Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 16:25:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/07_2023/6ytk_10917.pdb" } resolution = 4.07 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= 0.001 sd= 0.007 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 400 5.16 5 C 26800 2.51 5 N 6980 2.21 5 O 7440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 228": "OE1" <-> "OE2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J GLU 176": "OE1" <-> "OE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J GLU 228": "OE1" <-> "OE2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "K GLU 154": "OE1" <-> "OE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N GLU 233": "OE1" <-> "OE2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "O GLU 154": "OE1" <-> "OE2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O GLU 176": "OE1" <-> "OE2" Residue "O ARG 182": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 174": "NH1" <-> "NH2" Residue "P GLU 176": "OE1" <-> "OE2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 247": "NH1" <-> "NH2" Residue "Q GLU 154": "OE1" <-> "OE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q ARG 247": "NH1" <-> "NH2" Residue "R GLU 154": "OE1" <-> "OE2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 174": "NH1" <-> "NH2" Residue "R GLU 176": "OE1" <-> "OE2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 174": "NH1" <-> "NH2" Residue "S GLU 176": "OE1" <-> "OE2" Residue "S ARG 182": "NH1" <-> "NH2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "T GLU 154": "OE1" <-> "OE2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 174": "NH1" <-> "NH2" Residue "T GLU 176": "OE1" <-> "OE2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "T ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 41620 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "E" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "F" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "G" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "I" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "J" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "K" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "M" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "O" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "P" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "Q" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "T" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Time building chain proxies: 18.94, per 1000 atoms: 0.46 Number of scatterers: 41620 At special positions: 0 Unit cell: (132.66, 132.66, 207.7, 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 400 16.00 O 7440 8.00 N 6980 7.00 C 26800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=1.97 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.03 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: 16.30 Conformation dependent library (CDL) restraints added in 6.0 seconds 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10160 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.514A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.895A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.710A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.692A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 211 Processing helix chain 'A' and resid 214 through 253 removed outlier: 3.564A pdb=" N HIS A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 38 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.693A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 Processing helix chain 'B' and resid 167 through 211 Processing helix chain 'B' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 38 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.895A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.693A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 211 Processing helix chain 'C' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 38 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.545A pdb=" N GLY D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.692A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 167 through 211 Processing helix chain 'D' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 38 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.708A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.692A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 167 through 211 Processing helix chain 'E' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 38 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.895A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.692A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 167 through 211 Processing helix chain 'F' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS F 218 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL F 277 " --> pdb=" O LYS F 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 38 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.545A pdb=" N GLY G 126 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.694A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 167 through 211 Processing helix chain 'G' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS G 218 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 38 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.545A pdb=" N GLY H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.693A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 158 Processing helix chain 'H' and resid 167 through 211 Processing helix chain 'H' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS H 218 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS H 219 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.546A pdb=" N GLY I 126 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.692A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 167 through 211 Processing helix chain 'I' and resid 214 through 253 removed outlier: 3.563A pdb=" N HIS I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 277 removed outlier: 4.268A pdb=" N VAL I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 38 Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.896A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.709A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.544A pdb=" N GLY J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.693A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 167 through 211 Processing helix chain 'J' and resid 214 through 253 removed outlier: 3.562A pdb=" N HIS J 218 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 277 removed outlier: 4.267A pdb=" N VAL J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 38 Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.889A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.725A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY K 126 " --> pdb=" O THR K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS K 219 " --> pdb=" O SER K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 38 Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.890A pdb=" N PHE L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.725A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 112 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY L 126 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS L 218 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS L 219 " --> pdb=" O SER L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 277 removed outlier: 4.327A pdb=" N VAL L 277 " --> pdb=" O LYS L 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 38 Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.890A pdb=" N PHE M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.725A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.594A pdb=" N GLY M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS M 218 " --> pdb=" O THR M 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL M 277 " --> pdb=" O LYS M 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 39 removed outlier: 3.693A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 70 removed outlier: 3.579A pdb=" N TYR N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.716A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.533A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.736A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 158 Processing helix chain 'N' and resid 167 through 211 Processing helix chain 'N' and resid 216 through 253 Processing helix chain 'N' and resid 268 through 277 removed outlier: 4.019A pdb=" N TRP N 272 " --> pdb=" O SER N 268 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS N 273 " --> pdb=" O CYS N 269 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL N 277 " --> pdb=" O LYS N 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 38 Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.890A pdb=" N PHE O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.724A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 112 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY O 126 " --> pdb=" O THR O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS O 218 " --> pdb=" O THR O 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS O 219 " --> pdb=" O SER O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 277 removed outlier: 4.327A pdb=" N VAL O 277 " --> pdb=" O LYS O 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 38 Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.889A pdb=" N PHE P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.725A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 112 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY P 126 " --> pdb=" O THR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 159 removed outlier: 3.517A pdb=" N GLY P 159 " --> pdb=" O GLU P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS P 218 " --> pdb=" O THR P 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL P 277 " --> pdb=" O LYS P 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 38 Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.890A pdb=" N PHE Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.724A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 112 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY Q 126 " --> pdb=" O THR Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS Q 218 " --> pdb=" O THR Q 214 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL Q 277 " --> pdb=" O LYS Q 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 38 Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.889A pdb=" N PHE R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.724A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 112 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.592A pdb=" N GLY R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY R 159 " --> pdb=" O GLU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 38 Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.890A pdb=" N PHE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.724A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 112 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.594A pdb=" N GLY S 126 " --> pdb=" O THR S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.712A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY S 159 " --> pdb=" O GLU S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 214 through 253 removed outlier: 3.613A pdb=" N HIS S 218 " --> pdb=" O THR S 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS S 219 " --> pdb=" O SER S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL S 277 " --> pdb=" O LYS S 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 38 Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.889A pdb=" N PHE T 55 " --> pdb=" O TYR T 51 " (cutoff:3.500A) Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.724A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 112 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.593A pdb=" N GLY T 126 " --> pdb=" O THR T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.711A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 159 removed outlier: 3.516A pdb=" N GLY T 159 " --> pdb=" O GLU T 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 214 through 253 removed outlier: 3.612A pdb=" N HIS T 218 " --> pdb=" O THR T 214 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS T 219 " --> pdb=" O SER T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 277 removed outlier: 4.328A pdb=" N VAL T 277 " --> pdb=" O LYS T 273 " (cutoff:3.500A) 3191 hydrogen bonds defined for protein. 