Starting phenix.real_space_refine on Fri May 17 07:52:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rjl_19251/05_2024/8rjl_19251.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 144 5.16 5 C 23388 2.51 5 N 6207 2.21 5 O 6561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 355": "OE1" <-> "OE2" Residue "G ARG 369": "NH1" <-> "NH2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H GLU 67": "OE1" <-> "OE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 167": "OE1" <-> "OE2" Residue "I ARG 168": "NH1" <-> "NH2" Residue "I ARG 176": "NH1" <-> "NH2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K ARG 112": "NH1" <-> "NH2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K GLU 351": "OE1" <-> "OE2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 113": "NH1" <-> "NH2" Residue "M GLU 167": "OE1" <-> "OE2" Residue "M ARG 168": "NH1" <-> "NH2" Residue "M ARG 324": "NH1" <-> "NH2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O GLU 69": "OE1" <-> "OE2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 355": "OE1" <-> "OE2" Residue "O ARG 369": "NH1" <-> "NH2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q GLU 12": "OE1" <-> "OE2" Residue "Q GLU 67": "OE1" <-> "OE2" Residue "Q PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 119": "OE1" <-> "OE2" Residue "Q GLU 154": "OE1" <-> "OE2" Residue "Q ARG 369": "NH1" <-> "NH2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "L PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 351": "OE1" <-> "OE2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N ARG 168": "NH1" <-> "NH2" Residue "N ARG 324": "NH1" <-> "NH2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P GLU 49": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 112": "NH1" <-> "NH2" Residue "P PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 355": "OE1" <-> "OE2" Residue "P ARG 369": "NH1" <-> "NH2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "R PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 119": "OE1" <-> "OE2" Residue "R GLU 154": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 36300 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1729 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1740 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2167 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2156 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2146 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2162 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 255} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 17.34, per 1000 atoms: 0.48 Number of scatterers: 36300 At special positions: 0 Unit cell: (207.77, 214.09, 107.44, 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 144 16.00 O 6561 8.00 N 6207 7.00 C 23388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.68 Conformation dependent library (CDL) restraints added in 6.3 seconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8706 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 18 sheets defined 63.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 61 through 72 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 94 through 110 removed outlier: 4.321A pdb=" N ALA A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 185 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 206 through 219 removed outlier: 3.833A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 4.340A pdb=" N TYR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.109A pdb=" N ALA A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.930A pdb=" N TYR B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Proline residue: B 133 - end of helix removed outlier: 3.622A pdb=" N VAL B 136 " --> pdb=" O ILE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 206 through 219 removed outlier: 3.564A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 4.198A pdb=" N TYR B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 352 removed outlier: 3.502A pdb=" N VAL B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 4.097A pdb=" N ARG C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.771A pdb=" N ALA C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 131 removed outlier: 3.721A pdb=" N VAL C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 185 " --> pdb=" O CYS C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 202 Processing helix chain 'C' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 219 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.715A pdb=" N LEU C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 327 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 352 removed outlier: 4.062A pdb=" N VAL C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 340 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 46 through 57 removed outlier: 3.852A pdb=" N THR D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.984A pdb=" N LEU D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.748A pdb=" N ALA D 98 " --> pdb=" O HIS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 131 through 145 removed outlier: 4.089A pdb=" N MET D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 191 through 202 Processing helix chain 'D' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 327 removed outlier: 3.508A pdb=" N VAL D 322 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU D 326 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 352 removed outlier: 3.795A pdb=" N PHE D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 340 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA D 343 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 122 through 145 Proline residue: G 133 - end of helix removed outlier: 4.652A pdb=" N PHE G 139 " --> pdb=" O MET G 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN G 140 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.814A pdb=" N ALA G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 202 Processing helix chain 'G' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL G 210 " --> pdb=" O ASP G 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA G 219 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER G 319 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU G 321 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 342 removed outlier: 3.601A pdb=" N ALA G 340 " --> pdb=" O VAL G 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 341 " --> pdb=" O PHE G 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA G 347 " --> pdb=" O ALA G 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP G 349 " --> pdb=" O TRP G 345 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN H 44 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 57 Processing helix chain 'H' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 removed outlier: 3.983A pdb=" N ARG H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 110 removed outlier: 3.542A pdb=" N ALA H 98 " --> pdb=" O HIS H 94 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 143 removed outlier: 4.230A pdb=" N ALA H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL H 125 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL H 126 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Proline residue: H 133 - end of helix Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 201 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 206 through 219 removed outlier: 3.889A pdb=" N VAL H 210 " --> pdb=" O ASP H 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 219 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 326 removed outlier: 4.109A pdb=" N LEU H 326 " --> pdb=" O VAL H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 341 removed outlier: 3.776A pdb=" N VAL H 336 " --> pdb=" O LEU H 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE H 337 " --> pdb=" O PHE H 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA H 338 " --> pdb=" O THR H 334 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE H 339 " --> pdb=" O PRO H 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA H 340 " --> pdb=" O VAL H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 352 removed outlier: 3.747A pdb=" N TRP H 345 " --> pdb=" O ARG H 341 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 346 " --> pdb=" O VAL H 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU H 351 " --> pdb=" O ALA H 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 94 through 110 removed outlier: 4.322A pdb=" N ALA E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL E 126 " --> pdb=" O ARG E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 139 " --> pdb=" O MET E 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE E 177 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 185 " --> pdb=" O CYS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.834A pdb=" N VAL E 210 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA E 219 " --> pdb=" O VAL E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 removed outlier: 4.339A pdb=" N TYR E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU E 332 " --> pdb=" O PRO E 329 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 333 " --> pdb=" O SER E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 334 through 351 removed outlier: 4.110A pdb=" N ALA E 340 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA E 343 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU I 71 " --> pdb=" O GLU I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 86 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 