Starting phenix.real_space_refine on Wed Apr 17 00:43:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/04_2024/6ytk_10917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/04_2024/6ytk_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_10917/04_2024/6ytk_10917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/04_2024/6ytk_10917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/04_2024/6ytk_10917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytk_10917/04_2024/6ytk_10917.pdb" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 20.93, per 1000 atoms: 0.50 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: 15.57 Conformation dependent library (CDL) restraints added in 7.1 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: 3.38 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: 15.50 Time building geometry restraints manager: 16.95 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: 0.790 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: 0.040 Extract box with map and model: 5.100 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 102.690 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.350 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:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.160 ------------------------------------------------------------------------------- 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 % Allowed : 6.67 % Favored : 93.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 221 HIS 0.003 0.001 HIS N 239 PHE 0.012 0.001 PHE O 232 TYR 0.006 0.001 TYR N 51 ARG 0.007 0.000 ARG N 247 *********************** 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 : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 ASN cc_start: 0.6947 (m-40) cc_final: 0.6704 (m-40) REVERT: A 45 VAL cc_start: 0.8474 (m) cc_final: 0.7425 (p) REVERT: A 51 TYR cc_start: 0.9104 (t80) cc_final: 0.8701 (t80) REVERT: B 51 TYR cc_start: 0.8922 (t80) cc_final: 0.8680 (t80) REVERT: B 74 MET cc_start: 0.7655 (tmm) cc_final: 0.7189 (tmm) REVERT: B 129 TYR cc_start: 0.9053 (t80) cc_final: 0.8799 (t80) REVERT: B 182 ARG cc_start: 0.7517 (mtp-110) cc_final: 0.6976 (ttt-90) REVERT: B 270 GLN cc_start: 0.7448 (tp40) cc_final: 0.6933 (tm-30) REVERT: C 44 GLN cc_start: 0.8293 (mm-40) cc_final: 0.8052 (mm110) REVERT: C 51 TYR cc_start: 0.8949 (t80) cc_final: 0.8747 (t80) REVERT: C 104 PHE cc_start: 0.8562 (t80) cc_final: 0.8347 (t80) REVERT: C 117 THR cc_start: 0.8844 (t) cc_final: 0.8471 (m) REVERT: C 144 MET cc_start: 0.6812 (ptp) cc_final: 0.6425 (ptp) REVERT: C 234 GLN cc_start: 0.8375 (tt0) cc_final: 0.7830 (tm-30) REVERT: C 249 LYS cc_start: 0.8677 (tttt) cc_final: 0.8442 (ttmm) REVERT: C 270 GLN cc_start: 0.7899 (tp40) cc_final: 0.7321 (tm-30) REVERT: D 13 GLN cc_start: 0.7244 (tp40) cc_final: 0.6951 (tm-30) REVERT: D 51 TYR cc_start: 0.9185 (t80) cc_final: 0.8889 (t80) REVERT: D 135 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7239 (mt-10) REVERT: D 145 PHE cc_start: 0.7233 (m-80) cc_final: 0.6934 (m-80) REVERT: D 234 GLN cc_start: 0.8266 (tt0) cc_final: 0.7820 (tm-30) REVERT: D 244 MET cc_start: 0.8114 (tpt) cc_final: 0.7913 (tpp) REVERT: E 13 GLN cc_start: 0.7718 (tp40) cc_final: 0.7394 (tm-30) REVERT: E 44 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8113 (mm110) REVERT: E 129 TYR cc_start: 0.9221 (t80) cc_final: 0.8862 (t80) REVERT: E 187 MET cc_start: 0.9396 (mmp) cc_final: 0.9136 (mmp) REVERT: E 234 GLN cc_start: 0.8202 (tt0) cc_final: 0.7779 (tm-30) REVERT: E 270 GLN cc_start: 0.7633 (tp40) cc_final: 0.7407 (tm-30) REVERT: F 145 PHE cc_start: 0.7405 (m-80) cc_final: 0.7116 (m-80) REVERT: F 270 GLN cc_start: 0.7616 (tp40) cc_final: 0.7166 (tm-30) REVERT: G 117 THR cc_start: 0.8733 (t) cc_final: 0.8432 (m) REVERT: G 129 TYR cc_start: 0.9197 (t80) cc_final: 0.8897 (t80) REVERT: G 144 MET cc_start: 0.6582 (ptp) cc_final: 0.6171 (ptp) REVERT: G 270 GLN cc_start: 0.7591 (tp40) cc_final: 0.7379 (tm-30) REVERT: H 14 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6376 (mmt180) REVERT: H 44 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7999 (mm110) REVERT: H 117 THR cc_start: 0.8872 (t) cc_final: 0.8469 (m) REVERT: H 144 MET cc_start: 0.6689 (ptp) cc_final: 0.6303 (ptp) REVERT: H 234 GLN cc_start: 0.8367 (tt0) cc_final: 0.8045 (tt0) REVERT: H 249 LYS cc_start: 0.8629 (tttt) cc_final: 0.8417 (ttmm) REVERT: H 270 GLN cc_start: 0.7890 (tp40) cc_final: 0.7321 (tm-30) REVERT: I 13 GLN cc_start: 0.7245 (tp40) cc_final: 0.6912 (tm-30) REVERT: I 135 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7257 (mt-10) REVERT: I 144 MET cc_start: 0.7103 (ptp) cc_final: 0.6700 (ptm) REVERT: I 145 PHE cc_start: 0.7168 (m-80) cc_final: 0.6876 (m-80) REVERT: I 234 GLN cc_start: 0.8218 (tt0) cc_final: 0.7926 (tm-30) REVERT: I 244 MET cc_start: 0.8200 (tpt) cc_final: 0.7964 (tpp) REVERT: I 270 GLN cc_start: 0.7588 (tp40) cc_final: 0.7377 (tm-30) REVERT: J 13 GLN cc_start: 0.7690 (tp40) cc_final: 0.7397 (tm-30) REVERT: J 44 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8115 (mm110) REVERT: J 129 TYR cc_start: 0.9246 (t80) cc_final: 0.8878 (t80) REVERT: J 187 MET cc_start: 0.9364 (mmp) cc_final: 0.9072 (mmp) REVERT: J 234 GLN cc_start: 0.8219 (tt0) cc_final: 0.7786 (tm-30) REVERT: J 270 GLN cc_start: 0.7651 (tp40) cc_final: 0.7444 (tm-30) REVERT: K 51 TYR cc_start: 0.9231 (t80) cc_final: 0.9027 (t80) REVERT: K 117 THR cc_start: 0.8850 (t) cc_final: 0.8511 (m) REVERT: K 129 TYR cc_start: 0.9211 (t80) cc_final: 0.8936 (t80) REVERT: K 144 MET cc_start: 0.6551 (ptp) cc_final: 0.6269 (ptp) REVERT: K 215 SER cc_start: 0.8790 (t) cc_final: 0.8528 (p) REVERT: K 234 GLN cc_start: 0.8393 (tt0) cc_final: 0.7977 (tm-30) REVERT: K 270 GLN cc_start: 0.7587 (tp40) cc_final: 0.7014 (tm-30) REVERT: L 44 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7987 (mm110) REVERT: L 135 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7607 (mt-10) REVERT: L 144 MET cc_start: 0.6982 (ptp) cc_final: 0.6575 (ptp) REVERT: L 187 MET cc_start: 0.9361 (mmp) cc_final: 0.9109 (mmm) REVERT: L 234 GLN cc_start: 0.8331 (tt0) cc_final: 0.7764 (tm-30) REVERT: L 249 LYS cc_start: 0.8607 (tttt) cc_final: 0.8347 (ttmm) REVERT: L 270 GLN cc_start: 0.7489 (tp40) cc_final: 0.6836 (tm-30) REVERT: M 13 GLN cc_start: 0.7418 (tp40) cc_final: 0.7143 (tm-30) REVERT: M 51 TYR cc_start: 0.9248 (t80) cc_final: 0.8964 (t80) REVERT: M 135 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7369 (mt-10) REVERT: M 144 MET cc_start: 0.6766 (ptp) cc_final: 0.6205 (ptm) REVERT: M 234 GLN cc_start: 0.8244 (tt0) cc_final: 0.7934 (tm-30) REVERT: M 270 GLN cc_start: 0.7628 (tp40) cc_final: 0.7277 (tm-30) REVERT: N 234 GLN cc_start: 0.8070 (tt0) cc_final: 0.7751 (tt0) REVERT: O 15 ASN cc_start: 0.7444 (m-40) cc_final: 0.7183 (m110) REVERT: O 234 GLN cc_start: 0.8060 (tt0) cc_final: 0.7782 (tt0) REVERT: O 270 GLN cc_start: 0.7749 (tp40) cc_final: 0.7147 (tm-30) REVERT: P 51 TYR cc_start: 0.9226 (t80) cc_final: 0.9018 (t80) REVERT: P 117 THR cc_start: 0.8847 (t) cc_final: 0.8513 (m) REVERT: P 129 TYR cc_start: 0.9217 (t80) cc_final: 0.8954 (t80) REVERT: P 144 MET cc_start: 0.6522 (ptp) cc_final: 0.6269 (ptp) REVERT: P 215 SER cc_start: 0.8768 (t) cc_final: 0.8563 (p) REVERT: P 234 GLN cc_start: 0.8426 (tt0) cc_final: 0.7984 (tm-30) REVERT: P 270 GLN cc_start: 0.7590 (tp40) cc_final: 0.7011 (tm-30) REVERT: Q 13 GLN cc_start: 0.7832 (tp40) cc_final: 0.7553 (tp40) REVERT: Q 14 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6257 (mmt-90) REVERT: Q 44 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8045 (mm110) REVERT: Q 51 TYR cc_start: 0.9057 (t80) cc_final: 0.8809 (t80) REVERT: Q 234 GLN cc_start: 0.8289 (tt0) cc_final: 0.7800 (tm-30) REVERT: Q 249 LYS cc_start: 0.8611 (tttt) cc_final: 0.8309 (ttmm) REVERT: Q 270 GLN cc_start: 0.7445 (tp40) cc_final: 0.6629 (tm-30) REVERT: R 51 TYR cc_start: 0.9262 (t80) cc_final: 0.9051 (t80) REVERT: R 234 GLN cc_start: 0.8353 (tt0) cc_final: 0.7959 (tm-30) REVERT: R 270 GLN cc_start: 0.7685 (tp40) cc_final: 0.7309 (tm-30) REVERT: S 13 GLN cc_start: 0.7772 (tp40) cc_final: 0.7484 (tm-30) REVERT: S 15 ASN cc_start: 0.7456 (m-40) cc_final: 0.7139 (m-40) REVERT: S 44 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8131 (mm110) REVERT: S 51 TYR cc_start: 0.9152 (t80) cc_final: 0.8776 (t80) REVERT: S 129 TYR cc_start: 0.9214 (t80) cc_final: 0.8849 (t80) REVERT: S 153 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7560 (ttp-110) REVERT: S 234 GLN cc_start: 0.8311 (tt0) cc_final: 0.7837 (tm-30) REVERT: S 270 GLN cc_start: 0.7746 (tp40) cc_final: 0.7013 (tm-30) REVERT: T 15 ASN cc_start: 0.7408 (m-40) cc_final: 0.7163 (m110) REVERT: T 234 GLN cc_start: 0.8013 (tt0) cc_final: 0.7710 (tt0) REVERT: T 270 GLN cc_start: 0.7744 (tp40) cc_final: 0.7190 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1232 average time/residue: 0.6193 time to fit residues: 1162.5282 Evaluate side-chains 725 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 4.743 ------------------------------------------------------------------------------- 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: 2.9990 chunk 218 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 407 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 chunk 303 optimal weight: 0.8980 chunk 472 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 184 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 20 ASN D 184 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN E 20 ASN E 184 GLN E 227 ASN E 234 GLN 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 184 GLN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN I 20 ASN I 184 GLN I 227 ASN I 234 GLN J 20 ASN J 184 GLN J 227 ASN J 234 GLN K 15 ASN K 20 ASN K 44 GLN K 184 GLN K 234 GLN L 20 ASN L 184 GLN L 186 GLN L 234 GLN M 15 ASN M 20 ASN M 184 GLN M 234 GLN N 20 ASN N 184 GLN N 227 ASN N 234 GLN O 20 ASN O 184 GLN O 217 GLN O 234 GLN P 15 ASN P 20 ASN P 44 GLN P 184 GLN P 234 GLN Q 20 ASN Q 184 GLN Q 186 GLN Q 217 GLN Q 234 GLN R 15 ASN R 20 ASN R 184 GLN R 234 GLN S 20 ASN S 184 GLN S 234 GLN T 20 ASN T 184 GLN T 217 GLN T 234 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42580 Z= 0.192 Angle : 0.532 7.420 57820 Z= 0.282 Chirality : 0.039 0.141 6740 Planarity : 0.005 0.075 7180 Dihedral : 3.921 14.914 5700 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.22 % Allowed : 6.32 % Favored : 93.46 % 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: 1.17 (0.12), residues: 5260 helix: 1.77 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -3.11 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 75 HIS 0.005 0.001 HIS E 224 PHE 0.016 0.001 PHE B 105 TYR 0.019 0.001 TYR H 51 ARG 0.006 0.001 ARG M 174 *********************** 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 986 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 976 time to evaluate : 5.074 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.9082 (t80) cc_final: 0.8625 (t80) REVERT: A 245 MET cc_start: 0.8496 (tpp) cc_final: 0.8295 (tpp) REVERT: B 15 ASN cc_start: 0.7367 (m-40) cc_final: 0.7121 (m-40) REVERT: B 19 ILE cc_start: 0.8029 (mm) cc_final: 0.7824 (tp) REVERT: B 74 MET cc_start: 0.7572 (tmm) cc_final: 0.7323 (tmm) REVERT: B 182 ARG cc_start: 0.7592 (mtp-110) cc_final: 0.7128 (ttt-90) REVERT: B 208 LYS cc_start: 0.8193 (tppt) cc_final: 0.7881 (tptp) REVERT: B 228 GLU cc_start: 0.7882 (tt0) cc_final: 0.7629 (tt0) REVERT: C 105 PHE cc_start: 0.8571 (t80) cc_final: 0.8338 (t80) REVERT: C 117 THR cc_start: 0.8865 (t) cc_final: 0.8607 (m) REVERT: C 144 MET cc_start: 0.6558 (ptp) cc_final: 0.6080 (ptp) REVERT: C 234 GLN cc_start: 0.8172 (tt0) cc_final: 0.7837 (tm-30) REVERT: D 45 VAL cc_start: 0.8547 (m) cc_final: 0.8150 (m) REVERT: D 135 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7125 (mt-10) REVERT: D 145 PHE cc_start: 0.7169 (m-80) cc_final: 0.6927 (m-80) REVERT: D 187 MET cc_start: 0.9309 (mmm) cc_final: 0.9081 (mmm) REVERT: E 129 TYR cc_start: 0.9291 (t80) cc_final: 0.8959 (t80) REVERT: E 187 MET cc_start: 0.9376 (mmp) cc_final: 0.9038 (mmp) REVERT: E 208 LYS cc_start: 0.8343 (tppt) cc_final: 0.8075 (tmmt) REVERT: E 229 ARG cc_start: 0.7416 (tpp80) cc_final: 0.6847 (ttp-110) REVERT: E 234 GLN cc_start: 0.7887 (tt0) cc_final: 0.7666 (tm-30) REVERT: E 270 GLN cc_start: 0.7664 (tp40) cc_final: 0.7347 (tm-30) REVERT: F 45 VAL cc_start: 0.8404 (m) cc_final: 0.7614 (p) REVERT: F 51 TYR cc_start: 0.9076 (t80) cc_final: 0.8718 (t80) REVERT: F 145 PHE cc_start: 0.7432 (m-80) cc_final: 0.7139 (m-80) REVERT: F 187 MET cc_start: 0.9336 (mmm) cc_final: 0.9002 (mmm) REVERT: G 117 THR cc_start: 0.8926 (t) cc_final: 0.8633 (m) REVERT: G 129 TYR cc_start: 0.9289 (t80) cc_final: 0.8970 (t80) REVERT: G 187 MET cc_start: 0.9353 (mmp) cc_final: 0.8989 (mmt) REVERT: G 255 ILE cc_start: 0.9115 (mm) cc_final: 0.8909 (mm) REVERT: H 14 ARG cc_start: 0.6409 (mtm110) cc_final: 0.6089 (mmt-90) REVERT: H 74 MET cc_start: 0.8441 (tpp) cc_final: 0.8185 (tpp) REVERT: H 117 THR cc_start: 0.8935 (t) cc_final: 0.8631 (m) REVERT: H 144 MET cc_start: 0.6898 (ptp) cc_final: 0.6641 (ptp) REVERT: H 208 LYS cc_start: 0.8589 (tppt) cc_final: 0.8328 (tmmt) REVERT: I 45 VAL cc_start: 0.8559 (m) cc_final: 0.8187 (m) REVERT: I 135 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7158 (mt-10) REVERT: I 145 PHE cc_start: 0.7160 (m-80) cc_final: 0.6895 (m-80) REVERT: I 249 LYS cc_start: 0.8600 (tttp) cc_final: 0.8393 (ttmm) REVERT: I 270 GLN cc_start: 0.7747 (tp40) cc_final: 0.7438 (tm-30) REVERT: J 129 TYR cc_start: 0.9296 (t80) cc_final: 0.8966 (t80) REVERT: J 187 MET cc_start: 0.9346 (mmp) cc_final: 0.9021 (mmp) REVERT: J 208 LYS cc_start: 0.8338 (tppt) cc_final: 0.8089 (tmmt) REVERT: J 229 ARG cc_start: 0.7442 (tpp80) cc_final: 0.6853 (ttp-110) REVERT: J 234 GLN cc_start: 0.7897 (tt0) cc_final: 0.7663 (tm-30) REVERT: J 263 HIS cc_start: 0.7226 (m90) cc_final: 0.7007 (m90) REVERT: J 270 GLN cc_start: 0.7711 (tp40) cc_final: 0.7364 (tm-30) REVERT: K 129 TYR cc_start: 0.9282 (t80) cc_final: 0.8972 (t80) REVERT: K 208 LYS cc_start: 0.8199 (tppt) cc_final: 0.7758 (tptp) REVERT: K 229 ARG cc_start: 0.7881 (tpp80) cc_final: 0.6992 (ttp-110) REVERT: K 270 GLN cc_start: 0.7740 (tp40) cc_final: 0.7043 (tm-30) REVERT: L 14 ARG cc_start: 0.6620 (mtm110) cc_final: 0.6272 (mmt-90) REVERT: L 144 MET cc_start: 0.6794 (ptp) cc_final: 0.6565 (ptp) REVERT: L 270 GLN cc_start: 0.7262 (tp40) cc_final: 0.6592 (tm-30) REVERT: M 45 VAL cc_start: 0.8637 (m) cc_final: 0.8341 (m) REVERT: M 153 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7487 (ttp-110) REVERT: M 187 MET cc_start: 0.9310 (mmm) cc_final: 0.9089 (mmm) REVERT: M 238 GLN cc_start: 0.7783 (tt0) cc_final: 0.7517 (tt0) REVERT: M 245 MET cc_start: 0.8564 (tpp) cc_final: 0.8256 (tpp) REVERT: M 270 GLN cc_start: 0.7739 (tp40) cc_final: 0.7276 (tm-30) REVERT: N 187 MET cc_start: 0.9256 (mmp) cc_final: 0.9033 (mmp) REVERT: N 234 GLN cc_start: 0.8108 (tt0) cc_final: 0.7726 (tm-30) REVERT: O 31 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8918 (tm-30) REVERT: O 32 GLN cc_start: 0.7937 (tp40) cc_final: 0.7213 (mm-40) REVERT: O 45 VAL cc_start: 0.8540 (m) cc_final: 0.8095 (m) REVERT: O 187 MET cc_start: 0.9325 (mmm) cc_final: 0.9002 (mmm) REVERT: O 245 MET cc_start: 0.8647 (tpp) cc_final: 0.8368 (tpp) REVERT: O 270 GLN cc_start: 0.7801 (tp40) cc_final: 0.7160 (tm-30) REVERT: P 129 TYR cc_start: 0.9299 (t80) cc_final: 0.8985 (t80) REVERT: P 208 LYS cc_start: 0.8189 (tppt) cc_final: 0.7733 (tptp) REVERT: P 229 ARG cc_start: 0.7870 (tpp80) cc_final: 0.6975 (ttp-110) REVERT: P 270 GLN cc_start: 0.7619 (tp40) cc_final: 0.7032 (tm-30) REVERT: Q 117 THR cc_start: 0.8830 (t) cc_final: 0.8414 (m) REVERT: Q 155 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7227 (mt-10) REVERT: Q 270 GLN cc_start: 0.7256 (tp40) cc_final: 0.6553 (tm-30) REVERT: R 153 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7528 (ttp-110) REVERT: R 187 MET cc_start: 0.9300 (mmm) cc_final: 0.9063 (mmm) REVERT: R 229 ARG cc_start: 0.7506 (tpp80) cc_final: 0.6992 (ttp-110) REVERT: R 245 MET cc_start: 0.8566 (tpp) cc_final: 0.8266 (tpp) REVERT: R 270 GLN cc_start: 0.7798 (tp40) cc_final: 0.7302 (tm-30) REVERT: S 47 LYS cc_start: 0.7786 (mttp) cc_final: 0.7578 (mttp) REVERT: S 51 TYR cc_start: 0.9033 (t80) cc_final: 0.8758 (t80) REVERT: S 129 TYR cc_start: 0.9280 (t80) cc_final: 0.8939 (t80) REVERT: S 153 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7621 (ttp-110) REVERT: S 229 ARG cc_start: 0.7817 (tpp80) cc_final: 0.6982 (ttp-110) REVERT: S 238 GLN cc_start: 0.7945 (tt0) cc_final: 0.7602 (tp40) REVERT: S 270 GLN cc_start: 0.7877 (tp40) cc_final: 0.7042 (tm-30) REVERT: T 31 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8930 (tm-30) REVERT: T 32 GLN cc_start: 0.7946 (tp40) cc_final: 0.7208 (mm-40) REVERT: T 187 MET cc_start: 0.9338 (mmp) cc_final: 0.9114 (mmm) REVERT: T 238 GLN cc_start: 0.8000 (tt0) cc_final: 0.7793 (tt0) REVERT: T 245 MET cc_start: 0.8290 (tpp) cc_final: 0.7937 (tpp) REVERT: T 270 GLN cc_start: 0.7804 (tp40) cc_final: 0.7165 (tm-30) outliers start: 10 outliers final: 0 residues processed: 977 average time/residue: 0.5315 time to fit residues: 844.9745 Evaluate side-chains 687 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.663 ------------------------------------------------------------------------------- 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: 2.9990 chunk 146 optimal weight: 3.9990 chunk 393 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 473 optimal weight: 0.0270 chunk 511 optimal weight: 0.9990 chunk 421 optimal weight: 0.2980 chunk 469 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 379 optimal weight: 9.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN C 227 ASN D 227 ASN H 15 ASN H 44 GLN H 227 ASN I 15 ASN K 15 ASN K 238 GLN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 ASN P 238 GLN Q 15 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42580 Z= 0.168 Angle : 0.501 5.974 57820 Z= 0.265 Chirality : 0.038 0.160 6740 Planarity : 0.004 0.061 7180 Dihedral : 3.863 15.724 5700 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % 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: 1.72 (0.12), residues: 5260 helix: 2.12 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.82 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 118 HIS 0.004 0.000 HIS E 224 PHE 0.020 0.001 PHE L 232 TYR 0.017 0.001 TYR S 128 ARG 0.005 0.001 ARG E 153 *********************** 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 919 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 918 time to evaluate : 5.241 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.6018 (ptp) cc_final: 0.5719 (ptm) REVERT: B 15 ASN cc_start: 0.7392 (m110) cc_final: 0.6990 (m-40) REVERT: B 105 PHE cc_start: 0.8380 (t80) cc_final: 0.7918 (t80) REVERT: B 153 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.8008 (ttp-110) REVERT: B 182 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7209 (ttt-90) REVERT: B 208 LYS cc_start: 0.8273 (tppt) cc_final: 0.7950 (tptp) REVERT: C 128 TYR cc_start: 0.8595 (m-10) cc_final: 0.8388 (m-80) REVERT: C 144 MET cc_start: 0.6215 (ptp) cc_final: 0.5978 (ptp) REVERT: C 234 GLN cc_start: 0.8073 (tt0) cc_final: 0.7786 (tm-30) REVERT: D 45 VAL cc_start: 0.8570 (m) cc_final: 0.8140 (m) REVERT: D 135 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7101 (mt-10) REVERT: D 145 PHE cc_start: 0.7224 (m-80) cc_final: 0.6875 (m-80) REVERT: D 233 GLU cc_start: 0.8390 (tp30) cc_final: 0.8152 (tp30) REVERT: D 234 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7756 (tm-30) REVERT: E 187 MET cc_start: 0.9349 (mmp) cc_final: 0.9002 (mmp) REVERT: E 208 LYS cc_start: 0.8304 (tppt) cc_final: 0.8018 (tmmt) REVERT: E 229 ARG cc_start: 0.7223 (tpp80) cc_final: 0.6727 (ttp-110) REVERT: F 45 VAL cc_start: 0.8324 (m) cc_final: 0.7597 (p) REVERT: F 187 MET cc_start: 0.9242 (mmm) cc_final: 0.8909 (mmm) REVERT: G 117 THR cc_start: 0.8896 (t) cc_final: 0.8574 (m) REVERT: H 144 MET cc_start: 0.6544 (ptp) cc_final: 0.6293 (ptp) REVERT: H 208 LYS cc_start: 0.8553 (tppt) cc_final: 0.8235 (tmmt) REVERT: I 45 VAL cc_start: 0.8628 (m) cc_final: 0.8274 (m) REVERT: I 135 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7134 (mt-10) REVERT: I 145 PHE cc_start: 0.7200 (m-80) cc_final: 0.6892 (m-80) REVERT: I 187 MET cc_start: 0.9266 (mmm) cc_final: 0.9029 (mmm) REVERT: I 234 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 270 GLN cc_start: 0.7814 (tp40) cc_final: 0.7461 (tm-30) REVERT: J 208 LYS cc_start: 0.8331 (tppt) cc_final: 0.8035 (tmmt) REVERT: J 229 ARG cc_start: 0.7266 (tpp80) cc_final: 0.6772 (ttp-110) REVERT: K 129 TYR cc_start: 0.9300 (t80) cc_final: 0.8997 (t80) REVERT: K 187 MET cc_start: 0.9472 (mmp) cc_final: 0.9142 (mmp) REVERT: K 208 LYS cc_start: 0.8296 (tppt) cc_final: 0.7819 (tptp) REVERT: K 229 ARG cc_start: 0.7719 (tpp80) cc_final: 0.7084 (ttp-110) REVERT: K 270 GLN cc_start: 0.7657 (tp40) cc_final: 0.7013 (tm-30) REVERT: L 74 MET cc_start: 0.8401 (tpp) cc_final: 0.8184 (tpp) REVERT: L 144 MET cc_start: 0.6061 (ptp) cc_final: 0.5814 (ptp) REVERT: L 270 GLN cc_start: 0.7367 (tp40) cc_final: 0.6548 (tm-30) REVERT: M 45 VAL cc_start: 0.8639 (m) cc_final: 0.8196 (p) REVERT: M 141 HIS cc_start: 0.5786 (p-80) cc_final: 0.4843 (p-80) REVERT: N 234 GLN cc_start: 0.8051 (tt0) cc_final: 0.7719 (tm-30) REVERT: O 32 GLN cc_start: 0.7962 (tp40) cc_final: 0.7445 (mm-40) REVERT: O 45 VAL cc_start: 0.8460 (m) cc_final: 0.8080 (m) REVERT: O 187 MET cc_start: 0.9234 (mmm) cc_final: 0.8980 (mmm) REVERT: P 129 TYR cc_start: 0.9327 (t80) cc_final: 0.9018 (t80) REVERT: P 187 MET cc_start: 0.9476 (mmp) cc_final: 0.9197 (mmp) REVERT: P 208 LYS cc_start: 0.8273 (tppt) cc_final: 0.7802 (tptp) REVERT: P 229 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7022 (ttp-110) REVERT: P 270 GLN