Starting phenix.real_space_refine on Sat Mar 23 23:21:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yt5_10912/03_2024/6yt5_10912.pdb" } resolution = 3.0 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= 0.004 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 186 5.16 5 C 24180 2.51 5 N 6882 2.21 5 O 7830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 541": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C ARG 541": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 603": "OE1" <-> "OE2" Residue "C GLU 694": "OE1" <-> "OE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 541": "NH1" <-> "NH2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D GLU 603": "OE1" <-> "OE2" Residue "D GLU 694": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 279": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 485": "OE1" <-> "OE2" Residue "E ARG 486": "NH1" <-> "NH2" Residue "E ARG 541": "NH1" <-> "NH2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E ARG 577": "NH1" <-> "NH2" Residue "E GLU 603": "OE1" <-> "OE2" Residue "E GLU 694": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 485": "OE1" <-> "OE2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 541": "NH1" <-> "NH2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F ARG 577": "NH1" <-> "NH2" Residue "F GLU 603": "OE1" <-> "OE2" Residue "F GLU 694": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 198": "OE1" <-> "OE2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 198": "OE1" <-> "OE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "K ARG 39": "NH1" <-> "NH2" Residue "K GLU 112": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "K GLU 133": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L GLU 112": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 216": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39078 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5116 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 620} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "K" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1397 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 18.63, per 1000 atoms: 0.48 Number of scatterers: 39078 At special positions: 0 Unit cell: (149.721, 147.627, 221.964, 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 186 16.00 O 7830 8.00 N 6882 7.00 C 24180 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: 14.20 Conformation dependent library (CDL) restraints added in 6.6 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9432 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 18 sheets defined 68.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 61 through 78 removed outlier: 3.776A pdb=" N ASP A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.629A pdb=" N GLU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 155 removed outlier: 4.104A pdb=" N ALA A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 170 through 201 removed outlier: 4.350A pdb=" N PHE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.501A pdb=" N THR A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 4.089A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.756A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.911A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.575A pdb=" N TRP A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 372 removed outlier: 3.740A pdb=" N ILE A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.306A pdb=" N LEU A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.044A pdb=" N MET A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 434 removed outlier: 3.509A pdb=" N VAL A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 removed outlier: 4.281A pdb=" N LYS A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 481 Processing helix chain 'A' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 4.145A pdb=" N ALA A 506 " --> pdb=" O GLN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 Processing helix chain 'A' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.940A pdb=" N PHE A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.832A pdb=" N ILE A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 651 removed outlier: 3.706A pdb=" N ILE A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'B' and resid 61 through 78 removed outlier: 3.775A pdb=" N ASP B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.629A pdb=" N GLU B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 155 removed outlier: 4.104A pdb=" N ALA B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 170 through 201 removed outlier: 4.350A pdb=" N PHE B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 236 through 253 removed outlier: 3.501A pdb=" N THR B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 4.089A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.755A pdb=" N ILE B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.910A pdb=" N ASN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.575A pdb=" N TRP B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 372 removed outlier: 3.741A pdb=" N ILE B 353 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 396 removed outlier: 4.305A pdb=" N LEU B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 4.044A pdb=" N MET B 407 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 434 removed outlier: 3.509A pdb=" N VAL B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 452 removed outlier: 4.280A pdb=" N LYS B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 481 Processing helix chain 'B' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 4.146A pdb=" N ALA B 506 " --> pdb=" O GLN B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 523 Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 558 removed outlier: 3.940A pdb=" N PHE B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.833A pdb=" N ILE B 579 " --> pdb=" O SER B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 651 removed outlier: 3.706A pdb=" N ILE B 641 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 697 Processing helix chain 'C' and resid 61 through 78 removed outlier: 3.776A pdb=" N ASP C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.629A pdb=" N GLU C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 155 removed outlier: 4.104A pdb=" N ALA C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 170 through 201 removed outlier: 4.350A pdb=" N PHE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 236 through 253 removed outlier: 3.500A pdb=" N THR C 241 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 4.089A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.755A pdb=" N ILE C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 302 through 318 removed outlier: 3.910A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.575A pdb=" N TRP C 326 " --> pdb=" O PRO C 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 372 removed outlier: 3.741A pdb=" N ILE C 353 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS C 368 " --> pdb=" O ASN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 396 removed outlier: 4.305A pdb=" N LEU C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.044A pdb=" N MET C 407 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 434 removed outlier: 3.510A pdb=" N VAL