94 through 110 removed outlier: 3.930A pdb=" N TYR I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 123 Processing helix chain 'I' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) Proline residue: I 133 - end of helix removed outlier: 3.622A pdb=" N VAL I 136 " --> pdb=" O ILE I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 142 No H-bonds generated for 'chain 'I' and resid 140 through 142' Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 171 through 185 Processing helix chain 'I' and resid 192 through 202 Processing helix chain 'I' and resid 206 through 219 removed outlier: 3.564A pdb=" N VAL I 210 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA I 219 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 327 removed outlier: 4.197A pdb=" N TYR I 318 " --> pdb=" O ASN I 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU I 321 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 352 removed outlier: 3.502A pdb=" N VAL I 336 " --> pdb=" O LEU I 332 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA I 338 " --> pdb=" O THR I 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA I 340 " --> pdb=" O VAL I 336 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA I 343 " --> pdb=" O ILE I 339 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLY I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP I 345 " --> pdb=" O ARG I 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU I 351 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN I 352 " --> pdb=" O HIS I 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU K 65 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 88 removed outlier: 4.097A pdb=" N ARG K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 removed outlier: 3.771A pdb=" N ALA K 98 " --> pdb=" O HIS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.720A pdb=" N VAL K 126 " --> pdb=" O ARG K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS K 144 " --> pdb=" O GLN K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 167 Processing helix chain 'K' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS K 185 " --> pdb=" O CYS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 202 Processing helix chain 'K' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL K 210 " --> pdb=" O ASP K 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA K 219 " --> pdb=" O VAL K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 327 removed outlier: 4.716A pdb=" N LEU K 321 " --> pdb=" O PHE K 317 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU K 326 " --> pdb=" O VAL K 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY K 327 " --> pdb=" O TYR K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 352 removed outlier: 4.061A pdb=" N VAL K 336 " --> pdb=" O LEU K 332 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 337 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 340 " --> pdb=" O VAL K 336 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG K 341 " --> pdb=" O PHE K 337 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA K 343 " --> pdb=" O ILE K 339 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY K 344 " --> pdb=" O ALA K 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP K 345 " --> pdb=" O ARG K 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.852A pdb=" N THR M 50 " --> pdb=" O SER M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 removed outlier: 3.984A pdb=" N LEU M 65 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG M 83 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS M 87 " --> pdb=" O ARG M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 106 removed outlier: 3.747A pdb=" N ALA M 98 " --> pdb=" O HIS M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 131 Processing helix chain 'M' and resid 131 through 145 removed outlier: 4.088A pdb=" N MET M 135 " --> pdb=" O LYS M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 167 Processing helix chain 'M' and resid 171 through 184 Processing helix chain 'M' and resid 191 through 202 Processing helix chain 'M' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL M 210 " --> pdb=" O ASP M 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA M 212 " --> pdb=" O TYR M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 327 removed outlier: 3.507A pdb=" N VAL M 322 " --> pdb=" O TYR M 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU M 326 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY M 327 " --> pdb=" O TYR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 352 removed outlier: 3.796A pdb=" N PHE M 337 " --> pdb=" O PHE M 333 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA M 340 " --> pdb=" O VAL M 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA M 343 " --> pdb=" O ILE M 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY M 344 " --> pdb=" O ALA M 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA M 347 " --> pdb=" O ALA M 343 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS M 348 " --> pdb=" O GLY M 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 350 " --> pdb=" O LEU M 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR O 50 " --> pdb=" O SER O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 94 through 104 Processing helix chain 'O' and resid 122 through 145 Proline residue: O 133 - end of helix removed outlier: 4.653A pdb=" N PHE O 139 " --> pdb=" O MET O 135 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS O 144 " --> pdb=" O GLN O 140 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY O 145 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU O 165 " --> pdb=" O PHE O 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 184 removed outlier: 3.814A pdb=" N ALA O 175 " --> pdb=" O ASP O 171 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 202 Processing helix chain 'O' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL O 210 " --> pdb=" O ASP O 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA O 219 " --> pdb=" O VAL O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER O 319 " --> pdb=" O VAL O 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU O 321 " --> pdb=" O PHE O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 342 removed outlier: 3.600A pdb=" N ALA O 340 " --> pdb=" O VAL O 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG O 341 " --> pdb=" O PHE O 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL O 342 " --> pdb=" O ALA O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA O 347 " --> pdb=" O ALA O 343 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP O 349 " --> pdb=" O TRP O 345 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU O 351 " --> pdb=" O ALA O 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.748A pdb=" N LEU Q 11 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU Q 12 " --> pdb=" O PRO Q 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 8 through 12' Processing helix chain 'Q' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU Q 41 " --> pdb=" O SER Q 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU Q 65 " --> pdb=" O THR Q 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 87 removed outlier: 3.829A pdb=" N ARG Q 83 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 110 removed outlier: 3.543A pdb=" N ALA Q 98 " --> pdb=" O HIS Q 94 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR Q 110 " --> pdb=" O LEU Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 143 removed outlier: 4.231A pdb=" N ALA Q 124 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL Q 125 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL Q 126 " --> pdb=" O ARG Q 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE Q 132 " --> pdb=" O LEU Q 128 " (cutoff:3.500A) Proline residue: Q 133 - end of helix Processing helix chain 'Q' and resid 156 through 167 Processing helix chain 'Q' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA Q 175 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 201 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 206 through 219 removed outlier: 3.806A pdb=" N VAL Q 210 " --> pdb=" O ASP Q 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA Q 219 " --> pdb=" O VAL Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 326 removed outlier: 4.109A pdb=" N LEU Q 326 " --> pdb=" O VAL Q 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 332 through 341 removed outlier: 3.775A pdb=" N VAL Q 336 " --> pdb=" O LEU Q 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE Q 337 " --> pdb=" O PHE Q 333 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA Q 338 " --> pdb=" O THR Q 334 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE Q 339 " --> pdb=" O PRO Q 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA Q 340 " --> pdb=" O VAL Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 352 removed outlier: 3.748A pdb=" N TRP Q 345 " --> pdb=" O ARG Q 341 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU Q 346 " --> pdb=" O VAL Q 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU Q 351 " --> pdb=" O ALA Q 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 61 through 72 Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 94 through 110 removed outlier: 4.321A pdb=" N ALA F 98 " --> pdb=" O HIS F 94 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 4.142A pdb=" N VAL F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 145 removed outlier: 3.549A pdb=" N MET F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE F 139 " --> pdb=" O MET F 