cc_start: 0.7657 (tp40) cc_final: 0.7035 (tm-30) REVERT: Q 31 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8919 (tm-30) REVERT: Q 117 THR cc_start: 0.8778 (t) cc_final: 0.8381 (m) REVERT: Q 174 ARG cc_start: 0.8811 (tmm-80) cc_final: 0.8181 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7062 (tp40) cc_final: 0.6290 (tm-30) REVERT: R 45 VAL cc_start: 0.8655 (m) cc_final: 0.8210 (p) REVERT: R 141 HIS cc_start: 0.5619 (p-80) cc_final: 0.4656 (p-80) REVERT: R 229 ARG cc_start: 0.7048 (tpp80) cc_final: 0.6797 (ttp-110) REVERT: R 270 GLN cc_start: 0.7852 (tp40) cc_final: 0.7508 (tp40) REVERT: S 45 VAL cc_start: 0.8393 (m) cc_final: 0.8027 (p) REVERT: S 229 ARG cc_start: 0.7461 (tpp80) cc_final: 0.6981 (ttp-110) REVERT: S 234 GLN cc_start: 0.8159 (tt0) cc_final: 0.7560 (tm-30) REVERT: S 270 GLN cc_start: 0.7923 (tp40) cc_final: 0.7114 (tm-30) REVERT: T 45 VAL cc_start: 0.8485 (m) cc_final: 0.8115 (m) outliers start: 1 outliers final: 0 residues processed: 919 average time/residue: 0.5389 time to fit residues: 803.9739 Evaluate side-chains 638 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 638 time to evaluate : 4.581 ------------------------------------------------------------------------------- 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: 3.9990 chunk 355 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 317 optimal weight: 0.5980 chunk 474 optimal weight: 0.7980 chunk 502 optimal weight: 1.9990 chunk 248 optimal weight: 0.0470 chunk 449 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 42580 Z= 0.156 Angle : 0.491 6.115 57820 Z= 0.256 Chirality : 0.038 0.151 6740 Planarity : 0.004 0.064 7180 Dihedral : 3.833 15.118 5700 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 2.07 (0.12), residues: 5260 helix: 2.35 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 118 HIS 0.004 0.000 HIS N 224 PHE 0.017 0.001 PHE L 232 TYR 0.013 0.001 TYR D 51 ARG 0.006 0.001 ARG N 265 *********************** 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 883 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 883 time to evaluate : 4.582 Fit side-chains revert: symmetry clash REVERT: A 245 MET cc_start: 0.8534 (tpp) cc_final: 0.8234 (tpp) REVERT: B 51 TYR cc_start: 0.9087 (t80) cc_final: 0.8804 (t80) REVERT: B 105 PHE cc_start: 0.8542 (t80) cc_final: 0.8181 (t80) REVERT: B 208 LYS cc_start: 0.8368 (tppt) cc_final: 0.7948 (tptp) REVERT: C 128 TYR cc_start: 0.8548 (m-10) cc_final: 0.8336 (m-80) REVERT: C 144 MET cc_start: 0.6174 (ptp) cc_final: 0.5802 (ptp) REVERT: D 45 VAL cc_start: 0.8577 (m) cc_final: 0.8298 (m) REVERT: D 135 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7200 (mt-10) REVERT: D 145 PHE cc_start: 0.7231 (m-80) cc_final: 0.6819 (m-80) REVERT: D 234 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 245 MET cc_start: 0.8522 (tpp) cc_final: 0.8253 (tpp) REVERT: E 208 LYS cc_start: 0.8298 (tppt) cc_final: 0.8020 (tmmt) REVERT: E 229 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6885 (ttp-110) REVERT: E 244 MET cc_start: 0.7898 (tpp) cc_final: 0.7682 (tpp) REVERT: E 263 HIS cc_start: 0.7349 (m90) cc_final: 0.6984 (m90) REVERT: F 45 VAL cc_start: 0.8350 (m) cc_final: 0.7531 (p) REVERT: F 187 MET cc_start: 0.9218 (mmm) cc_final: 0.8950 (mmm) REVERT: G 117 THR cc_start: 0.8877 (t) cc_final: 0.8481 (m) REVERT: G 187 MET cc_start: 0.9406 (mmp) cc_final: 0.9056 (mmp) REVERT: H 51 TYR cc_start: 0.9270 (t80) cc_final: 0.9024 (t80) REVERT: H 208 LYS cc_start: 0.8497 (tppt) cc_final: 0.8269 (tmmt) REVERT: I 45 VAL cc_start: 0.8589 (m) cc_final: 0.8217 (m) REVERT: I 135 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7089 (mt-10) REVERT: I 145 PHE cc_start: 0.7253 (m-80) cc_final: 0.6825 (m-80) REVERT: I 234 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7862 (tm-30) REVERT: I 270 GLN cc_start: 0.7842 (tp40) cc_final: 0.7492 (tm-30) REVERT: J 208 LYS cc_start: 0.8289 (tppt) cc_final: 0.8025 (tmmt) REVERT: J 229 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6942 (ttp-110) REVERT: J 244 MET cc_start: 0.7987 (tpp) cc_final: 0.7634 (tpp) REVERT: J 263 HIS cc_start: 0.7285 (m90) cc_final: 0.6792 (m90) REVERT: K 129 TYR cc_start: 0.9315 (t80) cc_final: 0.8989 (t80) REVERT: K 208 LYS cc_start: 0.8348 (tppt) cc_final: 0.7853 (tptp) REVERT: K 229 ARG cc_start: 0.7604 (tpp80) cc_final: 0.7089 (ttp-110) REVERT: K 270 GLN cc_start: 0.7653 (tp40) cc_final: 0.6999 (tm-30) REVERT: L 45 VAL cc_start: 0.8720 (m) cc_final: 0.8416 (p) REVERT: L 117 THR cc_start: 0.8803 (t) cc_final: 0.8462 (m) REVERT: L 270 GLN cc_start: 0.7137 (tp40) cc_final: 0.6387 (tm-30) REVERT: M 45 VAL cc_start: 0.8585 (m) cc_final: 0.8167 (p) REVERT: M 153 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7545 (ttp-110) REVERT: M 154 GLU cc_start: 0.7735 (pp20) cc_final: 0.7433 (pp20) REVERT: N 234 GLN cc_start: 0.8001 (tt0) cc_final: 0.7761 (tm-30) REVERT: N 265 ARG cc_start: 0.6718 (ttt-90) cc_final: 0.6402 (tmm-80) REVERT: O 45 VAL cc_start: 0.8434 (m) cc_final: 0.8030 (m) REVERT: O 187 MET cc_start: 0.9246 (mmm) cc_final: 0.8980 (mmm) REVERT: O 245 MET cc_start: 0.8466 (tpp) cc_final: 0.8261 (tpp) REVERT: P 129 TYR cc_start: 0.9285 (t80) cc_final: 0.8993 (t80) REVERT: P 208 LYS cc_start: 0.8323 (tppt) cc_final: 0.7821 (tptp) REVERT: P 229 ARG cc_start: 0.7543 (tpp80) cc_final: 0.6981 (ttp-110) REVERT: P 270 GLN cc_start: 0.7623 (tp40) cc_final: 0.7024 (tm-30) REVERT: Q 117 THR cc_start: 0.8818 (t) cc_final: 0.8493 (m) REVERT: Q 174 ARG cc_start: 0.8781 (tmm-80) cc_final: 0.8149 (ttp-170) REVERT: Q 241 ARG cc_start: 0.8412 (ttt90) cc_final: 0.8142 (ttt90) REVERT: Q 270 GLN cc_start: 0.7092 (tp40) cc_final: 0.6312 (tm-30) REVERT: R 45 VAL cc_start: 0.8572 (m) cc_final: 0.8138 (p) REVERT: R 141 HIS cc_start: 0.5820 (p-80) cc_final: 0.4810 (p-80) REVERT: R 154 GLU cc_start: 0.7699 (pp20) cc_final: 0.7365 (pp20) REVERT: R 265 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7111 (ttp80) REVERT: R 270 GLN cc_start: 0.7849 (tp40) cc_final: 0.7510 (tp40) REVERT: S 154 GLU cc_start: 0.7773 (pp20) cc_final: 0.7461 (pp20) REVERT: S 229 ARG cc_start: 0.7400 (tpp80) cc_final: 0.6974 (ttp-110) REVERT: S 234 GLN cc_start: 0.8060 (tt0) cc_final: 0.7661 (tm-30) REVERT: S 270 GLN cc_start: 0.7888 (tp40) cc_final: 0.7167 (tm-30) REVERT: T 45 VAL cc_start: 0.8492 (m) cc_final: 0.8045 (m) REVERT: T 187 MET cc_start: 0.9225 (mmm) cc_final: 0.9023 (mmm) REVERT: T 245 MET cc_start: 0.8085 (tpp) cc_final: 0.7843 (tpp) outliers start: 0 outliers final: 0 residues processed: 883 average time/residue: 0.5423 time to fit residues: 770.2012 Evaluate side-chains 610 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 610 time to evaluate : 4.533 ------------------------------------------------------------------------------- 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: 0.7980 chunk 374 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 428 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 2.9990 chunk 451 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.7949 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42580 Z= 0.197 Angle : 0.527 6.751 57820 Z= 0.275 Chirality : 0.039 0.148 6740 Planarity : 0.004 0.056 7180 Dihedral : 3.870 15.384 5700 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 2.15 (0.12), residues: 