C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 452 removed outlier: 4.280A pdb=" N LYS C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 481 Processing helix chain 'C' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 4.146A pdb=" N ALA C 506 " --> pdb=" O GLN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 Processing helix chain 'C' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 558 removed outlier: 3.939A pdb=" N PHE C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.832A pdb=" N ILE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 634 through 651 removed outlier: 3.706A pdb=" N ILE C 641 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 647 " --> pdb=" O GLU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'D' and resid 61 through 78 removed outlier: 3.776A pdb=" N ASP D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 3.629A pdb=" N GLU D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 155 removed outlier: 4.104A pdb=" N ALA D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 170 through 201 removed outlier: 4.350A pdb=" N PHE D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 231 Processing helix chain 'D' and resid 236 through 253 removed outlier: 3.501A pdb=" N THR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 4.089A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.756A pdb=" N ILE D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.911A pdb=" N ASN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.575A pdb=" N TRP D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 372 removed outlier: 3.740A pdb=" N ILE D 353 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 368 " --> pdb=" O ASN D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 396 removed outlier: 4.306A pdb=" N LEU D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 removed outlier: 4.044A pdb=" N MET D 407 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 434 removed outlier: 3.509A pdb=" N VAL D 422 " --> pdb=" O HIS D 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 452 removed outlier: 4.281A pdb=" N LYS D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 481 Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP D 491 " --> pdb=" O THR D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 508 removed outlier: 4.145A pdb=" N ALA D 506 " --> pdb=" O GLN D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 523 Processing helix chain 'D' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 540 " --> pdb=" O ARG D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 558 removed outlier: 3.940A pdb=" N PHE D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 569 through 587 removed outlier: 3.832A pdb=" N ILE D 579 " --> pdb=" O SER D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 634 through 651 removed outlier: 3.706A pdb=" N ILE D 641 " --> pdb=" O GLN D 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 647 " --> pdb=" O GLU D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'E' and resid 61 through 78 removed outlier: 3.776A pdb=" N ASP E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 87 removed outlier: 3.628A pdb=" N GLU E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS E 123 " --> pdb=" O ASP E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 155 removed outlier: 4.105A pdb=" N ALA E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 170 through 201 removed outlier: 4.350A pdb=" N PHE E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 205 Processing helix chain 'E' and resid 216 through 231 Processing helix chain 'E' and resid 236 through 253 removed outlier: 3.501A pdb=" N THR E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 4.090A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.755A pdb=" N ILE E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 283 through 297 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.910A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.575A pdb=" N TRP E 326 " --> pdb=" O PRO E 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP E 337 " --> pdb=" O LYS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 372 removed outlier: 3.741A pdb=" N ILE E 353 " --> pdb=" O ARG E 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 396 removed outlier: 4.306A pdb=" N LEU E 384 " --> pdb=" O SER E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 4.044A pdb=" N MET E 407 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 434 removed outlier: 3.509A pdb=" N VAL E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 452 removed outlier: 4.281A pdb=" N LYS E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 481 Processing helix chain 'E' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP E 491 " --> pdb=" O THR E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 508 removed outlier: 4.145A pdb=" N ALA E 506 " --> pdb=" O GLN E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 523 Processing helix chain 'E' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG E 536 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 558 removed outlier: 3.940A pdb=" N PHE E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 569 through 587 removed outlier: 3.832A pdb=" N ILE E 579 " --> pdb=" O SER E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 604 Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 634 through 651 removed outlier: 3.706A pdb=" N ILE E 641 " --> pdb=" O GLN E 637 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 642 " --> pdb=" O GLY E 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS E 647 " --> pdb=" O GLU E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 697 Processing helix chain 'F' and resid 61 through 78 removed outlier: 3.776A pdb=" N ASP F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 87 removed outlier: 3.628A pdb=" N GLU F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 127 removed outlier: 3.636A pdb=" N ALA F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 155 removed outlier: 4.104A pdb=" N ALA F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'F' and resid 170 through 201 removed outlier: 4.351A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL F 200 " --> pdb=" O MET F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 Processing helix chain 'F' and resid 216 through 231 Processing helix chain 'F' and resid 236 through 253 removed outlier: 3.501A pdb=" N THR F 241 " --> pdb=" O ASP F 237 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER F 249 " --> pdb=" O SER F 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 4.088A pdb=" N PHE F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.756A pdb=" N ILE F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 283 through 297 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.910A pdb=" N ASN F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.576A pdb=" N TRP F 326 " --> pdb=" O PRO F 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP F 337 " --> pdb=" O LYS F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 372 removed outlier: 3.741A pdb=" N ILE F 353 " --> pdb=" O ARG F 349 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 396 removed outlier: 4.305A pdb=" N LEU F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 407 removed outlier: 4.043A pdb=" N MET F 407 