9573 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: 14.05 Time building geometry restraints manager: 17.26 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: 13110 1.34 - 1.46: 8323 1.46 - 1.58: 20647 1.58 - 1.70: 0 1.70 - 1.82: 500 Bond restraints: 42580 Sorted by residual: bond pdb=" CA ILE A 255 " pdb=" CB ILE A 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.51e+00 bond pdb=" CA ILE H 255 " pdb=" CB ILE H 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.48e+00 bond pdb=" CA ILE G 255 " pdb=" CB ILE G 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.48e+00 bond pdb=" CA ILE E 255 " pdb=" CB ILE E 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.45e+00 bond pdb=" CA ILE C 255 " pdb=" CB ILE C 255 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.43e+00 ... (remaining 42575 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.09: 1260 107.09 - 113.83: 24631 113.83 - 120.57: 17957 120.57 - 127.31: 13492 127.31 - 134.05: 480 Bond angle restraints: 57820 Sorted by residual: angle pdb=" N ARG A 164 " pdb=" CA ARG A 164 " pdb=" C ARG A 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG C 164 " pdb=" CA ARG C 164 " pdb=" C ARG C 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG E 164 " pdb=" CA ARG E 164 " pdb=" C ARG E 164 " ideal model delta sigma weight residual 108.76 115.27 -6.51 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG J 164 " pdb=" CA ARG J 164 " pdb=" C ARG J 164 " ideal model delta sigma weight residual 108.76 115.26 -6.50 1.69e+00 3.50e-01 1.48e+01 angle pdb=" N ARG D 164 " pdb=" CA ARG D 164 " pdb=" C ARG D 164 " ideal model delta sigma weight residual 108.76 115.25 -6.49 1.69e+00 3.50e-01 1.48e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 23160 18.03 - 36.06: 1796 36.06 - 54.09: 366 54.09 - 72.12: 19 72.12 - 90.15: 99 Dihedral angle restraints: 25440 sinusoidal: 9820 harmonic: 15620 Sorted by residual: dihedral pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " pdb=" SG CYS F 131 " pdb=" CB CYS F 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.15 90.15 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS J 41 " pdb=" SG CYS J 41 " pdb=" SG CYS J 131 " pdb=" CB CYS J 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.15 90.15 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS I 41 " pdb=" SG CYS I 41 " pdb=" SG CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sinusoidal sigma weight residual -86.00 -176.14 90.14 1 1.00e+01 1.00e-02 9.62e+01 ... (remaining 25437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5655 0.051 - 0.101: 915 0.101 - 0.152: 151 0.152 - 0.202: 0 0.202 - 0.253: 19 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA SER H 165 " pdb=" N SER H 165 " pdb=" C SER H 165 " pdb=" CB SER H 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA SER J 165 " pdb=" N SER J 165 " pdb=" C SER J 165 " pdb=" CB SER J 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA SER F 165 " pdb=" N SER F 165 " pdb=" C SER F 165 " pdb=" CB SER F 165 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6737 not shown) Planarity restraints: 7180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 166 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 166 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO D 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 166 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO F 167 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 167 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 167 " -0.028 5.00e-02 4.00e+02 ... (remaining 7177 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 48 2.46 - 3.07: 28771 3.07 - 3.68: 62109 3.68 - 4.29: 82937 4.29 - 4.90: 138161 Nonbonded interactions: 312026 Sorted by model distance: nonbonded pdb=" NH1 ARG N 182 " pdb=" OG SER O 40 " model vdw 1.844 2.520 nonbonded pdb=" OH TYR N 142 " pdb=" OE1 GLU N 176 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR R 142 " pdb=" OE1 GLU R 176 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR K 142 " pdb=" OE1 GLU K 176 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR L 142 " pdb=" OE1 GLU L 176 " model vdw 2.234 2.440 ... (remaining 312021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.030 Extract box with map and model: 6.880 Check model and map are aligned: 0.630 Set scattering table: 0.360 Process input model: 94.920 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.320 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 42580 Z= 0.183 Angle : 0.583 6.507 57820 Z= 0.353 Chirality : 0.039 0.253 6740 Planarity : 0.004 0.051 7180 Dihedral : 13.760 87.971 15160 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5260 helix: 0.70 (0.07), residues: 3980 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1232 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1232 average time/residue: 0.6137 time to fit residues: 1153.7960 Evaluate side-chains 704 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 4.691 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 3.9990 chunk 394 optimal weight: 0.0270 chunk 218 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 407 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 chunk 303 optimal weight: 0.7980 chunk 472 optimal weight: 0.0980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 184 GLN A 227 ASN B 20 ASN B 184 GLN B 227 ASN C 20 ASN C 44 GLN C 184 GLN C 227 ASN D 20 ASN D 184 GLN D 227 ASN E 20 ASN E 44 GLN E 184 GLN E 227 ASN F 20 ASN F 184 GLN F 217 GLN F 227 ASN G 20 ASN G 44 GLN G 184 GLN G 227 ASN H 20 ASN H 44 GLN H 184 GLN H 227 ASN I 20 ASN I 184 GLN I 227 ASN J 20 ASN J 44 GLN J 184 GLN J 227 ASN K 15 ASN K 20 ASN K 44 GLN K 184 GLN L 20 ASN L 44 GLN L 184 GLN L 186 GLN M 15 ASN M 20 ASN M 184 GLN N 20 ASN N 184 GLN N 227 ASN O 15 ASN O 20 ASN O 184 GLN O 217 GLN P 15 ASN P 20 ASN P 44 GLN P 184 GLN Q 15 ASN Q 20 ASN Q 44 GLN Q 184 GLN Q 186 GLN R 15 ASN R 20 ASN R 184 GLN S 20 ASN S 44 GLN S 184 GLN T 15 ASN T 20 ASN T 184 GLN T 217 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 42580 Z= 0.164 Angle : 0.526 7.697 57820 Z= 0.277 Chirality : 0.039 0.138 6740 Planarity : 0.005 0.066 7180 Dihedral : 3.929 15.208 5700 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 5260 helix: 1.87 (0.08), residues: 4100 sheet: None (None), residues: 0 loop : -2.75 (0.17), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 976 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 976 average time/residue: 0.5282 time to fit residues: 845.1682 Evaluate side-chains 656 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 656 time to evaluate : 4.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 393 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 473 optimal weight: 0.8980 chunk 511 optimal weight: 3.9990 chunk 421 optimal weight: 0.5980 chunk 469 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN H 15 ASN I 15 ASN K 15 ASN K 238 GLN L 15 ASN M 238 GLN O 15 ASN P 15 ASN P 238 GLN T 15 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 42580 Z= 0.158 Angle : 0.498 5.488 57820 Z= 0.263 Chirality : 0.038 0.138 6740 Planarity : 0.004 0.061 7180 Dihedral : 3.833 15.342 5700 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.12), residues: 5260 helix: 2.17 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.77 (0.16), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 895 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.4967 time to fit residues: 739.8262 Evaluate side-chains 615 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 615 time to evaluate : 4.711 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 2.9990 chunk 355 optimal weight: 0.9980 chunk 245 optimal weight: 0.4980 chunk 52 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 317 optimal