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS F 144 " --> pdb=" O GLN F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 173 through 185 removed outlier: 3.902A pdb=" N ILE F 177 " --> pdb=" O VAL F 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 185 " --> pdb=" O CYS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 206 through 219 removed outlier: 3.834A pdb=" N VAL F 210 " --> pdb=" O ASP F 206 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA F 219 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 327 removed outlier: 4.339A pdb=" N TYR F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.728A pdb=" N LEU F 332 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE F 333 " --> pdb=" O SER F 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 333' Processing helix chain 'F' and resid 334 through 351 removed outlier: 4.109A pdb=" N ALA F 340 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 343 " --> pdb=" O ILE F 339 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLY F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 350 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 44 removed outlier: 3.593A pdb=" N GLN J 44 " --> pdb=" O GLN J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 Processing helix chain 'J' and resid 64 through 75 removed outlier: 4.798A pdb=" N HIS J 70 " --> pdb=" O THR J 66 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU J 71 " --> pdb=" O GLU J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 86 Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'J' and resid 94 through 110 removed outlier: 3.929A pdb=" N TYR J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 123 Processing helix chain 'J' and resid 124 through 139 removed outlier: 3.615A pdb=" N LEU J 128 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU J 129 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Proline residue: J 133 - end of helix removed outlier: 3.622A pdb=" N VAL J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 171 through 185 Processing helix chain 'J' and resid 192 through 202 Processing helix chain 'J' and resid 206 through 219 removed outlier: 3.565A pdb=" N VAL J 210 " --> pdb=" O ASP J 206 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA J 219 " --> pdb=" O VAL J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 removed outlier: 4.198A pdb=" N TYR J 318 " --> pdb=" O ASN J 314 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU J 321 " --> pdb=" O PHE J 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 352 removed outlier: 3.501A pdb=" N VAL J 336 " --> pdb=" O LEU J 332 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA J 338 " --> pdb=" O THR J 334 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA J 340 " --> pdb=" O VAL J 336 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA J 343 " --> pdb=" O ILE J 339 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY J 344 " --> pdb=" O ALA J 340 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP J 345 " --> pdb=" O ARG J 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 350 " --> pdb=" O LEU J 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU J 351 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN J 352 " --> pdb=" O HIS J 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 43 Processing helix chain 'L' and resid 46 through 57 removed outlier: 3.516A pdb=" N LEU L 53 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 72 removed outlier: 3.711A pdb=" N LEU L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 88 removed outlier: 4.096A pdb=" N ARG L 83 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 104 removed outlier: 3.770A pdb=" N ALA L 98 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 131 removed outlier: 3.721A pdb=" N VAL L 126 " --> pdb=" O ARG L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 144 removed outlier: 4.529A pdb=" N LYS L 144 " --> pdb=" O GLN L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 167 Processing helix chain 'L' and resid 171 through 185 removed outlier: 3.598A pdb=" N ALA L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS L 185 " --> pdb=" O CYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 Processing helix chain 'L' and resid 206 through 219 removed outlier: 3.915A pdb=" N VAL L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 327 removed outlier: 4.716A pdb=" N LEU L 321 " --> pdb=" O PHE L 317 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU L 326 " --> pdb=" O VAL L 322 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY L 327 " --> pdb=" O TYR L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 352 removed outlier: 4.061A pdb=" N VAL L 336 " --> pdb=" O LEU L 332 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE L 337 " --> pdb=" O PHE L 333 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA L 340 " --> pdb=" O VAL L 336 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG L 341 " --> pdb=" O PHE L 337 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA L 343 " --> pdb=" O ILE L 339 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY L 344 " --> pdb=" O ALA L 340 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP L 345 " --> pdb=" O ARG L 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA L 347 " --> pdb=" O ALA L 343 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 42 Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.851A pdb=" N THR N 50 " --> pdb=" O SER N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 75 removed outlier: 3.983A pdb=" N LEU N 65 " --> pdb=" O THR N 61 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.885A pdb=" N ARG N 83 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 106 removed outlier: 3.747A pdb=" N ALA N 98 " --> pdb=" O HIS N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 131 Processing helix chain 'N' and resid 131 through 145 removed outlier: 4.089A pdb=" N MET N 135 " --> pdb=" O LYS N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 167 Processing helix chain 'N' and resid 171 through 184 Processing helix chain 'N' and resid 191 through 202 Processing helix chain 'N' and resid 206 through 215 removed outlier: 4.028A pdb=" N VAL N 210 " --> pdb=" O ASP N 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA N 212 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 327 removed outlier: 3.509A pdb=" N VAL N 322 " --> pdb=" O TYR N 318 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU N 326 " --> pdb=" O VAL N 322 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY N 327 " --> pdb=" O TYR N 323 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 352 removed outlier: 3.794A pdb=" N PHE N 337 " --> pdb=" O PHE N 333 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA N 340 " --> pdb=" O VAL N 336 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA N 343 " --> pdb=" O ILE N 339 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY N 344 " --> pdb=" O ALA N 340 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 347 " --> pdb=" O ALA N 343 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS N 348 " --> pdb=" O GLY N 344 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS N 350 " --> pdb=" O LEU N 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 57 removed outlier: 4.065A pdb=" N THR P 50 " --> pdb=" O SER P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 74 removed outlier: 3.557A pdb=" N LEU P 65 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 Processing helix chain 'P' and resid 94 through 104 Processing helix chain 'P' and resid 122 through 145 Proline residue: P 133 - end of helix removed outlier: 4.652A pdb=" N PHE P 139 " --> pdb=" O MET P 135 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS P 144 " --> pdb=" O GLN P 140 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY P 145 " --> pdb=" O LEU P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 167 removed outlier: 3.513A pdb=" N LEU P 165 " --> pdb=" O PHE P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 184 removed outlier: 3.813A pdb=" N ALA P 175 " --> pdb=" O ASP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 Processing helix chain 'P' and resid 206 through 219 removed outlier: 3.860A pdb=" N VAL P 210 " --> pdb=" O ASP P 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 326 removed outlier: 3.729A pdb=" N SER P 319 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU P 321 " --> pdb=" O PHE P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 342 removed outlier: 3.601A pdb=" N ALA P 340 " --> pdb=" O VAL P 336 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG P 341 " --> pdb=" O PHE P 337 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL P 342 " --> pdb=" O ALA P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 352 removed outlier: 3.551A pdb=" N ALA P 347 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP P 349 " --> pdb=" O TRP P 345 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU P 351 " --> pdb=" O ALA P 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 44 removed outlier: 3.751A pdb=" N LEU R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN R 44 " --> pdb=" O GLN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 57 Processing helix chain 'R' and resid 61 through 75 removed outlier: 3.871A pdb=" N LEU R 65 " --> pdb=" O THR R 61 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 87 removed outlier: 3.983A pdb=" N ARG R 83 " --> pdb=" O LYS R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 110 removed