5260 helix: 2.41 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.62 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 118 HIS 0.004 0.001 HIS S 224 PHE 0.029 0.002 PHE S 68 TYR 0.009 0.001 TYR J 129 ARG 0.006 0.000 ARG J 103 *********************** 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 844 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 844 time to evaluate : 4.509 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9226 (mmm) cc_final: 0.8748 (mmm) REVERT: B 32 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 51 TYR cc_start: 0.9091 (t80) cc_final: 0.8851 (t80) REVERT: C 208 LYS cc_start: 0.7897 (tmmt) cc_final: 0.7675 (tmmt) REVERT: D 45 VAL cc_start: 0.8614 (m) cc_final: 0.8241 (m) REVERT: D 135 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7250 (mt-10) REVERT: D 145 PHE cc_start: 0.7144 (m-80) cc_final: 0.6634 (m-80) REVERT: D 234 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 45 VAL cc_start: 0.8372 (m) cc_final: 0.8040 (p) REVERT: E 208 LYS cc_start: 0.8287 (tppt) cc_final: 0.7978 (tmmt) REVERT: E 229 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6958 (ttp-110) REVERT: E 263 HIS cc_start: 0.7377 (m90) cc_final: 0.7010 (m90) REVERT: F 45 VAL cc_start: 0.8329 (m) cc_final: 0.7569 (p) REVERT: F 187 MET cc_start: 0.9230 (mmm) cc_final: 0.8942 (mmm) REVERT: G 117 THR cc_start: 0.8797 (t) cc_final: 0.8457 (m) REVERT: G 187 MET cc_start: 0.9397 (mmp) cc_final: 0.9052 (mmp) REVERT: H 51 TYR cc_start: 0.9288 (t80) cc_final: 0.9033 (t80) REVERT: H 208 LYS cc_start: 0.8448 (tppt) cc_final: 0.8149 (tmmt) REVERT: I 45 VAL cc_start: 0.8618 (m) cc_final: 0.8242 (m) REVERT: I 135 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7205 (mt-10) REVERT: I 145 PHE cc_start: 0.7312 (m-80) cc_final: 0.6877 (m-80) REVERT: I 234 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7834 (tm-30) REVERT: J 45 VAL cc_start: 0.8390 (m) cc_final: 0.8060 (p) REVERT: J 208 LYS cc_start: 0.8268 (tppt) cc_final: 0.7989 (tmmt) REVERT: J 229 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6951 (ttp-110) REVERT: J 263 HIS cc_start: 0.7281 (m90) cc_final: 0.6827 (m90) REVERT: K 187 MET cc_start: 0.9455 (mmp) cc_final: 0.9060 (mmm) REVERT: K 229 ARG cc_start: 0.7522 (tpp80) cc_final: 0.7011 (ttp-110) REVERT: K 270 GLN cc_start: 0.7762 (tp40) cc_final: 0.7142 (tm-30) REVERT: L 45 VAL cc_start: 0.8726 (m) cc_final: 0.8418 (p) REVERT: L 117 THR cc_start: 0.8836 (t) cc_final: 0.8443 (m) REVERT: L 144 MET cc_start: 0.5683 (ptp) cc_final: 0.5465 (ptt) REVERT: L 270 GLN cc_start: 0.7246 (tp40) cc_final: 0.6572 (tm-30) REVERT: M 45 VAL cc_start: 0.8602 (m) cc_final: 0.8234 (p) REVERT: M 154 GLU cc_start: 0.7780 (pp20) cc_final: 0.7509 (pp20) REVERT: N 234 GLN cc_start: 0.8038 (tt0) cc_final: 0.7713 (tm-30) REVERT: N 265 ARG cc_start: 0.6828 (ttt-90) cc_final: 0.6561 (tmm-80) REVERT: O 45 VAL cc_start: 0.8387 (m) cc_final: 0.8057 (m) REVERT: O 144 MET cc_start: 0.6419 (ptm) cc_final: 0.6054 (ptm) REVERT: O 187 MET cc_start: 0.9231 (mmm) cc_final: 0.8776 (mmm) REVERT: O 245 MET cc_start: 0.8532 (tpp) cc_final: 0.8291 (tpp) REVERT: P 187 MET cc_start: 0.9447 (mmp) cc_final: 0.9061 (mmm) REVERT: P 229 ARG cc_start: 0.7563 (tpp80) cc_final: 0.6995 (ttp-110) REVERT: P 270 GLN cc_start: 0.7740 (tp40) cc_final: 0.7165 (tm-30) REVERT: Q 45 VAL cc_start: 0.8613 (m) cc_final: 0.8396 (p) REVERT: Q 117 THR cc_start: 0.8844 (t) cc_final: 0.8471 (m) REVERT: Q 154 GLU cc_start: 0.7767 (pp20) cc_final: 0.7493 (pp20) REVERT: Q 174 ARG cc_start: 0.8795 (tmm-80) cc_final: 0.8167 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7292 (tp40) cc_final: 0.6482 (tm-30) REVERT: R 45 VAL cc_start: 0.8605 (m) cc_final: 0.8230 (p) REVERT: R 154 GLU cc_start: 0.7675 (pp20) cc_final: 0.7455 (pp20) REVERT: R 234 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7873 (tm-30) REVERT: R 270 GLN cc_start: 0.7914 (tp40) cc_final: 0.7535 (tp40) REVERT: S 229 ARG cc_start: 0.7440 (tpp80) cc_final: 0.7050 (ttp-110) REVERT: S 234 GLN cc_start: 0.8108 (tt0) cc_final: 0.7649 (tm-30) REVERT: S 270 GLN cc_start: 0.7937 (tp40) cc_final: 0.7207 (tm-30) REVERT: T 45 VAL cc_start: 0.8505 (m) cc_final: 0.8133 (m) REVERT: T 144 MET cc_start: 0.6497 (ptm) cc_final: 0.6130 (ptm) REVERT: T 187 MET cc_start: 0.9307 (mmm) cc_final: 0.9049 (mmm) REVERT: T 245 MET cc_start: 0.8143 (tpp) cc_final: 0.7770 (tpp) outliers start: 0 outliers final: 0 residues processed: 844 average time/residue: 0.5336 time to fit residues: 730.1639 Evaluate side-chains 584 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 4.921 ------------------------------------------------------------------------------- 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: 8.9990 chunk 452 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 503 optimal weight: 0.8980 chunk 417 optimal weight: 0.9990 chunk 232 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7924 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42580 Z= 0.160 Angle : 0.509 6.137 57820 Z= 0.262 Chirality : 0.038 0.162 6740 Planarity : 0.004 0.052 7180 Dihedral : 3.853 17.199 5700 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 2.34 (0.12), residues: 5260 helix: 2.54 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.53 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 272 HIS 0.005 0.000 HIS S 224 PHE 0.020 0.001 PHE L 232 TYR 0.010 0.001 TYR S 129 ARG 0.004 0.000 ARG G 153 *********************** 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 851 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 4.240 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9252 (mmm) cc_final: 0.9045 (mmm) REVERT: B 32 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 51 TYR cc_start: 0.9113 (t80) cc_final: 0.8886 (t80) REVERT: D 45 VAL cc_start: 0.8684 (m) cc_final: 0.8101 (p) REVERT: D 145 PHE cc_start: 0.7153 (m-80) cc_final: 0.6643 (m-80) REVERT: D 154 GLU cc_start: 0.7771 (pp20) cc_final: 0.7488 (pp20) REVERT: D 234 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 154 GLU cc_start: 0.7606 (pp20) cc_final: 0.7224 (pp20) REVERT: E 208 LYS cc_start: 0.8290 (tppt) cc_final: 0.8038 (tmmt) REVERT: E 263 HIS cc_start: 0.7336 (m90) cc_final: 0.6946 (m90) REVERT: F 45 VAL cc_start: 0.8199 (m) cc_final: 0.7551 (p) REVERT: G 117 THR cc_start: 0.8876 (t) cc_final: 0.8553 (m) REVERT: G 187 MET cc_start: 0.9299 (mmp) cc_final: 0.9034 (mmp) REVERT: H 51 TYR cc_start: 0.9284 (t80) cc_final: 0.9004 (t80) REVERT: H 208 LYS cc_start: 0.8485 (tppt) cc_final: 0.8164 (tmmt) REVERT: I 45 VAL cc_start: 0.8640 (m) cc_final: 0.8012 (p) REVERT: J 154 GLU cc_start: 0.7642 (pp20) cc_final: 0.7287 (pp20) REVERT: J 208 LYS cc_start: 0.8278 (tppt) cc_final: 0.8046 (tmmt) REVERT: J 244 MET cc_start: 0.7871 (tpp) cc_final: 0.7592 (tpp) REVERT: J 263 HIS cc_start: 0.7269 (m90) cc_final: 0.6766 (m90) REVERT: K 129 TYR cc_start: 0.9263 (t80) cc_final: 0.8971 (t80) REVERT: K 174 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8000 (ttp-170) REVERT: K 187 MET cc_start: 0.9449 (mmp) cc_final: 0.9128 (mmm) REVERT: K 229 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6991 (ttp-110) REVERT: K 270 GLN cc_start: 0.7739 (tp40) cc_final: 0.7119 (tm-30) REVERT: L 45 VAL cc_start: 0.8701 (m) cc_final: 0.8389 (p) REVERT: L 117 THR cc_start: 