weight: 0.9980 chunk 474 optimal weight: 7.9990 chunk 502 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 42580 Z= 0.162 Angle : 0.493 6.478 57820 Z= 0.259 Chirality : 0.038 0.163 6740 Planarity : 0.004 0.052 7180 Dihedral : 3.803 15.255 5700 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.12), residues: 5260 helix: 2.35 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.61 (0.16), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 862 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 862 average time/residue: 0.5324 time to fit residues: 760.3278 Evaluate side-chains 588 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 374 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 428 optimal weight: 0.0040 chunk 347 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 451 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 ASN Q 44 GLN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 42580 Z= 0.250 Angle : 0.564 6.703 57820 Z= 0.294 Chirality : 0.040 0.156 6740 Planarity : 0.004 0.055 7180 Dihedral : 3.899 16.586 5700 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.12), residues: 5260 helix: 2.35 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 808 time to evaluate : 5.842 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 808 average time/residue: 0.5035 time to fit residues: 679.2800 Evaluate side-chains 593 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 4.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 3.9990 chunk 452 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 124 optimal weight: 0.1980 chunk 503 optimal weight: 2.9990 chunk 417 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 15 ASN M 44 GLN N 73 GLN ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 42580 Z= 0.199 Angle : 0.531 6.231 57820 Z= 0.276 Chirality : 0.039 0.155 6740 Planarity : 0.004 0.055 7180 Dihedral : 3.948 17.203 5700 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.12), residues: 5260 helix: 2.45 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.62 (0.16), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 4.713 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 821 average time/residue: 0.5268 time to fit residues: 707.7248 Evaluate side-chains 579 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 4.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 367 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 280 optimal weight: 0.0570 chunk 501 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN B 44 GLN ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 42580 Z= 0.169 Angle : 0.523 6.838 57820 Z= 0.269 Chirality : 0.038 0.157 6740 Planarity : 0.004 0.051 7180 Dihedral : 3.901 17.050 5700 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.12), residues: 5260 helix: 2.58 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.56 (0.17), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 807 time to evaluate : 4.377 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 807 average time/residue: 0.5044 time to fit residues: 676.4128 Evaluate side-chains 573 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 341 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 chunk 393 optimal weight: 4.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 15 ASN ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 42580 Z= 0.257 Angle : 0.576 6.607 57820 Z= 0.299 Chirality : 0.041 0.153 6740 Planarity : 0.004 0.052 7180 Dihedral : 3.958 16.673 5700 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.12), residues: 5260 helix: 2.48 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.62 (0.16), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 4.810 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 776 average time/residue: 0.4971 time to fit residues: 646.1874 Evaluate side-chains 554 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 0.7980 chunk 480 optimal weight: 7.9990 chunk 438 optimal weight: 0.7980 chunk 467 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 366 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 422 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 465 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 42580 Z= 0.163 Angle : 0.534 7.684 57820 Z= 0.273 Chirality : 0.038 0.173 6740 Planarity : 0.004 0.052 7180 Dihedral : 3.907 16.634 5700 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.12), residues: 5260 helix: 2.65 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 1120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 779 time to evaluate : 4.390 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 779 average time/residue: 0.4819 time to fit residues: 630.9890 Evaluate side-chains 569 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 4.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 2.9990 chunk 493 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 343 optimal weight: 0.0870 chunk 518 optimal weight: 10.0000 chunk 476 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 318 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 42580 Z= 0.177 Angle : 0.548 7.980 57820 Z= 0.280 Chirality : 0.039 0.154 6740 Planarity : 0.004 0.049 7180 Dihedral : 3.890 16.237 5700 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.12), residues: 5260 helix: 2.67 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.44 (0.17), residues: 1120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 4.579 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 759 average time/residue: 0.4917 time to fit residues: 624.2608 Evaluate side-chains 577 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 577 time to evaluate : 4.275 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 3.9990 chunk 439 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 380 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 413 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 424 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.150478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124890 restraints weight = 57251.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125717 restraints weight = 45294.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126102 restraints weight = 39573.944| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 42580 Z= 0.183 Angle : 0.544 7.767 57820 Z= 0.278 Chirality : 0.039 0.155 6740 Planarity : 0.004 0.050 7180 Dihedral : 3.875 16.252 5700 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.12), residues: 5260 helix: 2.65 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.39 (0.17), residues: 1120 =============================================================================== Job complete usr+sys time: 10533.55 seconds wall clock time: 190 minutes 38.66 seconds (11438.66 seconds total)