outlier: 3.543A pdb=" N ALA R 98 " --> pdb=" O HIS R 94 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 143 removed outlier: 4.230A pdb=" N ALA R 124 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Proline residue: R 133 - end of helix Processing helix chain 'R' and resid 156 through 167 Processing helix chain 'R' and resid 171 through 184 removed outlier: 3.649A pdb=" N ALA R 175 " --> pdb=" O ASP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 206 through 219 removed outlier: 3.810A pdb=" N VAL R 210 " --> pdb=" O ASP R 206 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 326 removed outlier: 4.110A pdb=" N LEU R 326 " --> pdb=" O VAL R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 341 removed outlier: 3.776A pdb=" N VAL R 336 " --> pdb=" O LEU R 332 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE R 337 " --> pdb=" O PHE R 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 338 " --> pdb=" O THR R 334 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 339 " --> pdb=" O PRO R 335 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA R 340 " --> pdb=" O VAL R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 352 removed outlier: 3.748A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU R 346 " --> pdb=" O VAL R 342 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU R 351 " --> pdb=" O ALA R 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AA3, first strand: chain 'C' and resid 360 through 364 removed outlier: 8.046A pdb=" N ARG C 360 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA D 16 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 362 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU D 18 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE C 364 " --> pdb=" O LEU D 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.501A pdb=" N PHE D 23 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA7, first strand: chain 'K' and resid 15 through 17 Processing sheet with id=AA8, first strand: chain 'K' and resid 22 through 25 Processing sheet with id=AA9, first strand: chain 'K' and resid 360 through 365 removed outlier: 8.045A pdb=" N ARG K 360 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ALA M 16 " --> pdb=" O ARG K 360 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR K 362 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU M 18 " --> pdb=" O THR K 362 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE K 364 " --> pdb=" O LEU M 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 22 through 23 removed outlier: 3.500A pdb=" N PHE M 23 " --> pdb=" O GLU M 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 22 through 25 Processing sheet with id=AB3, first strand: chain 'Q' and resid 22 through 24 Processing sheet with id=AB4, first strand: chain 'L' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'L' and resid 22 through 25 Processing sheet with id=AB6, first strand: chain 'L' and resid 360 through 365 removed outlier: 8.047A pdb=" N ARG L 360 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA N 16 " --> pdb=" O ARG L 360 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR L 362 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU N 18 " --> pdb=" O THR L 362 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE L 364 " --> pdb=" O LEU N 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.501A pdb=" N PHE N 23 " --> pdb=" O GLU N 32 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 22 through 25 Processing sheet with id=AB9, first strand: chain 'R' and resid 22 through 24 1578 hydrogen bonds defined for protein. 4698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 13.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5832 1.30 - 1.43: 10215 1.43 - 1.56: 20896 1.56 - 1.69: 0 1.69 - 1.82: 254 Bond restraints: 37197 Sorted by residual: bond pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 1.469 1.708 -0.239 1.28e-02 6.10e+03 3.49e+02 bond pdb=" N PRO O 15 " pdb=" CA PRO O 15 " ideal model delta sigma weight residual 1.469 1.705 -0.236 1.28e-02 6.10e+03 3.40e+02 bond pdb=" C ASN L 146 " pdb=" N ASP L 147 " ideal model delta sigma weight residual 1.331 1.242 0.089 1.59e-02 3.96e+03 3.16e+01 bond pdb=" C ASN C 146 " pdb=" N ASP C 147 " ideal model delta sigma weight residual 1.331 1.243 0.089 1.59e-02 3.96e+03 3.10e+01 bond pdb=" C ASN K 146 " pdb=" N ASP K 147 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.59e-02 3.96e+03 3.07e+01 ... (remaining 37192 not shown) Histogram of bond angle deviations from ideal: 96.08 - 104.51: 859 104.51 - 112.93: 19388 112.93 - 121.36: 22138 121.36 - 129.78: 7888 129.78 - 138.21: 274 Bond angle restraints: 50547 Sorted by residual: angle pdb=" C VAL O 14 " pdb=" N PRO O 15 " pdb=" CA PRO O 15 " ideal model delta sigma weight residual 119.84 138.21 -18.37 1.25e+00 6.40e-01 2.16e+02 angle pdb=" C VAL D 14 " pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 119.84 138.10 -18.26 1.25e+00 6.40e-01 2.13e+02 angle pdb=" CA PRO O 15 " pdb=" N PRO O 15 " pdb=" CD PRO O 15 " ideal model delta sigma weight residual 112.00 99.52 12.48 1.40e+00 5.10e-01 7.95e+01 angle pdb=" CA PRO D 15 " pdb=" N PRO D 15 " pdb=" CD PRO D 15 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" N TYR K 74 " pdb=" CA TYR K 74 " pdb=" C TYR K 74 " ideal model delta sigma weight residual 113.16 103.07 10.09 1.24e+00 6.50e-01 6.62e+01 ... (remaining 50542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 18849 16.84 - 33.68: 2499 33.68 - 50.52: 610 50.52 - 67.36: 155 67.36 - 84.20: 60 Dihedral angle restraints: 22173 sinusoidal: 8748 harmonic: 13425 Sorted by residual: dihedral pdb=" CA LYS J 79 " pdb=" C LYS J 79 " pdb=" N PHE J 80 " pdb=" CA PHE J 80 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA LYS B 79 " pdb=" C LYS B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LYS I 79 " pdb=" C LYS I 79 " pdb=" N PHE I 80 " pdb=" CA PHE I 80 " ideal model delta harmonic sigma weight residual -180.00 -147.49 -32.51 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 22170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4897 0.092 - 0.184: 664 0.184 - 0.275: 76 0.275 - 0.367: 25 0.367 - 0.459: 14 Chirality restraints: 5676 Sorted by residual: chirality pdb=" CA PRO O 15 " pdb=" N PRO O 15 " pdb=" C PRO O 15 " pdb=" CB PRO O 15 " both_signs ideal model delta sigma weight residual False 2.72 3.18 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA TYR Q 120 " pdb=" N TYR Q 120 " pdb=" C TYR Q 120 " pdb=" CB TYR Q 120 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CA TYR H 120 " pdb=" N TYR H 120 " pdb=" C TYR H 120 " pdb=" CB TYR H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 5673 not shown) Planarity restraints: 6465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 367 " -0.032 2.00e-02 2.50e+03 6.46e-02 4.17e+01 pdb=" C GLY P 367 " 0.112 2.00e-02 2.50e+03 pdb=" O GLY P 367 " -0.043 2.00e-02 2.50e+03 pdb=" N SER P 368 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 367 " 0.032 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C GLY G 367 " -0.112 2.00e-02 2.50e+03 pdb=" O GLY G 367 " 0.043 2.00e-02 2.50e+03 pdb=" N SER G 368 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 367 " -0.032 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C GLY O 367 " 0.111 2.00e-02 2.50e+03 pdb=" O GLY O 367 " -0.043 2.00e-02 2.50e+03 pdb=" N SER O 368 " -0.037 2.00e-02 2.50e+03 ... (remaining 6462 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 38 2.27 - 2.92: 16626 2.92 - 3.58: 44562 3.58 - 4.24: 66865 4.24 - 4.90: 111979 Nonbonded interactions: 240070 Sorted by model distance: nonbonded pdb=" O VAL B 322 " pdb=" CD1 LEU B 326 " model vdw 1.607 3.460 nonbonded pdb=" O VAL J 322 " pdb=" CD1 LEU J 326 " model vdw 1.607 3.460 nonbonded pdb=" O VAL I 322 " pdb=" CD1 LEU I 326 " model vdw 1.608 3.460 nonbonded pdb=" OH TYR C 365 " pdb=" O SER D 20 " model vdw 1.631 2.440 nonbonded pdb=" O PHE O 109 " pdb=" NH1 ARG O 112 " model vdw 2.034 2.520 ... (remaining 240065 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' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'B' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) selection = (chain 'E' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'F' and (resid 33 through 111 or resid 119 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 352)) selection = (chain 'I' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) selection = (chain 'J' and (resid 33 through 42 or resid 47 through 167 or (resid 168 and (n \ ame N or name CA or name C or name O or name CB )) or resid 169 through 175 or ( \ resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 \ through 352)) } ncs_group { reference = (chain 'C' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'D' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'G' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'H' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) selection = (chain 'K' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'L' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 371 or (resid 372 and (name N or name CA or name C or name O \ or name CB )) or resid 373 through 375)) selection = (chain 'M' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'N' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 112 or resid 119 throu \ gh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 219 or resid 314 through 324 or (resid 325 and (name N or nam \ e CA or name C or name O or name CB )) or resid 326 through 375)) selection = (chain 