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 434 removed outlier: 3.510A pdb=" N VAL F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR F 424 " --> pdb=" O ASP F 420 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 452 removed outlier: 4.280A pdb=" N LYS F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 481 Processing helix chain 'F' and resid 487 through 500 removed outlier: 3.604A pdb=" N ASP F 491 " --> pdb=" O THR F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 508 removed outlier: 4.145A pdb=" N ALA F 506 " --> pdb=" O GLN F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 523 Processing helix chain 'F' and resid 528 through 540 removed outlier: 4.139A pdb=" N ARG F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 540 " --> pdb=" O ARG F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 558 removed outlier: 3.940A pdb=" N PHE F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 Processing helix chain 'F' and resid 569 through 587 removed outlier: 3.832A pdb=" N ILE F 579 " --> pdb=" O SER F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 604 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 634 through 651 removed outlier: 3.705A pdb=" N ILE F 641 " --> pdb=" O GLN F 637 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 642 " --> pdb=" O GLY F 638 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS F 647 " --> pdb=" O GLU F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 697 Processing helix chain 'G' and resid 11 through 21 removed outlier: 3.780A pdb=" N LYS G 18 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.605A pdb=" N ALA G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP G 35 " --> pdb=" O ARG G 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU G 37 " --> pdb=" O VAL G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 66 Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 100 through 110 removed outlier: 3.754A pdb=" N ASN G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 124 removed outlier: 3.619A pdb=" N ALA G 122 " --> pdb=" O PRO G 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.563A pdb=" N ILE G 131 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 removed outlier: 3.585A pdb=" N ASN G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 155 Processing helix chain 'G' and resid 168 through 173 removed outlier: 3.541A pdb=" N GLY G 172 " --> pdb=" O PRO G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 217 through 223 Processing helix chain 'H' and resid 11 through 21 removed outlier: 3.781A pdb=" N LYS H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.604A pdb=" N ALA H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 37 " --> pdb=" O VAL H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'H' and resid 100 through 110 removed outlier: 3.755A pdb=" N ASN H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 124 removed outlier: 3.619A pdb=" N ALA H 122 " --> pdb=" O PRO H 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 131 removed outlier: 3.563A pdb=" N ILE H 131 " --> pdb=" O PHE H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 143 removed outlier: 3.586A pdb=" N ASN H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 155 Processing helix chain 'H' and resid 168 through 173 removed outlier: 3.540A pdb=" N GLY H 172 " --> pdb=" O PRO H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 217 through 223 Processing helix chain 'I' and resid 11 through 21 removed outlier: 3.780A pdb=" N LYS I 18 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 38 removed outlier: 3.605A pdb=" N ALA I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU I 37 " --> pdb=" O VAL I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 66 Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'I' and resid 100 through 110 removed outlier: 3.754A pdb=" N ASN I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 removed outlier: 3.619A pdb=" N ALA I 122 " --> pdb=" O PRO I 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 131 removed outlier: 3.563A pdb=" N ILE I 131 " --> pdb=" O PHE I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.585A pdb=" N ASN I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 155 Processing helix chain 'I' and resid 168 through 173 removed outlier: 3.542A pdb=" N GLY I 172 " --> pdb=" O PRO I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 215 Processing helix chain 'I' and resid 217 through 223 Processing helix chain 'J' and resid 11 through 21 removed outlier: 3.781A pdb=" N LYS J 18 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.604A pdb=" N ALA J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP J 35 " --> pdb=" O ARG J 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU J 37 " --> pdb=" O VAL J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 66 Processing helix chain 'J' and resid 81 through 94 Processing helix chain 'J' and resid 100 through 110 removed outlier: 3.754A pdb=" N ASN J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 124 removed outlier: 3.620A pdb=" N ALA J 122 " --> pdb=" O PRO J 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 131 removed outlier: 3.564A pdb=" N ILE J 131 " --> pdb=" O PHE J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 143 removed outlier: 3.585A pdb=" N ASN J 141 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 Processing helix chain 'J' and resid 168 through 173 removed outlier: 3.541A pdb=" N GLY J 172 " --> pdb=" O PRO J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 215 Processing helix chain 'J' and resid 217 through 223 Processing helix chain 'K' and resid 11 through 21 removed outlier: 3.780A pdb=" N LYS K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 38 removed outlier: 3.605A pdb=" N ALA K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP K 35 " --> pdb=" O ARG K 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU K 37 " --> pdb=" O VAL K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 66 Processing helix chain 'K' and resid 81 through 94 Processing helix chain 'K' and resid 100 through 110 removed outlier: 3.753A pdb=" N ASN K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 124 removed outlier: 3.620A pdb=" N ALA K 122 " --> pdb=" O PRO K 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 131 removed outlier: 3.564A pdb=" N ILE K 131 " --> pdb=" O PHE K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.585A pdb=" N ASN K 141 " --> pdb=" O ASN K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 Processing helix chain 'K' and resid 168 through 173 removed outlier: 3.541A pdb=" N GLY K 172 " --> pdb=" O PRO K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 215 Processing helix chain 'K' and resid 217 through 223 Processing helix chain 'L' and resid 11 through 21 removed outlier: 3.781A pdb=" N LYS L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 38 removed outlier: 3.605A pdb=" N ALA L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP L 35 " --> pdb=" O ARG L 31 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 66 Processing helix chain 'L' and resid 81 through 94 Processing helix chain 'L' and resid 100 through 110 removed outlier: 3.753A pdb=" N ASN L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 124 removed outlier: 3.619A pdb=" N ALA L 122 " --> pdb=" O PRO L 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 131 removed outlier: 3.563A pdb=" N ILE L 131 " --> pdb=" O PHE L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.585A pdb=" N ASN L 141 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 Processing helix chain 'L' and resid 168 through 173 removed outlier: 3.541A pdb=" N GLY L 172 " --> pdb=" O PRO L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 215 Processing helix chain 'L' and resid 217 through 223 Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 605 through 607 Processing sheet with id=AA3, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AA4, first strand: chain 'B' and resid 268 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AA6, first strand: chain 'B' and resid 670 through 671 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 605 through 607 Processing sheet with id=AA9, first strand: chain 'C' and resid 670 through 671 Processing sheet with id=AB1, first strand: chain 'D' and resid 268 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 605 through 607 Processing sheet with id=AB3, first strand: chain 'D' and resid 670 through 671 Processing sheet with id=AB4, first strand: chain 'E' and resid 268 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 605 through 607 Processing sheet with id=AB6, first strand: chain 'E' and resid 670 through 671 Processing sheet with id=AB7, first strand: chain 'F' and resid 268 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 605 through 607 Processing sheet with id=AB9, first strand: chain 'F' and resid 670 through 671 2148 hydrogen bonds defined for protein. 6354 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: 12.49 Time building geometry restraints manager: 15.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13456 1.34 - 1.45: 4938 1.45 - 1.57: 20912 1.57 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 39678 Sorted by residual: bond pdb=" CB TRP C 326 " pdb=" CG TRP C 326 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.52e+00 bond pdb=" CB TRP D 326 " pdb=" CG TRP D 326 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.50e+00 bond pdb=" CB TRP A 326 " pdb=" CG TRP A 326 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.50e+00 bond pdb=" CB TRP F 326 " pdb=" CG TRP F 326 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.47e+00 bond pdb=" CB TRP E 326 " pdb=" CG TRP E 326 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.44e+00 ... (remaining 39673 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.73: 738 105.73 - 112.84: 20789 112.84 - 119.96: 14860 119.96 - 127.07: 16790 127.07 - 134.18: 319 Bond angle restraints: 53496 Sorted by residual: angle pdb=" CA LYS E 584 " pdb=" CB LYS E 584 " pdb=" CG LYS E 584 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.03e+00 angle pdb=" CA LYS C 584 " pdb=" CB LYS C 584 " pdb=" CG LYS C 584 " ideal model delta sigma weight residual 114.10 119.38 -5.28 2.00e+00 2.50e-01 6.98e+00 angle pdb=" CA LYS A 584 " pdb=" CB LYS A 584 " pdb=" CG LYS A 584 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA LYS D 584 " pdb=" CB LYS D 584 " pdb=" CG LYS D 584 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.95e+00 angle pdb=" CA LYS B 584 " pdb=" CB LYS B 584 " pdb=" CG LYS B 584 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 ... (remaining 53491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21473 17.96 - 35.93: 2461 35.93 - 53.89: 384 53.89 - 71.86: 78 71.86 - 89.82: 48 Dihedral angle restraints: 24444 sinusoidal: 9852 harmonic: 14592 Sorted by residual: dihedral pdb=" CA GLU L 170 " pdb=" C GLU L 170 " pdb=" N VAL L 171 " pdb=" CA VAL L 171 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLU I 170 " pdb=" C GLU I 170 " pdb=" N VAL I 171 " pdb=" CA VAL I 171 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLU G 170 " pdb=" C GLU G 170 " pdb=" N VAL G 171 " pdb=" CA VAL G 171 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 24441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2659 0.030 - 0.061: 1965 0.061 - 0.091: 785 0.091 - 0.121: 256 0.121 - 0.151: 89 Chirality restraints: 5754 Sorted by residual: chirality pdb=" CB VAL J 171 " pdb=" CA VAL J 171 " pdb=" CG1 VAL J 171 " pdb=" CG2 VAL J 171 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE B 437 " pdb=" N ILE B 437 " pdb=" C ILE B 437 " pdb=" CB ILE B 437 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB VAL H 171 " pdb=" CA VAL H 171 " pdb=" CG1 VAL H 171 " pdb=" CG2 VAL H 171 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 5751 not shown) Planarity restraints: 7182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 79 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO E 80 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 80 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 79 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO C 80 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 79 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO A 80 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " 0.031 5.00e-02 4.00e+02 ... (remaining 7179 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5665 2.74 - 3.28: 40053 3.28 - 3.82: 64517 3.82 - 4.36: 78058 4.36 - 4.90: 132339 Nonbonded interactions: 320632 Sorted by model distance: nonbonded pdb=" OD2 ASP C 403 " pdb=" NZ LYS C 405 " model vdw 2.196 2.520 nonbonded pdb=" OD2 ASP F 403 " pdb=" NZ LYS F 405 " model vdw 2.196 2.520 nonbonded pdb=" OD2 ASP E 403 " pdb=" NZ LYS E 405 " model vdw 2.196 2.520 nonbonded pdb=" OD2 ASP B 403 " pdb=" NZ LYS B 405 " model vdw 2.196 2.520 nonbonded pdb=" OD2 ASP A 403 " pdb=" NZ LYS A 405 " model vdw 2.197 2.520 ... (remaining 320627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.200 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 92.310 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.290 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:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.010 0.072 39678 Z= 0.615 Angle : 0.731 9.740 53496 Z= 0.407 Chirality : 0.049 0.151 5754 Planarity : 0.005 0.057 7182 Dihedral : 15.513 89.819 15012 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.15 % Allowed : 8.23 % Favored : 91.62 % 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: -4.28 (0.09), residues: 4980 helix: -2.56 (0.07), residues: 3270 sheet: None (None), residues: 0 loop : -3.09 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 366 HIS 0.005 0.002 HIS E 182 PHE 0.014 0.002 PHE C 404 TYR 0.017 0.002 TYR E 664 ARG 0.008 0.001 ARG C 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 956 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8359 (t) cc_final: 0.8125 (p) REVERT: A 519 ASP cc_start: 0.7294 (m-30) cc_final: 0.6848 (m-30) REVERT: B 149 VAL cc_start: 0.8483 (t) cc_final: 0.8232 (p) REVERT: B 496 ILE cc_start: 0.8453 (mt) cc_final: 0.8239 (mp) REVERT: B 698 LYS cc_start: 0.8592 (mttm) cc_final: 0.8387 (mttp) REVERT: C 149 VAL cc_start: 0.8462 (t) cc_final: 0.8229 (p) REVERT: C 421 MET cc_start: 0.7789 (tpp) cc_final: 0.7528 (tpp) REVERT: D 149 VAL cc_start: 0.8345 (t) cc_final: 0.8106 (p) REVERT: D 519 ASP cc_start: 0.7302 (m-30) cc_final: 0.6856 (m-30) REVERT: D 661 LEU cc_start: 0.8519 (mt) cc_final: 0.8270 (mt) REVERT: E 149 VAL cc_start: 0.8478 (t) cc_final: 0.8232 (p) REVERT: E 