634 Evaluate side-chains 507 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 494 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4421 time to fit residues: 18.7392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 670 optimal weight: 5.9990 chunk 706 optimal weight: 8.9990 chunk 644 optimal weight: 4.9990 chunk 687 optimal weight: 20.0000 chunk 413 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 539 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 620 optimal weight: 9.9990 chunk 649 optimal weight: 0.8980 chunk 684 optimal weight: 50.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** G 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 190 GLN ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 297 GLN W 196 HIS ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 61278 Z= 0.325 Angle : 0.588 13.120 82935 Z= 0.288 Chirality : 0.040 0.214 9750 Planarity : 0.003 0.059 11082 Dihedral : 4.340 24.586 8424 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Rotamer Outliers : 0.44 % 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: 0.43 (0.11), residues: 7617 helix: 2.20 (0.11), residues: 2376 sheet: -0.23 (0.11), residues: 3033 loop : -0.96 (0.14), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 502 time to evaluate : 6.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 522 average time/residue: 0.6233 time to fit residues: 542.9864 Evaluate side-chains 500 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 486 time to evaluate : 5.735 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5089 time to fit residues: 21.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 451 optimal weight: 6.9990 chunk 726 optimal weight: 7.9990 chunk 443 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 505 optimal weight: 1.9990 chunk 762 optimal weight: 6.9990 chunk 701 optimal weight: 3.9990 chunk 606 optimal weight: 60.0000 chunk 63 optimal weight: 4.9990 chunk 468 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 HIS K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 222 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 297 GLN ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 61278 Z= 0.276 Angle : 0.581 13.014 82935 Z= 0.282 Chirality : 0.040 0.200 9750 Planarity : 0.003 0.058 11082 Dihedral : 4.297 24.470 8424 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer Outliers : 0.12 % 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: 0.50 (0.11), residues: 7617 helix: 2.24 (0.11), residues: 2394 sheet: -0.22 (0.11), residues: 3069 loop : -0.88 (0.14), residues: 2154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15234 Ramachandran restraints generated. 7617 Oldfield, 0 Emsley, 7617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 498 time to evaluate : 5.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 502 average time/residue: 0.6390 time to fit residues: 531.1701 Evaluate side-chains 490 residues out of total 6801 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 485 time to evaluate : 5.802 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4510 time to fit residues: 12.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 482 optimal weight: 2.9990 chunk 646 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 559 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 168 optimal weight: 60.0000 chunk 607 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 624 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 218 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN G 231 ASN ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 297 GLN ** W 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.108118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070145 restraints weight = 142548.810| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.68 r_work: 0.3124 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 61278 Z= 0.238 Angle : 0.566 12.906 82935 Z= 0.274 Chirality : 0.040 0.179 9750 Planarity : 0.003 0.058 11082 Dihedral : 4.221 24.504 8424 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer Outliers : 0.21 % 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: 0.63 (0.11), residues: 7617 helix: 2.32 (0.11), residues: 2406 sheet: -0.08 (0.11), residues: 3021 loop : -0.92 (0.14), residues: 2190 =============================================================================== Job complete usr+sys time: 13139.23 seconds wall clock time: 232 minutes 13.02 seconds (13933.02 seconds total)