'O' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'P' and (resid 9 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 219 or resid 314 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) \ or resid 326 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 375)) selection = (chain 'Q' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) selection = (chain 'R' and (resid 9 through 39 or (resid 40 and (name N or name CA or name C \ or name O or name CB )) or resid 41 through 112 or resid 119 through 167 or (re \ sid 168 and (name N or name CA or name C or name O or name CB )) or resid 169 th \ rough 219 or resid 314 through 371 or (resid 372 and (name N or name CA or name \ C or name O or name CB )) or resid 373 through 375)) } 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.280 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: 0.050 Extract box with map and model: 28.020 Check model and map are aligned: 0.290 Set scattering table: 0.330 Process input model: 83.650 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.170 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.012 0.239 37197 Z= 0.778 Angle : 1.324 18.368 50547 Z= 0.791 Chirality : 0.070 0.459 5676 Planarity : 0.009 0.108 6465 Dihedral : 16.843 84.196 13467 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 1.08 % Allowed : 12.55 % Favored : 86.37 % Rotamer: Outliers : 4.59 % Allowed : 16.46 % Favored : 78.95 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.23 (0.09), residues: 4455 helix: -2.72 (0.08), residues: 2598 sheet: None (None), residues: 0 loop : -4.61 (0.10), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP Q 345 HIS 0.010 0.002 HIS Q 188 PHE 0.044 0.004 PHE D 337 TYR 0.045 0.004 TYR N 318 ARG 0.011 0.001 ARG G 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 430 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5959 (mmm160) REVERT: A 143 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8323 (ttp-170) REVERT: A 171 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6351 (m-30) REVERT: A 324 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6559 (tpt90) REVERT: B 187 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 176 ARG cc_start: 0.7159 (tpm170) cc_final: 0.6796 (mmp-170) REVERT: D 325 LYS cc_start: 0.7637 (tppp) cc_final: 0.6783 (ttmt) REVERT: G 167 GLU cc_start: 0.6898 (pm20) cc_final: 0.6549 (pm20) REVERT: G 359 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: H 74 TYR cc_start: 0.6356 (t80) cc_final: 0.6120 (t80) REVERT: H 120 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: H 324 ARG cc_start: 0.7347 (tpt-90) cc_final: 0.6651 (tmm160) REVERT: E 81 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5982 (mmm160) REVERT: E 171 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6063 (m-30) REVERT: E 324 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6274 (tpt90) REVERT: I 142 ILE cc_start: 0.7540 (mm) cc_final: 0.7282 (mt) REVERT: I 187 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: K 356 ASN cc_start: 0.7779 (p0) cc_final: 0.7576 (p0) REVERT: M 112 ARG cc_start: 0.6538 (mmt-90) cc_final: 0.6133 (mtm110) REVERT: M 325 LYS cc_start: 0.7801 (tppp) cc_final: 0.6952 (ttmt) REVERT: O 121 ILE cc_start: 0.8325 (mp) cc_final: 0.8007 (mm) REVERT: Q 74 TYR cc_start: 0.6411 (t80) cc_final: 0.6132 (t80) REVERT: Q 120 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6397 (t80) REVERT: Q 324 ARG cc_start: 0.7331 (tpt-90) cc_final: 0.6744 (tmm160) REVERT: F 81 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5754 (mmm160) REVERT: F 143 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8268 (ttp-170) REVERT: F 171 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.6113 (m-30) REVERT: F 324 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6206 (tpt90) REVERT: J 142 ILE cc_start: 0.7584 (mm) cc_final: 0.7258 (mt) REVERT: J 187 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: N 325 LYS cc_start: 0.7823 (tppp) cc_final: 0.6927 (ttmt) REVERT: P 167 GLU cc_start: 0.7016 (pm20) cc_final: 0.6645 (tp30) REVERT: P 184 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5828 (mp) REVERT: P 359 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: R 74 TYR cc_start: 0.6520 (t80) cc_final: 0.6256 (t80) REVERT: R 120 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: R 324 ARG cc_start: 0.7345 (tpt-90) cc_final: 0.6717 (tmm160) outliers start: 175 outliers final: 93 residues processed: 589 average time/residue: 0.6083 time to fit residues: 532.8629 Evaluate side-chains 410 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 297 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 359 PHE Chi-restraints excluded: chain G residue 368 SER Chi-restraints excluded: chain G residue 369 ARG Chi-restraints excluded: chain H residue 8 ARG Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 112 ARG Chi-restraints excluded: chain H residue 120 TYR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 152 ARG Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 325 LYS Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 77 ARG Chi-restraints excluded: chain M residue 146 ASN Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 369 ARG Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 359 PHE Chi-restraints excluded: chain O residue 369 ARG Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 79 LYS Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 112 ARG Chi-restraints excluded: chain Q residue 120 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 206 ASP Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 369 ARG Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain F residue 325 LYS Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain L residue 5 SER Chi-restraints excluded: chain L residue 6 GLU Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 77 ARG Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain N residue 369 ARG Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 359 PHE Chi-restraints excluded: chain P residue 369 ARG Chi-restraints excluded: chain R residue 6 GLU Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 112 ARG Chi-restraints excluded: chain R residue 120 TYR Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 152 ARG Chi-restraints excluded: chain R residue 206 ASP Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 0.9990 chunk 341 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 352 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 408 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 188 HIS B 140 GLN B 146 ASN C 40 GLN C 314 ASN C 356 ASN D 58 HIS D 140 GLN D 160 ASN G 100 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 HIS G 363 GLN H 58 HIS E 188 HIS I 146 ASN K 40 GLN K 314 ASN M 58 HIS M 140 GLN M 160 ASN O 100 GLN O 160 ASN O 188 HIS O 363 GLN Q 58 HIS F 188 HIS J 146 ASN L 40 GLN L 356 ASN N 58 HIS N 140 GLN N 160 ASN P 100 GLN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 HIS P 363 GLN R 58 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37197 Z= 0.201 Angle : 0.673 11.422 50547 Z= 0.354 Chirality : 0.042 0.186 5676 Planarity : 0.006 0.056 6465 Dihedral : 8.380 59.576 5317 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.58 % Rotamer: Outliers : 3.96 % Allowed : 19.84 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 4455 helix: -0.81 (0.10), residues: 2610 sheet: None (None), residues: 0 loop : -3.65 (0.12), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 349 HIS 0.007 0.001 HIS N 58 PHE 0.016 0.001 PHE K 68 TYR 0.019 0.001 TYR C 365 ARG 0.007 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 389 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5825 (mmm160) REVERT: C 176 ARG cc_start: 0.6462 (tpm170) cc_final: 0.6103 (mmp-170) REVERT: C 356 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.6787 (p0) REVERT: D 360 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6675 (ppt-90) REVERT: G 182 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8025 (mp) REVERT: G 187 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: H 110 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.6125 (p90) REVERT: H 188 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6139 (t-170) REVERT: H 324 ARG cc_start: 0.7189 (tpt-90) cc_final: 0.6591 (tmm160) REVERT: E 81 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5808 (mmm160) REVERT: E 171 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6163 (m-30) REVERT: M 112 ARG cc_start: 0.6436 (mmt-90) cc_final: 0.6203 (mtm110) REVERT: M 187 GLU cc_start: 0.7924 (tp30) cc_final: 0.7631 (tp30) REVERT: M 360 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6805 (ppt-90) REVERT: O 187 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: Q 110 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.6218 (p90) REVERT: Q 188 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6281 (t-170) REVERT: Q 324 ARG cc_start: 0.7317 (tpt-90) cc_final: 0.6753 (tmm160) REVERT: Q 371 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7342 (mt) REVERT: F 81 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5785 (mmm160) REVERT: F 171 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6277 (m-30) REVERT: J 142 ILE cc_start: 0.7513 (mm) cc_final: 0.7236 (mt) REVERT: N 360 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6629 (ppt-90) REVERT: P 184 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6059 (mp) REVERT: P 187 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: R 110 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.5789 (p90) REVERT: R 324 ARG cc_start: 0.7231 (tpt-90) cc_final: 0.6668 (tmm160) outliers start: 151 outliers final: 87 residues processed: 518 average time/residue: 0.4763 time to fit residues: 404.4405 Evaluate side-chains 423 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 316 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 363 GLN Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 111 SER Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 77 ARG Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain Q residue 91 ASP Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 188 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 366 THR Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 217 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 363 GLN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 409 optimal weight: 0.0070 chunk 442 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 HIS K 356 ASN M 354 ASN O 160 ASN L 314 ASN N 354 ASN ** P 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37197 Z= 0.273 Angle : 0.702 12.918 50547 Z= 0.364 Chirality : 0.043 0.162 5676 Planarity : 0.006 0.050 6465 Dihedral : 6.832 59.905 5136 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.28 % Favored : 91.58 % Rotamer: Outliers : 5.17 % Allowed : 21.31 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.12), residues: 4455 helix: -0.29 (0.10), residues: 2601 sheet: None (None), residues: 0 loop : -3.27 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 349 HIS 0.005 0.001 HIS M 185 PHE 0.022 0.002 PHE M 80 TYR 0.029 0.002 TYR O 74 ARG 0.006 0.000 ARG R 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 325 time to evaluate : 4.179 Fit side-chains REVERT: A 81 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5864 (mmm160) REVERT: B 187 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: C 176 ARG cc_start: 0.6623 (tpm170) cc_final: 0.6255 (mmp-170) REVERT: C 356 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6681 (p0) REVERT: D 360 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6602 (ppt-90) REVERT: G 182 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7856 (mp) REVERT: G 187 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: G 363 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.5426 (pm20) REVERT: H 17 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7305 (p) REVERT: H 110 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.5798 (p90) REVERT: H 188 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6112 (t-170) REVERT: H 324 ARG cc_start: 0.7195 (tpt-90) cc_final: 0.6598 (tmm160) REVERT: E 81 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5867 (mmm160) REVERT: E 171 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.6268 (m-30) REVERT: E 324 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6632 (tpt90) REVERT: I 187 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: K 106 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7003 (mp) REVERT: K 358 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7827 (pt) REVERT: M 360 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6607 (ppt-90) REVERT: O 128 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6592 (mm) REVERT: O 187 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: O 363 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: Q 110 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.5962 (p90) REVERT: Q 188 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6328 (t-170) REVERT: Q 324 ARG cc_start: 0.7261 (tpt-90) cc_final: 0.6765 (tmm160) REVERT: Q 371 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7584 (mt) REVERT: F 81 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5865 (mmm160) REVERT: J 142 ILE cc_start: 0.7747 (mm) cc_final: 0.7464 (mt) REVERT: J 187 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: L 356 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.6720 (p0) REVERT: N 360 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6531 (ppt-90) REVERT: P 128 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6344 (mm) REVERT: P 184 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.5873 (mp) REVERT: P 187 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: P 363 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.5941 (pm20) REVERT: R 74 TYR cc_start: 0.5929 (t80) cc_final: 0.5719 (t80) REVERT: R 110 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.6055 (p90) REVERT: R 188 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6975 (t-90) REVERT: R 324 ARG cc_start: 0.7186 (tpt-90) cc_final: 0.6625 (tmm160) outliers start: 197 outliers final: 119 residues processed: 484 average time/residue: 0.4726 time to fit residues: 374.6223 Evaluate side-chains 446 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 294 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 360 ARG Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 165 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 363 GLN Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 188 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 324 ARG Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain K residue 358 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 324 ARG Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain M residue 366 THR Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain O residue 165 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 187 GLU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 188 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 204 LEU Chi-restraints excluded: chain Q residue 217 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 366 THR Chi-restraints excluded: chain Q residue 371 LEU Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 368 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain N residue 366 THR Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain P residue 363 GLN Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 188 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 217 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.0020 chunk 307 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 195 optimal weight: 0.4980 chunk 274 optimal weight: 0.0980 chunk 410 optimal weight: 0.0980 chunk 434 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 389 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.1506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN O 160 ASN L 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 37197 Z= 0.142 Angle : 0.544 12.609 50547 Z= 0.276 Chirality : 0.038 0.150 5676 Planarity : 0.005 0.044 6465 Dihedral : 5.628 56.096 5125 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 3.23 % Allowed : 23.70 % Favored : 73.07 % 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: -1.09 (0.13), residues: 4455 helix: 0.54 (0.10), residues: 2613 sheet: None (None), residues: 0 loop : -2.70 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 349 HIS 0.004 0.001 HIS J 348 PHE 0.012 0.001 PHE L 68 TYR 0.021 0.001 TYR G 74 ARG 0.018 0.000 ARG K 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 432 time to evaluate : 3.862 Fit side-chains REVERT: B 109 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.4870 (t80) REVERT: B 187 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: C 176 ARG cc_start: 0.6097 (tpm170) cc_final: 0.5842 (mmp-170) REVERT: C 356 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6714 (p0) REVERT: D 112 ARG cc_start: 0.6478 (mmt-90) cc_final: 0.6252 (mtm110) REVERT: H 110 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6054 (p90) REVERT: H 324 ARG cc_start: 0.7026 (tpt-90) cc_final: 0.6415 (tmm160) REVERT: I 187 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: M 112 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.6193 (mtm110) REVERT: M 360 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7215 (ptp90) REVERT: Q 110 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6043 (p90) REVERT: Q 324 ARG cc_start: 0.7199 (tpt-90) cc_final: 0.6666 (tmm160) REVERT: J 187 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6829 (tt0) REVERT: L 86 MET cc_start: 0.6805 (ttt) cc_final: 0.6531 (ttt) REVERT: L 356 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.6858 (p0) REVERT: N 324 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5680 (ttp-170) REVERT: N 360 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7148 (ptp90) REVERT: P 121 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6528 (mm) REVERT: R 110 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.5721 (p90) REVERT: R 324 ARG cc_start: 0.7127 (tpt-90) cc_final: 0.6611 (tmm160) outliers start: 123 outliers final: 56 residues processed: 538 average time/residue: 0.5021 time to fit residues: 446.8493 Evaluate side-chains 409 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 340 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 360 ARG Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain N residue 360 ARG Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 91 ASP Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 371 optimal weight: 0.0070 chunk 300 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 0.0370 chunk 390 optimal weight: 0.0980 chunk 109 optimal weight: 0.0270 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN G 356 ASN K 356 ASN O 160 ASN J 352 GLN L 356 ASN P 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 37197 Z= 0.137 Angle : 0.549 12.247 50547 Z= 0.275 Chirality : 0.038 0.136 5676 Planarity : 0.004 0.043 6465 Dihedral : 4.858 56.676 5073 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 3.28 % Allowed : 25.28 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4455 helix: 0.82 (0.10), residues: 2628 sheet: None (None), residues: 0 loop : -2.48 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 349 HIS 0.002 0.000 HIS E 94 PHE 0.009 0.001 PHE D 80 TYR 0.017 0.001 TYR H 163 ARG 0.006 0.000 ARG J 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 363 time to evaluate : 4.