496 ILE cc_start: 0.8452 (mt) cc_final: 0.8237 (mp) REVERT: E 698 LYS cc_start: 0.8588 (mttm) cc_final: 0.8384 (mttp) REVERT: F 149 VAL cc_start: 0.8463 (t) cc_final: 0.8231 (p) REVERT: F 421 MET cc_start: 0.7786 (tpp) cc_final: 0.7533 (tpp) REVERT: G 136 ARG cc_start: 0.6857 (mtm180) cc_final: 0.6639 (mtp180) REVERT: H 112 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6648 (tm-30) REVERT: H 134 GLU cc_start: 0.7527 (mp0) cc_final: 0.7255 (mp0) REVERT: I 102 LEU cc_start: 0.8462 (mm) cc_final: 0.8260 (mm) REVERT: I 134 GLU cc_start: 0.7439 (mp0) cc_final: 0.7053 (mp0) REVERT: J 112 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6648 (tm-30) REVERT: J 134 GLU cc_start: 0.7526 (mp0) cc_final: 0.7250 (mp0) REVERT: K 136 ARG cc_start: 0.6912 (mtm180) cc_final: 0.6679 (mtp180) REVERT: L 102 LEU cc_start: 0.8458 (mm) cc_final: 0.8254 (mm) REVERT: L 134 GLU cc_start: 0.7437 (mp0) cc_final: 0.7049 (mp0) outliers start: 6 outliers final: 6 residues processed: 960 average time/residue: 1.7053 time to fit residues: 1936.4866 Evaluate side-chains 739 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 733 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 411 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 3.9990 chunk 377 optimal weight: 0.4980 chunk 209 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 254 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 390 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 237 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 452 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 191 GLN A 272 ASN A 286 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN A 418 HIS A 426 ASN A 472 GLN A 529 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 418 HIS B 426 ASN B 472 GLN B 529 GLN B 658 ASN B 696 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 272 ASN C 286 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN C 418 HIS C 426 ASN C 472 GLN C 529 GLN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 191 GLN D 272 ASN D 286 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN D 418 HIS D 426 ASN D 472 GLN D 529 GLN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 GLN ** E 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN E 418 HIS E 426 ASN E 472 GLN E 529 GLN E 658 ASN E 696 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 272 ASN F 286 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 GLN F 418 HIS F 426 ASN F 472 GLN F 529 GLN G 7 ASN G 141 ASN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN H 141 ASN H 214 HIS I 7 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 ASN J 141 ASN J 214 HIS K 7 ASN K 141 ASN ** K 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39678 Z= 0.193 Angle : 0.538 8.784 53496 Z= 0.285 Chirality : 0.040 0.157 5754 Planarity : 0.004 0.058 7182 Dihedral : 5.750 164.974 5452 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.07 % Allowed : 19.26 % Favored : 77.67 % 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: -2.42 (0.11), residues: 4980 helix: -1.06 (0.08), residues: 3390 sheet: -4.01 (0.58), residues: 60 loop : -2.50 (0.13), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.002 0.001 HIS D 418 PHE 0.009 0.001 PHE B 167 TYR 0.018 0.001 TYR G 138 ARG 0.007 0.000 ARG I 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 822 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.7113 (m-30) cc_final: 0.6724 (m-30) REVERT: B 149 VAL cc_start: 0.8336 (t) cc_final: 0.8034 (p) REVERT: B 335 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6071 (mt-10) REVERT: B 647 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7414 (mtpt) REVERT: C 149 VAL cc_start: 0.8467 (t) cc_final: 0.8140 (p) REVERT: C 490 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7530 (ttm) REVERT: C 494 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7493 (mtt-85) REVERT: D 519 ASP cc_start: 0.7128 (m-30) cc_final: 0.6813 (m-30) REVERT: E 149 VAL cc_start: 0.8334 (t) cc_final: 0.8035 (p) REVERT: E 335 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6066 (mt-10) REVERT: E 625 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: E 647 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7410 (mtpt) REVERT: F 149 VAL cc_start: 0.8465 (t) cc_final: 0.8139 (p) REVERT: F 490 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7540 (ttm) REVERT: F 494 ARG cc_start: 0.7730 (mtt-85) cc_final: 0.7489 (mtt-85) REVERT: H 115 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7722 (tm) REVERT: I 102 LEU cc_start: 0.8296 (mm) cc_final: 0.8093 (mm) REVERT: J 115 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7704 (tm) REVERT: L 102 LEU cc_start: 0.8292 (mm) cc_final: 0.8082 (mm) outliers start: 123 outliers final: 36 residues processed: 884 average time/residue: 1.5784 time to fit residues: 1677.2408 Evaluate side-chains 772 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 727 time to evaluate : 4.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 445 MET Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 625 MET Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain E residue 684 ASP Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 688 LEU Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 376 optimal weight: 0.0270 chunk 307 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 453 optimal weight: 7.9990 chunk 489 optimal weight: 0.0170 chunk 403 optimal weight: 6.9990 chunk 449 optimal weight: 0.0470 chunk 154 optimal weight: 3.9990 chunk 363 optimal weight: 0.8980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN B 340 GLN B 348 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN D 298 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN E 340 GLN E 348 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 ASN G 214 HIS H 141 ASN H 180 GLN ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS J 141 ASN J 180 GLN K 141 ASN K 214 HIS ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39678 Z= 0.145 Angle : 0.506 8.055 53496 Z= 0.264 Chirality : 0.038 0.168 5754 Planarity : 0.004 0.053 7182 Dihedral : 4.350 36.162 5452 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.67 % Allowed : 20.61 % Favored : 75.72 % 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: -1.20 (0.11), residues: 4980 helix: -0.16 (0.09), residues: 3390 sheet: -3.61 (0.55), residues: 60 loop : -1.96 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.001 0.000 HIS F 140 PHE 0.009 0.001 PHE B 167 TYR 0.021 0.001 TYR J 138 ARG 0.008 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 790 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6939 (m-30) cc_final: 0.6612 (m-30) REVERT: B 149 VAL cc_start: 0.8345 (t) cc_final: 0.8080 (p) REVERT: B 550 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6971 (t70) REVERT: B 647 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7229 (mtpt) REVERT: C 149 VAL cc_start: 0.8390 (t) cc_final: 0.8140 (p) REVERT: C 335 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6084 (mt-10) REVERT: C 568 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6639 (mtm) REVERT: C 594 MET cc_start: 0.6333 (tpp) cc_final: 0.5386 (tpt) REVERT: D 519 ASP cc_start: 0.6945 (m-30) cc_final: 0.6618 (m-30) REVERT: E 149 VAL cc_start: 0.8347 (t) cc_final: 0.8096 (p) REVERT: E 550 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6976 (t70) REVERT: E 647 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7226 (mtpt) REVERT: F 149 VAL cc_start: 0.8392 (t) cc_final: 0.8143 (p) REVERT: F 323 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6418 (mtp85) REVERT: F 335 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6078 (mt-10) REVERT: F 594 MET cc_start: 0.6331 (tpp) cc_final: 0.5362 (tpt) REVERT: I 102 LEU cc_start: 0.8268 (mm) cc_final: 0.8040 (mm) REVERT: L 102 LEU cc_start: 0.8261 (mm) cc_final: 0.8034 (mm) outliers start: 147 outliers final: 35 residues processed: 859 average time/residue: 1.5077 time to fit residues: 1564.2416 Evaluate side-chains 757 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 714 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 568 MET Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain F residue 565 ILE Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 6.9990 chunk 340 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 454 optimal weight: 3.9990 chunk 481 optimal weight: 10.0000 chunk 237 optimal weight: 0.7980 chunk 430 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 318 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 39678 Z= 0.179 Angle : 0.519 8.169 53496 Z= 0.268 Chirality : 0.040 0.219 5754 Planarity : 0.004 0.051 7182 Dihedral : 4.144 35.131 5446 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.74 % Allowed : 22.11 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4980 helix: 0.28 (0.09), residues: 3384 sheet: -3.08 (0.58), residues: 60 loop : -1.72 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 351 HIS 0.002 0.001 HIS C 182 PHE 0.010 0.001 PHE K 210 TYR 0.022 0.001 TYR I 138 ARG 0.007 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 759 time to evaluate : 4.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6856 (m-30) cc_final: 0.6569 (m-30) REVERT: A 592 MET cc_start: 0.6543 (tmm) cc_final: 0.5219 (tmt) REVERT: B 149 VAL cc_start: 0.8346 (t) cc_final: 0.8034 (p) REVERT: B 363 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6315 (ttt) REVERT: B 550 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6979 (t70) REVERT: B 592 MET cc_start: 0.6561 (tmm) cc_final: 0.4909 (ttt) REVERT: B 647 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7166 (mtpt) REVERT: C 335 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6140 (mt-10) REVERT: C 407 MET cc_start: 0.7368 (mmt) cc_final: 0.7157 (mmt) REVERT: C 592 MET cc_start: 0.6645 (tmm) cc_final: 0.6350 (tmm) REVERT: C 594 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5482 (tpt) REVERT: D 519 ASP cc_start: 0.6945 (m-30) cc_final: 0.6655 (m-30) REVERT: E 149 VAL cc_start: 0.8351 (t) cc_final: 0.8037 (p) REVERT: E 363 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6315 (ttt) REVERT: E 550 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6965 (t70) REVERT: E 625 MET cc_start: 0.8256 (mtt) cc_final: 0.8013 (mtt) REVERT: F 335 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6131 (mt-10) REVERT: F 407 MET cc_start: 0.7368 (mmt) cc_final: 0.7153 (mmt) REVERT: F 592 MET cc_start: 0.6639 (tmm) cc_final: 0.6348 (tmm) REVERT: F 594 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5463 (tpt) REVERT: I 102 LEU cc_start: 0.8240 (mm) cc_final: 0.8004 (mm) REVERT: J 112 GLU cc_start: 0.7987 (mp0) cc_final: 0.7196 (pp20) REVERT: L 102 LEU cc_start: 0.8232 (mm) cc_final: 0.7985 (mm) outliers start: 150 outliers final: 56 residues processed: 819 average time/residue: 1.5496 time to fit residues: 1531.1891 Evaluate side-chains 784 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 719 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 647 LYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 482 LYS Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 565 ILE Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain L residue 194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 0.9990 chunk 273 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 358 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 410 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 432 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN E 272 ASN E 318 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN G 180 GLN H 180 GLN J 180 GLN K 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39678 Z= 0.188 Angle : 0.535 8.426 53496 Z= 0.271 Chirality : 0.040 0.209 5754 Planarity : 0.004 0.049 7182 Dihedral : 4.053 34.774 5446 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.94 % Allowed : 23.33 % Favored : 72.73 % 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: -0.17 (0.12), residues: 4980 helix: 0.56 (0.09), residues: 3420 sheet: -2.53 (0.63), residues: 60 loop : -1.46 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 351 HIS 0.002 0.001 HIS C 182 PHE 0.011 0.001 PHE E 220 TYR 0.020 0.001 TYR I 138 ARG 0.008 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 738 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6701 (m-30) cc_final: 0.6379 (m-30) REVERT: A 592 MET cc_start: 0.6575 (tmm) cc_final: 0.5849 (tmt) REVERT: B 149 VAL cc_start: 0.8354 (t) cc_final: 0.8087 (p) REVERT: B 363 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6331 (ttt) REVERT: B 550 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7126 (t70) REVERT: C 149 VAL cc_start: 0.8401 (t) cc_final: 0.8126 (p) REVERT: C 592 MET cc_start: 0.6689 (tmm) cc_final: 0.6305 (tmm) REVERT: C 594 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5510 (tpt) REVERT: D 519 ASP cc_start: 0.6881 (m-30) cc_final: 0.6618 (m-30) REVERT: E 149 VAL cc_start: 0.8361 (t) cc_final: 0.8087 (p) REVERT: E 363 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6327 (ttt) REVERT: E 550 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7106 (t70) REVERT: E 647 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7093 (mtpt) REVERT: F 149 VAL cc_start: 0.8400 (t) cc_final: 0.8125 (p) REVERT: F 592 MET cc_start: 0.6686 (tmm) cc_final: 0.6295 (tmm) REVERT: F 594 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5493 (tpt) REVERT: F 673 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7590 (tpp) REVERT: H 112 GLU cc_start: 0.7980 (mp0) cc_final: 0.7181 (pp20) REVERT: I 102 LEU cc_start: 0.8298 (mm) cc_final: 0.8037 (mm) REVERT: J 112 GLU cc_start: 0.7971 (mp0) cc_final: 0.7149 (pp20) REVERT: L 102 LEU cc_start: 0.8294 (mm) cc_final: 0.8035 (mm) outliers start: 158 outliers final: 72 residues processed: 816 average time/residue: 1.5158 time to fit residues: 1499.5381 Evaluate side-chains 798 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 718 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 594 MET Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 323 ARG Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 0.8980 chunk 433 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 481 optimal weight: 5.9990 chunk 399 optimal weight: 4.9990 chunk 223 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 252 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 180 GLN ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN K 180 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39678 Z= 0.182 Angle : 0.545 8.809 53496 Z= 0.274 Chirality : 0.040 0.204 5754 Planarity : 0.004 0.049 7182 Dihedral : 3.959 34.517 5446 