0.8805 (t) cc_final: 0.8378 (m) REVERT: L 270 GLN cc_start: 0.7320 (tp40) cc_final: 0.6608 (tm-30) REVERT: M 45 VAL cc_start: 0.8684 (m) cc_final: 0.8307 (p) REVERT: M 154 GLU cc_start: 0.7764 (pp20) cc_final: 0.7534 (pp20) REVERT: N 234 GLN cc_start: 0.8039 (tt0) cc_final: 0.7728 (tm-30) REVERT: N 263 HIS cc_start: 0.7367 (m90) cc_final: 0.7105 (m90) REVERT: O 45 VAL cc_start: 0.8417 (m) cc_final: 0.7676 (p) REVERT: O 144 MET cc_start: 0.6492 (ptm) cc_final: 0.6156 (ptm) REVERT: O 154 GLU cc_start: 0.7702 (pp20) cc_final: 0.7328 (pp20) REVERT: O 187 MET cc_start: 0.9207 (mmm) cc_final: 0.8761 (mmm) REVERT: P 129 TYR cc_start: 0.9275 (t80) cc_final: 0.8958 (t80) REVERT: P 174 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8016 (ttp-170) REVERT: P 187 MET cc_start: 0.9428 (mmp) cc_final: 0.9115 (mmm) REVERT: P 229 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7074 (ttp-110) REVERT: P 270 GLN cc_start: 0.7734 (tp40) cc_final: 0.7141 (tm-30) REVERT: Q 45 VAL cc_start: 0.8618 (m) cc_final: 0.8365 (p) REVERT: Q 117 THR cc_start: 0.8810 (t) cc_final: 0.8439 (m) REVERT: Q 154 GLU cc_start: 0.7787 (pp20) cc_final: 0.7505 (pp20) REVERT: Q 174 ARG cc_start: 0.8779 (tmm-80) cc_final: 0.8164 (ttp-170) REVERT: R 45 VAL cc_start: 0.8651 (m) cc_final: 0.8265 (p) REVERT: R 234 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7744 (tm-30) REVERT: S 234 GLN cc_start: 0.8117 (tt0) cc_final: 0.7636 (tm-30) REVERT: S 270 GLN cc_start: 0.7935 (tp40) cc_final: 0.7205 (tm-30) REVERT: T 45 VAL cc_start: 0.8445 (m) cc_final: 0.8129 (m) REVERT: T 144 MET cc_start: 0.6532 (ptm) cc_final: 0.6204 (ptm) REVERT: T 187 MET cc_start: 0.9201 (mmm) cc_final: 0.8987 (mmm) REVERT: T 245 MET cc_start: 0.8125 (tpp) cc_final: 0.7852 (tpp) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.5328 time to fit residues: 735.3578 Evaluate side-chains 605 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 4.915 ------------------------------------------------------------------------------- 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: 0.8980 chunk 56 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 423 optimal weight: 1.9990 chunk 280 optimal weight: 0.8980 chunk 501 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN C 44 GLN S 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 42580 Z= 0.159 Angle : 0.510 6.468 57820 Z= 0.263 Chirality : 0.038 0.166 6740 Planarity : 0.004 0.056 7180 Dihedral : 3.834 17.727 5700 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.12), residues: 5260 helix: 2.61 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.44 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 272 HIS 0.003 0.000 HIS S 224 PHE 0.021 0.001 PHE T 232 TYR 0.010 0.001 TYR S 129 ARG 0.010 0.000 ARG B 153 *********************** 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 861 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 861 time to evaluate : 4.583 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7955 (pp20) cc_final: 0.7705 (pp20) REVERT: A 187 MET cc_start: 0.9245 (mmm) cc_final: 0.9020 (mmm) REVERT: B 51 TYR cc_start: 0.9132 (t80) cc_final: 0.8922 (t80) REVERT: B 144 MET cc_start: 0.4145 (ptt) cc_final: 0.3802 (ttp) REVERT: B 208 LYS cc_start: 0.8454 (tppt) cc_final: 0.8081 (tptp) REVERT: B 262 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7605 (mttm) REVERT: B 265 ARG cc_start: 0.6942 (ttt90) cc_final: 0.6708 (tmm-80) REVERT: C 233 GLU cc_start: 0.8364 (tp30) cc_final: 0.8156 (tp30) REVERT: D 13 GLN cc_start: 0.7415 (tp40) cc_final: 0.7182 (tp-100) REVERT: D 45 VAL cc_start: 0.8439 (m) cc_final: 0.8021 (p) REVERT: D 145 PHE cc_start: 0.7442 (m-80) cc_final: 0.6808 (m-80) REVERT: E 208 LYS cc_start: 0.8398 (tppt) cc_final: 0.8120 (tmmt) REVERT: E 263 HIS cc_start: 0.7397 (m90) cc_final: 0.6943 (m90) REVERT: F 45 VAL cc_start: 0.8247 (m) cc_final: 0.7532 (p) REVERT: F 144 MET cc_start: 0.6153 (ptm) cc_final: 0.5945 (ptm) REVERT: G 187 MET cc_start: 0.9363 (mmp) cc_final: 0.9084 (mmp) REVERT: H 51 TYR cc_start: 0.9184 (t80) cc_final: 0.8897 (t80) REVERT: H 208 LYS cc_start: 0.8493 (tppt) cc_final: 0.8089 (tmmt) REVERT: H 233 GLU cc_start: 0.8432 (tp30) cc_final: 0.8121 (tp30) REVERT: I 45 VAL cc_start: 0.8628 (m) cc_final: 0.8202 (p) REVERT: I 154 GLU cc_start: 0.7712 (pp20) cc_final: 0.7488 (pp20) REVERT: J 208 LYS cc_start: 0.8388 (tppt) cc_final: 0.8125 (tmmt) REVERT: J 244 MET cc_start: 0.7816 (tpp) cc_final: 0.7595 (tpp) REVERT: J 263 HIS cc_start: 0.7294 (m90) cc_final: 0.6783 (m90) REVERT: K 129 TYR cc_start: 0.9266 (t80) cc_final: 0.8975 (t80) REVERT: K 174 ARG cc_start: 0.8557 (tmm-80) cc_final: 0.8005 (ttp-170) REVERT: K 187 MET cc_start: 0.9442 (mmp) cc_final: 0.9142 (mmm) REVERT: K 208 LYS cc_start: 0.8315 (tppt) cc_final: 0.7817 (tptp) REVERT: K 229 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6910 (ttp-110) REVERT: L 45 VAL cc_start: 0.8615 (m) cc_final: 0.8408 (p) REVERT: L 117 THR cc_start: 0.8784 (t) cc_final: 0.8411 (m) REVERT: L 154 GLU cc_start: 0.7593 (pp20) cc_final: 0.7246 (pp20) REVERT: L 270 GLN cc_start: 0.7361 (tp40) cc_final: 0.6664 (tm-30) REVERT: M 45 VAL cc_start: 0.8587 (m) cc_final: 0.8231 (p) REVERT: M 154 GLU cc_start: 0.7897 (pp20) cc_final: 0.7660 (pp20) REVERT: N 263 HIS cc_start: 0.7401 (m90) cc_final: 0.7132 (m90) REVERT: N 265 ARG cc_start: 0.6861 (ttt-90) cc_final: 0.6523 (tmm-80) REVERT: O 45 VAL cc_start: 0.8307 (m) cc_final: 0.7678 (p) REVERT: O 144 MET cc_start: 0.6487 (ptm) cc_final: 0.6131 (ptm) REVERT: O 154 GLU cc_start: 0.7684 (pp20) cc_final: 0.7356 (pp20) REVERT: O 187 MET cc_start: 0.9258 (mmm) cc_final: 0.8838 (mmm) REVERT: O 245 MET cc_start: 0.8577 (tpp) cc_final: 0.8067 (tpp) REVERT: P 129 TYR cc_start: 0.9283 (t80) cc_final: 0.8995 (t80) REVERT: P 174 ARG cc_start: 0.8556 (tmm-80) cc_final: 0.8019 (ttp-170) REVERT: P 187 MET cc_start: 0.9409 (mmp) cc_final: 0.9105 (mmm) REVERT: P 208 LYS cc_start: 0.8274 (tppt) cc_final: 0.7771 (tptp) REVERT: P 229 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7026 (ttp-110) REVERT: Q 117 THR cc_start: 0.8785 (t) cc_final: 0.8422 (m) REVERT: Q 154 GLU cc_start: 0.7607 (pp20) cc_final: 0.7327 (pp20) REVERT: Q 174 ARG cc_start: 0.8755 (tmm-80) cc_final: 0.8141 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7284 (tp40) cc_final: 0.6555 (tm-30) REVERT: R 45 VAL cc_start: 0.8635 (m) cc_final: 0.8236 (p) REVERT: R 51 TYR cc_start: 0.9229 (t80) cc_final: 0.8999 (t80) REVERT: R 154 GLU cc_start: 0.7631 (pp20) cc_final: 0.7426 (pp20) REVERT: R 238 GLN cc_start: 0.7745 (tt0) cc_final: 0.7284 (tp40) REVERT: R 270 GLN cc_start: 0.7906 (tp40) cc_final: 0.7574 (tp40) REVERT: S 234 GLN cc_start: 0.8085 (tt0) cc_final: 0.7577 (tm-30) REVERT: S 270 GLN cc_start: 0.7832 (tp40) cc_final: 0.7274 (tm-30) REVERT: T 45 VAL cc_start: 0.8431 (m) cc_final: 0.7747 (p) REVERT: T 144 MET cc_start: 0.6507 (ptm) cc_final: 0.6159 (ptm) REVERT: T 154 GLU cc_start: 0.7624 (pp20) cc_final: 0.7250 (pp20) REVERT: T 187 MET cc_start: 0.9235 (mmm) cc_final: 0.8860 (mmm) outliers start: 0 outliers final: 0 residues processed: 861 average time/residue: 0.5291 time to fit residues: 741.6017 Evaluate side-chains 582 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 4.650 ------------------------------------------------------------------------------- 