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 187 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: C 356 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6920 (p0) REVERT: H 110 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6014 (p90) REVERT: H 324 ARG cc_start: 0.7047 (tpt-90) cc_final: 0.6414 (tmm160) REVERT: O 128 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5886 (mm) REVERT: Q 110 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6145 (p90) REVERT: Q 324 ARG cc_start: 0.7141 (tpt-90) cc_final: 0.6580 (tmm160) REVERT: L 356 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.6933 (p0) REVERT: N 324 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5881 (ttp-170) REVERT: P 106 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6878 (tt) REVERT: P 121 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6830 (mm) REVERT: P 128 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5785 (mm) REVERT: P 187 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: R 110 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.5744 (p90) REVERT: R 185 HIS cc_start: 0.7459 (OUTLIER) cc_final: 0.6897 (t-90) REVERT: R 324 ARG cc_start: 0.7137 (tpt-90) cc_final: 0.6594 (tmm160) outliers start: 125 outliers final: 83 residues processed: 466 average time/residue: 0.4390 time to fit residues: 340.5856 Evaluate side-chains 424 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 328 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 152 ARG Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 0.7980 chunk 391 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 435 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 356 ASN G 363 GLN I 352 GLN O 160 ASN O 363 GLN J 352 GLN P 150 GLN P 363 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37197 Z= 0.168 Angle : 0.575 12.681 50547 Z= 0.290 Chirality : 0.039 0.135 5676 Planarity : 0.004 0.065 6465 Dihedral : 4.759 56.357 5061 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 3.49 % Allowed : 25.91 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4455 helix: 0.84 (0.10), residues: 2625 sheet: None (None), residues: 0 loop : -2.39 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 349 HIS 0.003 0.001 HIS M 185 PHE 0.014 0.001 PHE D 80 TYR 0.017 0.001 TYR R 163 ARG 0.007 0.000 ARG O 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 327 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5943 (mmm160) REVERT: A 350 LYS cc_start: 0.7866 (tppp) cc_final: 0.7630 (tptt) REVERT: C 176 ARG cc_start: 0.6185 (tpm170) cc_final: 0.5874 (mmp-170) REVERT: C 356 ASN cc_start: 0.7671 (p0) cc_final: 0.7011 (p0) REVERT: H 110 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.5932 (p90) REVERT: H 185 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.6852 (t-90) REVERT: H 324 ARG cc_start: 0.7089 (tpt-90) cc_final: 0.6484 (tmm160) REVERT: O 128 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6218 (mm) REVERT: Q 110 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.5905 (p90) REVERT: Q 185 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6847 (t-90) REVERT: Q 324 ARG cc_start: 0.7178 (tpt-90) cc_final: 0.6630 (tmm160) REVERT: F 81 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5861 (mmt90) REVERT: L 86 MET cc_start: 0.7057 (ttt) cc_final: 0.6722 (ttt) REVERT: L 356 ASN cc_start: 0.7633 (p0) cc_final: 0.6976 (p0) REVERT: N 324 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5892 (ttp-170) REVERT: P 106 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6965 (tt) REVERT: P 121 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7109 (mm) REVERT: P 128 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5956 (mm) REVERT: P 187 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: R 110 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.5981 (p90) REVERT: R 165 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7634 (tt) REVERT: R 185 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6834 (t-90) REVERT: R 324 ARG cc_start: 0.7104 (tpt-90) cc_final: 0.6522 (tmm160) outliers start: 133 outliers final: 102 residues processed: 435 average time/residue: 0.4577 time to fit residues: 331.5792 Evaluate side-chains 428 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 311 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain G residue 363 GLN Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 43 GLN Chi-restraints excluded: chain O residue 128 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain O residue 363 GLN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain P residue 363 GLN Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 152 ARG Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 246 optimal weight: 0.0970 chunk 366 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 433 optimal weight: 4.9990 chunk 271 optimal weight: 0.3980 chunk 264 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 352 GLN K 356 ASN O 160 ASN J 352 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37197 Z= 0.135 Angle : 0.544 13.404 50547 Z= 0.272 Chirality : 0.038 0.136 5676 Planarity : 0.004 0.059 6465 Dihedral : 4.582 56.301 5061 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.44 % Allowed : 26.43 % Favored : 70.13 % 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: -0.33 (0.13), residues: 4455 helix: 1.05 (0.10), residues: 2613 sheet: None (None), residues: 0 loop : -2.18 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 349 HIS 0.002 0.000 HIS E 94 PHE 0.008 0.001 PHE D 80 TYR 0.016 0.001 TYR R 163 ARG 0.007 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 348 time to evaluate : 4.125 Fit side-chains REVERT: A 350 LYS cc_start: 0.7859 (tppp) cc_final: 0.7624 (tptt) REVERT: C 176 ARG cc_start: 0.6153 (tpm170) cc_final: 0.5840 (mmp-170) REVERT: H 110 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.5940 (p90) REVERT: H 185 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.6833 (t-90) REVERT: H 324 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.6442 (tmm160) REVERT: M 31 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7959 (tt) REVERT: Q 110 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.5985 (p90) REVERT: Q 185 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6785 (t-90) REVERT: Q 324 ARG cc_start: 0.7140 (tpt-90) cc_final: 0.6585 (tmm160) REVERT: L 356 ASN cc_start: 0.7505 (p0) cc_final: 0.6841 (p0) REVERT: N 31 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8027 (tt) REVERT: N 324 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5957 (ttp-170) REVERT: P 106 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6801 (tt) REVERT: P 121 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7023 (mm) REVERT: P 128 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5918 (mm) REVERT: P 187 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: R 110 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.5844 (p90) REVERT: R 185 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6837 (t-90) REVERT: R 324 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.6493 (tmm160) outliers start: 131 outliers final: 98 residues processed: 458 average time/residue: 0.4287 time to fit residues: 334.0454 Evaluate side-chains 429 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 318 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 210 VAL Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 317 PHE Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 314 ASN Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 2.9990 chunk 173 optimal weight: 0.1980 chunk 259 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 295 optimal weight: 4.9990 chunk 214 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 340 optimal weight: 0.0980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 ASN O 160 ASN J 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37197 Z= 0.142 Angle : 0.541 12.918 50547 Z= 0.271 Chirality : 0.038 0.135 5676 Planarity : 0.004 0.084 6465 Dihedral : 4.512 57.010 5061 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.72 % Favored : 94.21 % Rotamer: Outliers : 3.65 % Allowed : 26.46 % Favored : 69.90 % 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: -0.20 (0.13), residues: 4455 helix: 1.14 (0.10), residues: 2622 sheet: None (None), residues: 0 loop : -2.11 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 349 HIS 0.003 0.001 HIS E 94 PHE 0.011 0.001 PHE M 80 TYR 0.017 0.001 TYR R 163 ARG 0.008 0.000 ARG O 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 336 time to evaluate : 4.943 Fit side-chains revert: symmetry clash REVERT: A 81 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5957 (mmm160) REVERT: B 187 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: C 176 ARG cc_start: 0.6139 (tpm170) cc_final: 0.5827 (mmp-170) REVERT: H 185 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6846 (t-90) REVERT: H 324 ARG cc_start: 0.7009 (tpt-90) cc_final: 0.6404 (tmm160) REVERT: M 31 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7978 (tt) REVERT: Q 185 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6749 (t-90) REVERT: Q 324 ARG cc_start: 0.7152 (tpt-90) cc_final: 0.6552 (tmm160) REVERT: F 81 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5844 (mmt90) REVERT: L 356 ASN cc_start: 0.7479 (p0) cc_final: 0.6792 (p0) REVERT: N 31 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8031 (tt) REVERT: N 324 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5976 (ttp-170) REVERT: P 106 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6879 (tt) REVERT: P 121 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7135 (mm) REVERT: P 128 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5927 (mm) REVERT: P 187 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: R 110 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.5938 (p90) REVERT: R 185 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6797 (t-90) REVERT: R 324 ARG cc_start: 0.7060 (tpt-90) cc_final: 0.6484 (tmm160) outliers start: 139 outliers final: 109 residues processed: 450 average time/residue: 0.4376 time to fit residues: 334.9847 Evaluate side-chains 439 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 316 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 332 LEU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 352 GLN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain O residue 314 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 173 VAL Chi-restraints excluded: chain Q residue 185 HIS Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 164 MET Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 102 SER Chi-restraints excluded: chain N residue 206 ASP Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain N residue 324 ARG Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 128 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 210 VAL Chi-restraints excluded: chain P residue 314 ASN Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 0.1980 chunk 415 optimal weight: 0.4980 chunk 379 optimal weight: 3.9990 chunk 404 optimal weight: 0.0470 chunk 243 optimal weight: 0.0870 chunk 176 optimal weight: 0.9980 chunk 317 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 365 optimal weight: 0.5980 chunk 382 optimal weight: 0.8980 chunk 402 optimal weight: 4.9990 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 356 ASN K 356 ASN O 160 ASN J 352 GLN R 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37197 Z= 0.124 Angle : 0.519 14.239 50547 Z= 0.256 Chirality : 0.037 0.135 5676 Planarity : 0.004 0.079 6465 Dihedral : 4.229 57.219 5058 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 27.30 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4455 helix: 1.40 (0.11), residues: 2625 sheet: None (None), residues: 0 loop : -1.93 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 349 HIS 0.002 0.000 HIS Q 185 PHE 0.008 0.000 PHE K 68 TYR 0.021 0.001 TYR R 163 ARG 0.014 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 388 time to evaluate : 3.831 Fit side-chains REVERT: B 187 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: H 185 HIS cc_start: 0.7071 (OUTLIER) cc_final: 0.6706 (t-90) REVERT: H 324 ARG cc_start: 0.7050 (tpt-90) cc_final: 0.6410 (tmm160) REVERT: M 31 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7870 (tt) REVERT: O 27 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6840 (mm110) REVERT: Q 324 ARG cc_start: 0.7019 (tpt-90) cc_final: 0.6427 (tmm160) REVERT: F 81 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5831 (mmt90) REVERT: F 164 MET cc_start: 0.5742 (mtt) cc_final: 0.5462 (mtt) REVERT: F 352 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7211 (tp40) REVERT: L 356 ASN cc_start: 0.7386 (p0) cc_final: 0.6700 (p0) REVERT: N 31 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7948 (tt) REVERT: P 106 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6607 (tt) REVERT: P 121 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6763 (mm) REVERT: R 110 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.5840 (p90) REVERT: R 185 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6643 (t-90) REVERT: R 324 ARG cc_start: 0.7067 (tpt-90) cc_final: 0.6482 (tmm160) outliers start: 103 outliers final: 77 residues processed: 471 average time/residue: 0.4378 time to fit residues: 350.4810 Evaluate side-chains 429 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 343 time to evaluate : 3.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 1.9990 chunk 427 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 297 optimal weight: 0.5980 chunk 448 optimal weight: 0.0770 chunk 412 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 356 ASN O 160 ASN J 352 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.208 37197 Z= 0.185 Angle : 0.708 59.199 50547 Z= 0.392 Chirality : 0.038 0.413 5676 Planarity : 0.005 0.092 6465 Dihedral : 4.193 57.271 5052 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.47 % Allowed : 27.53 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4455 helix: 1.40 (0.11), residues: 2625 sheet: None (None), residues: 0 loop : -1.93 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 349 HIS 0.002 0.000 HIS H 185 PHE 0.007 0.001 PHE L 68 TYR 0.017 0.001 TYR R 163 ARG 0.018 0.000 ARG M 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 336 time to evaluate : 3.984 Fit side-chains revert: symmetry clash REVERT: B 187 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: H 185 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6706 (t-90) REVERT: H 324 ARG cc_start: 0.7057 (tpt-90) cc_final: 0.6412 (tmm160) REVERT: M 31 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7872 (tt) REVERT: O 27 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6842 (mm110) REVERT: Q 324 ARG cc_start: 0.7026 (tpt-90) cc_final: 0.6429 (tmm160) REVERT: F 81 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5833 (mmt90) REVERT: F 164 MET cc_start: 0.5746 (mtt) cc_final: 0.5469 (mtt) REVERT: F 352 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7210 (tp40) REVERT: L 356 ASN cc_start: 0.7400 (p0) cc_final: 0.6701 (p0) REVERT: N 31 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7946 (tt) REVERT: P 106 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6608 (tt) REVERT: P 121 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6769 (mm) REVERT: R 110 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.5861 (p90) REVERT: R 185 HIS cc_start: 0.6960 (OUTLIER) cc_final: 0.6625 (t-90) REVERT: R 324 ARG cc_start: 0.7073 (tpt-90) cc_final: 0.6482 (tmm160) outliers start: 94 outliers final: 78 residues processed: 415 average time/residue: 0.4391 time to fit residues: 313.7628 Evaluate side-chains 421 residues out of total 3834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 334 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 191 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 206 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain G residue 191 ASN Chi-restraints excluded: chain G residue 314 ASN Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 356 ASN Chi-restraints excluded: chain H residue 110 TYR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 156 ASP Chi-restraints excluded: chain H residue 171 ASP Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 185 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 374 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 142 ILE Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 184 LEU Chi-restraints excluded: chain O residue 191 ASN Chi-restraints excluded: chain O residue 356 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 110 TYR Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 171 ASP Chi-restraints excluded: chain Q residue 203 THR Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain Q residue 374 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 191 ASN Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 189 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 217 THR Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 191 ASN Chi-restraints excluded: chain P residue 356 ASN Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 185 HIS Chi-restraints excluded: chain R residue 203 THR Chi-restraints excluded: chain R residue 374 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 7.9990 chunk 380 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 329 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 357 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 367 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 160 ASN J 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.201676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.163088 restraints weight = 49929.771| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.32 r_work: 0.3930 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.208 37197 Z= 0.185 Angle : 0.704 55.086 50547 Z= 0.392 Chirality : 0.038 0.413 5676 Planarity : 0.005 0.094 6465 Dihedral : 4.193 57.271 5052 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 2.31 % Allowed : 27.74 % Favored : 69.95 % 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: 0.16 (0.13), residues: 4455 helix: 1.40 (0.11), residues: 2625 sheet: None (None), residues: 0 loop : -1.93 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 349 HIS 0.002 0.000 HIS H 185 PHE 0.007 0.001 PHE L 68 TYR 0.017 0.001 TYR R 163 ARG 0.018 0.000 ARG M 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9522.53 seconds wall clock time: 172 minutes 33.17 seconds (10353.17 seconds total)