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.74 % Allowed : 24.70 % Favored : 71.56 % 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: 0.19 (0.12), residues: 4980 helix: 0.82 (0.09), residues: 3414 sheet: -2.20 (0.64), residues: 60 loop : -1.28 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 351 HIS 0.002 0.001 HIS F 182 PHE 0.010 0.001 PHE J 210 TYR 0.017 0.001 TYR H 138 ARG 0.007 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 750 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6681 (m-30) cc_final: 0.6389 (m-30) REVERT: A 592 MET cc_start: 0.6603 (tmm) cc_final: 0.5901 (tmt) REVERT: B 149 VAL cc_start: 0.8340 (t) cc_final: 0.7965 (p) REVERT: B 335 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: B 363 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6246 (ttt) REVERT: B 550 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7099 (t70) REVERT: B 688 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7022 (mp) REVERT: C 550 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7092 (t70) REVERT: C 592 MET cc_start: 0.6628 (tmm) cc_final: 0.6309 (tmm) REVERT: C 594 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5964 (tpp) REVERT: D 519 ASP cc_start: 0.6676 (m-30) cc_final: 0.6381 (m-30) REVERT: D 573 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: E 149 VAL cc_start: 0.8345 (t) cc_final: 0.8026 (p) REVERT: E 335 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: E 363 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6241 (ttt) REVERT: E 550 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7104 (t70) REVERT: E 592 MET cc_start: 0.6528 (tmm) cc_final: 0.5396 (tmt) REVERT: E 625 MET cc_start: 0.8286 (mtt) cc_final: 0.8013 (mtt) REVERT: E 647 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7049 (mtpt) REVERT: E 688 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7022 (mp) REVERT: F 592 MET cc_start: 0.6618 (tmm) cc_final: 0.6206 (tmm) REVERT: F 594 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5946 (tpp) REVERT: F 673 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6458 (tmm) REVERT: H 112 GLU cc_start: 0.7957 (mp0) cc_final: 0.7172 (pp20) REVERT: I 102 LEU cc_start: 0.8314 (mm) cc_final: 0.8084 (mm) REVERT: J 112 GLU cc_start: 0.7953 (mp0) cc_final: 0.7191 (pp20) REVERT: K 180 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6788 (mt0) REVERT: L 102 LEU cc_start: 0.8308 (mm) cc_final: 0.8066 (mm) outliers start: 150 outliers final: 56 residues processed: 825 average time/residue: 1.5333 time to fit residues: 1535.3868 Evaluate side-chains 792 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 721 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 573 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain E residue 490 MET Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain E residue 688 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 351 optimal weight: 0.0970 chunk 272 optimal weight: 1.9990 chunk 405 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 479 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 221 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN E 318 ASN E 358 GLN F 298 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 180 GLN J 180 GLN L 109 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39678 Z= 0.188 Angle : 0.564 9.833 53496 Z= 0.282 Chirality : 0.040 0.209 5754 Planarity : 0.004 0.049 7182 Dihedral : 3.862 34.398 5444 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.52 % Allowed : 25.90 % Favored : 70.58 % 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: 0.45 (0.12), residues: 4980 helix: 0.96 (0.09), residues: 3432 sheet: -1.97 (0.65), residues: 60 loop : -1.06 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 351 HIS 0.002 0.001 HIS F 182 PHE 0.009 0.001 PHE E 167 TYR 0.015 0.001 TYR H 138 ARG 0.009 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 758 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6639 (m-30) cc_final: 0.6351 (m-30) REVERT: A 573 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7238 (ttp80) REVERT: A 592 MET cc_start: 0.6575 (tmm) cc_final: 0.5914 (tmt) REVERT: B 149 VAL cc_start: 0.8357 (t) cc_final: 0.8022 (p) REVERT: B 335 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: B 363 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6332 (ttt) REVERT: B 550 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7094 (t70) REVERT: B 590 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6346 (pm20) REVERT: B 592 MET cc_start: 0.6508 (tmt) cc_final: 0.5966 (tmt) REVERT: B 661 LEU cc_start: 0.8312 (mp) cc_final: 0.8102 (mt) REVERT: B 688 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7004 (mp) REVERT: C 335 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: C 550 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7092 (t70) REVERT: C 592 MET cc_start: 0.6602 (tmm) cc_final: 0.6316 (tmm) REVERT: C 594 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5958 (tpp) REVERT: D 519 ASP cc_start: 0.6695 (m-30) cc_final: 0.6403 (m-30) REVERT: E 149 VAL cc_start: 0.8361 (t) cc_final: 0.8025 (p) REVERT: E 335 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6217 (mp0) REVERT: E 363 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6328 (ttt) REVERT: E 550 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7104 (t70) REVERT: E 592 MET cc_start: 0.6518 (tmm) cc_final: 0.5393 (tmt) REVERT: E 625 MET cc_start: 0.8257 (mtt) cc_final: 0.7952 (mtt) REVERT: E 647 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7017 (mtpt) REVERT: E 661 LEU cc_start: 0.8434 (mp) cc_final: 0.8179 (mt) REVERT: E 688 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6999 (mp) REVERT: F 335 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: F 592 MET cc_start: 0.6604 (tmm) cc_final: 0.6294 (tmm) REVERT: F 594 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5951 (tpp) REVERT: F 673 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6464 (tmm) REVERT: F 674 ASP cc_start: 0.7283 (t0) cc_final: 0.6908 (t0) REVERT: G 112 GLU cc_start: 0.7874 (mp0) cc_final: 0.7342 (pp20) REVERT: I 102 LEU cc_start: 0.8321 (mm) cc_final: 0.8094 (mm) REVERT: K 112 GLU cc_start: 0.7891 (mp0) cc_final: 0.7365 (pp20) REVERT: L 102 LEU cc_start: 0.8319 (mm) cc_final: 0.8092 (mm) REVERT: L 127 ASP cc_start: 0.7142 (t0) cc_final: 0.6714 (t70) outliers start: 141 outliers final: 65 residues processed: 831 average time/residue: 1.5251 time to fit residues: 1527.9422 Evaluate side-chains 806 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 724 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 482 LYS Chi-restraints excluded: chain E residue 490 MET Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain E residue 688 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 565 ILE Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 305 optimal weight: 0.5980 chunk 327 optimal weight: 0.3980 chunk 237 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 377 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN C 298 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 180 GLN I 109 ASN J 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39678 Z= 0.189 Angle : 0.579 10.102 53496 Z= 0.289 Chirality : 0.040 0.157 5754 Planarity : 0.004 0.049 7182 Dihedral : 3.848 33.936 5444 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.39 % Allowed : 26.62 % Favored : 69.99 % 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 (0.12), residues: 4980 helix: 1.10 (0.09), residues: 3432 sheet: -1.85 (0.65), residues: 60 loop : -1.00 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 351 HIS 0.002 0.001 HIS D 182 PHE 0.010 0.001 PHE B 167 TYR 0.015 0.001 TYR F 664 ARG 0.010 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 741 time to evaluate : 4.