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: 2.9990 chunk 200 optimal weight: 0.9980 chunk 299 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 318 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 393 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42580 Z= 0.177 Angle : 0.528 7.863 57820 Z= 0.270 Chirality : 0.039 0.147 6740 Planarity : 0.004 0.051 7180 Dihedral : 3.844 17.333 5700 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.49 (0.12), residues: 5260 helix: 2.64 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.45 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 272 HIS 0.005 0.001 HIS N 224 PHE 0.020 0.001 PHE T 232 TYR 0.018 0.001 TYR D 51 ARG 0.007 0.000 ARG A 265 *********************** 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 813 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 813 time to evaluate : 4.640 Fit side-chains revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8206 (mttm) REVERT: B 51 TYR cc_start: 0.9174 (t80) cc_final: 0.8966 (t80) REVERT: B 208 LYS cc_start: 0.8399 (tppt) cc_final: 0.8184 (tppt) REVERT: B 262 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7650 (mttm) REVERT: B 265 ARG cc_start: 0.7006 (ttt90) cc_final: 0.6804 (tmm-80) REVERT: C 208 LYS cc_start: 0.8460 (tppt) cc_final: 0.8200 (tmmt) REVERT: D 45 VAL cc_start: 0.8464 (m) cc_final: 0.8013 (p) REVERT: D 145 PHE cc_start: 0.7417 (m-80) cc_final: 0.6769 (m-80) REVERT: D 154 GLU cc_start: 0.7870 (pp20) cc_final: 0.7645 (pp20) REVERT: E 208 LYS cc_start: 0.8429 (tppt) cc_final: 0.8109 (tmmt) REVERT: E 263 HIS cc_start: 0.7400 (m90) cc_final: 0.6865 (m90) REVERT: F 45 VAL cc_start: 0.8150 (m) cc_final: 0.7548 (p) REVERT: F 144 MET cc_start: 0.6235 (ptm) cc_final: 0.5906 (ptm) REVERT: G 129 TYR cc_start: 0.9315 (t80) cc_final: 0.9038 (t80) REVERT: G 144 MET cc_start: 0.5137 (ptt) cc_final: 0.4928 (ttp) REVERT: G 187 MET cc_start: 0.9362 (mmp) cc_final: 0.9119 (mmp) REVERT: H 208 LYS cc_start: 0.8482 (tppt) cc_final: 0.8075 (tmmt) REVERT: H 234 GLN cc_start: 0.7912 (tt0) cc_final: 0.7601 (tt0) REVERT: I 45 VAL cc_start: 0.8509 (m) cc_final: 0.8042 (p) REVERT: I 154 GLU cc_start: 0.7774 (pp20) cc_final: 0.7547 (pp20) REVERT: I 245 MET cc_start: 0.8451 (tpp) cc_final: 0.8150 (tpp) REVERT: J 208 LYS cc_start: 0.8420 (tppt) cc_final: 0.8131 (tmmt) REVERT: J 244 MET cc_start: 0.7765 (tpp) cc_final: 0.7537 (tpp) REVERT: J 263 HIS cc_start: 0.7327 (m90) cc_final: 0.6732 (m90) REVERT: K 129 TYR cc_start: 0.9273 (t80) cc_final: 0.9003 (t80) REVERT: K 187 MET cc_start: 0.9415 (mmp) cc_final: 0.9142 (mmm) REVERT: K 229 ARG cc_start: 0.7325 (tpp80) cc_final: 0.6923 (ttp-110) REVERT: L 154 GLU cc_start: 0.7618 (pp20) cc_final: 0.7265 (pp20) REVERT: L 270 GLN cc_start: 0.7436 (tp40) cc_final: 0.6725 (tm-30) REVERT: M 45 VAL cc_start: 0.8478 (m) cc_final: 0.8127 (p) REVERT: M 154 GLU cc_start: 0.8006 (pp20) cc_final: 0.7795 (pp20) REVERT: N 263 HIS cc_start: 0.7474 (m90) cc_final: 0.7155 (m90) REVERT: O 45 VAL cc_start: 0.8322 (m) cc_final: 0.7664 (p) REVERT: O 154 GLU cc_start: 0.7720 (pp20) cc_final: 0.7325 (pp20) REVERT: O 187 MET cc_start: 0.9205 (mmm) cc_final: 0.8951 (mmm) REVERT: O 245 MET cc_start: 0.8395 (tpp) cc_final: 0.8191 (tpp) REVERT: P 129 TYR cc_start: 0.9289 (t80) cc_final: 0.9010 (t80) REVERT: P 187 MET cc_start: 0.9404 (mmp) cc_final: 0.9129 (mmm) REVERT: P 229 ARG cc_start: 0.7424 (tpp80) cc_final: 0.7025 (ttp-110) REVERT: Q 117 THR cc_start: 0.8798 (t) cc_final: 0.8419 (m) REVERT: Q 174 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8158 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7463 (tp40) cc_final: 0.6653 (tm-30) REVERT: R 45 VAL cc_start: 0.8567 (m) cc_final: 0.8199 (p) REVERT: R 51 TYR cc_start: 0.9248 (t80) cc_final: 0.9015 (t80) REVERT: R 154 GLU cc_start: 0.7671 (pp20) cc_final: 0.7464 (pp20) REVERT: R 238 GLN cc_start: 0.7656 (tt0) cc_final: 0.7293 (tp40) REVERT: R 270 GLN cc_start: 0.7932 (tp40) cc_final: 0.7664 (tp40) REVERT: S 234 GLN cc_start: 0.8112 (tt0) cc_final: 0.7504 (tm-30) REVERT: S 263 HIS cc_start: 0.7471 (m90) cc_final: 0.6815 (m90) REVERT: S 270 GLN cc_start: 0.7884 (tp40) cc_final: 0.7284 (tm-30) REVERT: T 45 VAL cc_start: 0.8350 (m) cc_final: 0.7748 (p) REVERT: T 154 GLU cc_start: 0.7612 (pp20) cc_final: 0.7251 (pp20) REVERT: T 187 MET cc_start: 0.9229 (mmm) cc_final: 0.8878 (mmm) REVERT: T 245 MET cc_start: 0.8615 (tpp) cc_final: 0.8352 (tpp) outliers start: 0 outliers final: 0 residues processed: 813 average time/residue: 0.5129 time to fit residues: 685.2274 Evaluate side-chains 585 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 4.571 ------------------------------------------------------------------------------- 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: 8.9990 chunk 480 optimal weight: 10.0000 chunk 438 optimal weight: 5.9990 chunk 467 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 366 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 422 optimal weight: 5.9990 chunk 441 optimal weight: 1.9990 chunk 465 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 ASN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42580 Z= 0.192 Angle : 0.542 7.575 57820 Z= 0.278 Chirality : 0.039 0.181 6740 Planarity : 0.004 0.050 7180 Dihedral : 3.850 17.293 5700 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 2.48 (0.12), residues: 5260 helix: 2.62 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.43 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 272 HIS 0.005 0.001 HIS D 224 PHE 0.024 0.001 PHE N 105 TYR 0.022 0.001 TYR D 51 ARG 0.009 0.000 ARG A 153 *********************** 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 796 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 796 time to evaluate : 4.673 Fit side-chains revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8239 (mttm) REVERT: B 187 MET cc_start: 0.9123 (mmp) cc_final: 0.8809 (mmp) REVERT: B 208 LYS cc_start: 0.8437 (tppt) cc_final: 0.8228 (tppt) REVERT: B 229 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7053 (ttp-110) REVERT: B 262 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7690 (mttm) REVERT: B 265 ARG cc_start: 0.7099 (ttt90) cc_final: 0.6846 (tmm-80) REVERT: C 208 LYS cc_start: 0.8501 (tppt) cc_final: 0.8152 (tmmt) REVERT: D 45 VAL cc_start: 0.8480 (m) cc_final: 0.8089 (p) REVERT: D 145 PHE cc_start: 0.7245 (m-80) cc_final: 0.6630 (m-80) REVERT: D 154 GLU cc_start: 0.7898 (pp20) cc_final: 0.7685 (pp20) REVERT: E 208 LYS cc_start: 0.8432 (tppt) cc_final: 0.8108 (tmmt) REVERT: E 263 HIS cc_start: 0.7518 (m90) cc_final: 0.7039 (m90) REVERT: F 45 VAL cc_start: 0.8163 (m) cc_final: 0.7532 (p) REVERT: G 117 THR cc_start: 0.8869 (t) cc_final: 0.8438 (m) REVERT: G 129 TYR cc_start: 0.9317 (t80) cc_final: 0.9036 (t80) REVERT: G 144 MET cc_start: 0.4975 (ptt) cc_final: 0.4322 (ttp) REVERT: G 187 MET cc_start: 0.9385 (mmp) cc_final: 0.9063 (mmp) REVERT: H 51 TYR cc_start: 0.9293 (t80) cc_final: 0.8966 (t80) REVERT: H 234 GLN cc_start: 0.7916 (tt0) cc_final: 0.7659 (tt0) REVERT: I 45 VAL cc_start: 0.8447 (m) cc_final: 0.8051 (p) REVERT: I 51 TYR cc_start: 0.9201 (t80) cc_final: 0.8870 (t80) REVERT: I 154 GLU cc_start: 0.7760 (pp20) cc_final: 0.7547 (pp20) REVERT: J 208 LYS cc_start: 0.8426 (tppt) cc_final: 0.8130 (tmmt) REVERT: J 244 MET cc_start: 0.7856 (tpp) cc_final: 0.7606 (tpp) REVERT: J 263 HIS cc_start: 0.7378 (m90) cc_final: 0.6737 (m90) REVERT: K 129 TYR cc_start: 0.9280 (t80) cc_final: 0.9011 (t80) REVERT: K 144 MET cc_start: 0.4783 (ptt) cc_final: 0.4165 (ttp) REVERT: K 187 MET cc_start: 0.9386 (mmp) cc_final: 0.9127 (mmm) REVERT: K 229 ARG cc_start: 0.7406 (tpp80) cc_final: 0.7071 (ttp-110) REVERT: L 270 GLN cc_start: 0.7364 (tp40) cc_final: 0.6698 (tm-30) REVERT: M 45 VAL cc_start: 0.8506 (m) cc_final: 0.8120 (p) REVERT: N 244 MET cc_start: 0.8020 (tpp) cc_final: 0.7819 (tpp) REVERT: N 263 HIS cc_start: 0.7430 (m90) cc_final: 0.6865 (m90) REVERT: O 45 VAL cc_start: 0.8249 (m) cc_final: 0.7671 (p) REVERT: O 187 MET cc_start: 0.9245 (mmm) cc_final: 0.8993 (mmm) REVERT: P 129 TYR cc_start: 0.9293 (t80) cc_final: 0.9023 (t80) REVERT: P 144 MET cc_start: 0.4774 (ptt) cc_final: 0.4148 (ttp) REVERT: P 187 MET cc_start: 0.9402 (mmp) cc_final: 0.9151 (mmm) REVERT: P 229 ARG cc_start: 0.7503 (tpp80) cc_final: 0.7110 (ttp-110) REVERT: Q 174 ARG cc_start: 0.8788 (tmm-80) cc_final: 0.8170 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7517 (tp40) cc_final: 0.6708 (tm-30) REVERT: R 45 VAL cc_start: 0.8524 (m) cc_final: 0.8078 (p) REVERT: R 51 TYR cc_start: 0.9249 (t80) cc_final: 0.9017 (t80) REVERT: R 154 GLU cc_start: 0.7723 (pp20) cc_final: 0.7491 (pp20) REVERT: R 234 GLN cc_start: 0.8089 (tt0) cc_final: 0.7723 (tm-30) REVERT: S 234 GLN cc_start: 0.8064 (tt0) cc_final: 0.7600 (tm-30) REVERT: T 45 VAL cc_start: 0.8366 (m) cc_final: 0.7726 (p) REVERT: T 154 GLU cc_start: 0.7518 (pp20) cc_final: 0.7260 (pp20) REVERT: T 187 MET cc_start: 0.9218 (mmm) cc_final: 0.8762 (mmm) outliers start: 0 outliers final: 0 residues processed: 796 average time/residue: 0.5090 time to fit residues: 670.7773 Evaluate side-chains 601 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 4.917 ------------------------------------------------------------------------------- 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: 0.5980 chunk 493 optimal weight: 0.1980 chunk 301 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 343 optimal weight: 0.0770 chunk 518 optimal weight: 0.5980 chunk 476 optimal weight: 2.9990 chunk 412 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 318 optimal weight: 0.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3658 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= 0.149 Angle : 0.531 8.275 57820 Z= 0.269 Chirality : 0.038 0.193 6740 Planarity : 0.004 0.048 7180 Dihedral : 3.848 17.152 5700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 2.63 (0.12), residues: 5260 helix: 2.72 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 272 HIS 0.007 0.000 HIS M 218 PHE 0.021 0.001 PHE O 232 TYR 0.015 0.001 TYR D 51 ARG 0.008 0.000 ARG B 153 ********************** 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 800 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 800 time to evaluate : 5.097 Fit side-chains revert: symmetry clash REVERT: B 182 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7184 (ttm-80) REVERT: B 187 MET cc_start: 0.8916 (mmp) cc_final: 0.8483 (mmp) REVERT: B 229 ARG cc_start: 0.7618 (tpp80) cc_final: 0.6908 (ttp-110) REVERT: B 265 ARG cc_start: 0.7056 (ttt90) cc_final: 0.6820 (tmm-80) REVERT: C 208 LYS cc_start: 0.8453 (tppt) cc_final: 0.8140 (tmmt) REVERT: C 233 GLU cc_start: 0.8399 (tp30) cc_final: 0.8164 (tp30) REVERT: E 208 LYS cc_start: 0.8419 (tppt) cc_final: 0.8097 (tmmt) REVERT: E 263 HIS cc_start: 0.7354 (m90) cc_final: 0.6605 (m90) REVERT: F 45 VAL cc_start: 0.8248 (m) cc_final: 0.8035 (p) REVERT: G 129 TYR cc_start: 0.9297 (t80) cc_final: 0.9062 (t80) REVERT: G 144 MET cc_start: 0.4839 (ptt) cc_final: 0.4194 (ttp) REVERT: G 187 MET cc_start: 0.9339 (mmp) cc_final: 0.9033 (mmp) REVERT: H 51 TYR cc_start: 0.9194 (t80) cc_final: 0.8837 (t80) REVERT: H 208 LYS cc_start: 0.8455 (tppt) cc_final: 0.8184 (tmmt) REVERT: H 233 GLU cc_start: 0.8468 (tp30) cc_final: 0.8112 (tp30) REVERT: I 45 VAL cc_start: 0.8430 (m) cc_final: 0.8066 (p) REVERT: I 245 MET cc_start: 0.8337 (tpp) cc_final: 0.8106 (tpp) REVERT: J 208 LYS cc_start: 0.8410 (tppt) cc_final: 0.8113 (tmmt) REVERT: J 244 MET cc_start: 0.7738 (tpp) cc_final: 0.7518 (tpp) REVERT: J 263 HIS cc_start: 0.7278 (m90) cc_final: 0.6415 (m90) REVERT: K 129 TYR cc_start: 0.9248 (t80) cc_final: 0.9011 (t80) REVERT: K 144 MET cc_start: 0.4885 (ptt) cc_final: 0.4237 (ttp) REVERT: K 229 ARG cc_start: 0.7439 (tpp80) cc_final: 0.7077 (ttp-110) REVERT: L 117 THR cc_start: 0.8748 (t) cc_final: 0.8356 (m) REVERT: L 234 GLN cc_start: 0.7936 (tt0) cc_final: 0.7717 (tt0) REVERT: M 238 GLN cc_start: 0.7724 (tt0) cc_final: 0.7511 (tp40) REVERT: M 270 GLN cc_start: 0.7887 (tp40) cc_final: 0.7549 (tm-30) REVERT: N 45 VAL cc_start: 0.8534 (m) cc_final: 0.8035 (p) REVERT: N 47 LYS cc_start: 0.7849 (mttp) cc_final: 0.7583 (mttp) REVERT: N 263 HIS cc_start: 0.7381 (m90) cc_final: 0.6780 (m90) REVERT: O 187 MET cc_start: 0.9223 (mmm) cc_final: 0.8835 (mmm) REVERT: O 245 MET cc_start: 0.8316 (tpp) cc_final: 0.8074 (tpp) REVERT: P 129 TYR cc_start: 0.9268 (t80) cc_final: 0.9030 (t80) REVERT: P 144 MET cc_start: 0.4870 (ptt) cc_final: 0.4237 (ttp) REVERT: P 187 MET cc_start: 0.9387 (mmp) cc_final: 0.9109 (mmm) REVERT: P 229 ARG cc_start: 0.7373 (tpp80) cc_final: 0.7032 (ttp-110) REVERT: Q 117 THR cc_start: 0.8747 (t) cc_final: 0.8401 (m) REVERT: Q 174 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8150 (ttp-170) REVERT: Q 270 GLN cc_start: 0.7321 (tp40) cc_final: 0.6769 (tm-30) REVERT: R 45 VAL cc_start: 0.8525 (m) cc_final: 0.8218 (p) REVERT: R 51 TYR cc_start: 0.9204 (t80) cc_final: 0.8967 (t80) REVERT: R 154 GLU cc_start: 0.7716 (pp20) cc_final: 0.7479 (pp20) REVERT: S 263 HIS cc_start: 0.7462 (m90) cc_final: 0.6724 (m90) REVERT: T 187 MET cc_start: 0.9188 (mmm) cc_final: 0.8815 (mmm) outliers start: 0 outliers final: 0 residues processed: 800 average time/residue: 0.5738 time to fit residues: 763.5354 Evaluate side-chains 588 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 4.741 ------------------------------------------------------------------------------- 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: 7.9990 chunk 439 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 380 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 413 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 424 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127405 restraints weight = 57235.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128036 restraints weight = 45962.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128746 restraints weight = 39478.862| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 42580 Z= 0.172 Angle : 0.535 8.701 57820 Z= 0.273 Chirality : 0.039 0.143 6740 Planarity : 0.004 0.049 7180 Dihedral : 3.805 17.066 5700 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 2.63 (0.12), residues: 5260 helix: 2.72 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 272 HIS 0.004 0.001 HIS M 224 PHE 0.020 0.001 PHE L 145 TYR 0.018 0.001 TYR B 51 ARG 0.007 0.000 ARG B 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11235.08 seconds wall clock time: 203 minutes 48.27 seconds (12228.27 seconds total)