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 ASP cc_start: 0.6639 (m-30) cc_final: 0.6367 (m-30) REVERT: A 573 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7240 (ttp80) REVERT: B 149 VAL cc_start: 0.8346 (t) cc_final: 0.8092 (p) REVERT: B 335 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: B 363 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6330 (ttt) REVERT: B 550 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7089 (t70) REVERT: B 590 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6316 (pm20) REVERT: B 592 MET cc_start: 0.6544 (tmt) cc_final: 0.5966 (tmt) REVERT: B 594 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.5856 (tpp) REVERT: B 688 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6941 (mp) REVERT: C 149 VAL cc_start: 0.8435 (t) cc_final: 0.8233 (p) REVERT: C 335 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: C 363 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6144 (ttt) REVERT: C 550 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7104 (t70) REVERT: C 592 MET cc_start: 0.6594 (tmm) cc_final: 0.6253 (tmm) REVERT: C 594 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5922 (tpp) REVERT: D 519 ASP cc_start: 0.6692 (m-30) cc_final: 0.6427 (m-30) REVERT: D 573 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7868 (ttm-80) REVERT: D 592 MET cc_start: 0.6613 (tmt) cc_final: 0.5963 (tmt) REVERT: E 149 VAL cc_start: 0.8352 (t) cc_final: 0.8109 (p) REVERT: E 363 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6335 (ttt) REVERT: E 550 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7069 (t70) REVERT: E 592 MET cc_start: 0.6567 (tmm) cc_final: 0.5377 (tmt) REVERT: E 625 MET cc_start: 0.8244 (mtt) cc_final: 0.7926 (mtt) REVERT: E 647 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6942 (mtpt) REVERT: E 688 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6979 (mp) REVERT: E 698 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7717 (mttp) REVERT: F 335 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: F 520 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6660 (tpp) REVERT: F 550 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7099 (t70) REVERT: F 592 MET cc_start: 0.6652 (tmm) cc_final: 0.6363 (tmm) REVERT: F 594 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.5913 (tpp) REVERT: F 673 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6485 (tmm) REVERT: F 674 ASP cc_start: 0.7269 (t0) cc_final: 0.6977 (t0) REVERT: H 112 GLU cc_start: 0.7882 (mp0) cc_final: 0.7182 (pp20) REVERT: I 102 LEU cc_start: 0.8306 (mm) cc_final: 0.8092 (mm) REVERT: I 127 ASP cc_start: 0.7154 (t0) cc_final: 0.6596 (t0) REVERT: J 112 GLU cc_start: 0.7885 (mp0) cc_final: 0.7249 (pp20) REVERT: L 102 LEU cc_start: 0.8316 (mm) cc_final: 0.8101 (mm) REVERT: L 127 ASP cc_start: 0.7101 (t0) cc_final: 0.6664 (t70) outliers start: 136 outliers final: 63 residues processed: 810 average time/residue: 1.5666 time to fit residues: 1531.6293 Evaluate side-chains 800 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 717 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 574 GLU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 595 GLU Chi-restraints excluded: chain E residue 647 LYS Chi-restraints excluded: chain E residue 688 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 520 MET Chi-restraints excluded: chain F residue 550 ASP Chi-restraints excluded: chain F residue 565 ILE Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 3.9990 chunk 459 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 447 optimal weight: 10.0000 chunk 269 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 351 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 404 optimal weight: 20.0000 chunk 423 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 GLN B 88 ASN B 188 GLN B 330 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 330 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 GLN ** F 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 141 ASN H 180 GLN ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39678 Z= 0.278 Angle : 0.639 11.773 53496 Z= 0.319 Chirality : 0.043 0.234 5754 Planarity : 0.004 0.050 7182 Dihedral : 4.015 33.690 5444 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.22 % Allowed : 27.42 % Favored : 69.36 % 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: 0.52 (0.12), residues: 4980 helix: 1.00 (0.09), residues: 3426 sheet: -1.77 (0.66), residues: 60 loop : -1.00 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 351 HIS 0.003 0.001 HIS B 182 PHE 0.017 0.001 PHE E 167 TYR 0.017 0.001 TYR H 138 ARG 0.010 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 722 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7903 (ptpp) REVERT: A 519 ASP cc_start: 0.6922 (m-30) cc_final: 0.6565 (m-30) REVERT: B 149 VAL cc_start: 0.8343 (t) cc_final: 0.8133 (p) REVERT: B 335 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: B 363 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6256 (ttt) REVERT: B 550 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.7066 (t70) REVERT: B 590 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: B 592 MET cc_start: 0.6734 (tmt) cc_final: 0.6205 (tmt) REVERT: B 688 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6870 (mp) REVERT: B 698 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7743 (mttp) REVERT: C 335 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: C 363 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6163 (ttt) REVERT: C 594 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6039 (tpp) REVERT: C 663 MET cc_start: 0.7618 (ttp) cc_final: 0.7225 (ttp) REVERT: D 519 ASP cc_start: 0.6870 (m-30) cc_final: 0.6560 (m-30) REVERT: D 573 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7844 (ttm-80) REVERT: E 149 VAL cc_start: 0.8369 (t) cc_final: 0.8154 (p) REVERT: E 363 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6263 (ttt) REVERT: E 550 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.7051 (t70) REVERT: E 592 MET cc_start: 0.6755 (tmm) cc_final: 0.5774 (tmt) REVERT: E 625 MET cc_start: 0.8258 (mtt) cc_final: 0.7981 (mtt) REVERT: E 688 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6879 (mp) REVERT: E 698 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7744 (mttp) REVERT: F 335 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: F 363 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6026 (ttt) REVERT: F 594 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6034 (tpp) REVERT: F 673 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6612 (tmm) REVERT: H 112 GLU cc_start: 0.7898 (mp0) cc_final: 0.7166 (pp20) REVERT: H 141 ASN cc_start: 0.8330 (m-40) cc_final: 0.8092 (m110) REVERT: I 102 LEU cc_start: 0.8276 (mm) cc_final: 0.8023 (mm) REVERT: I 127 ASP cc_start: 0.7126 (t0) cc_final: 0.6546 (t0) REVERT: J 112 GLU cc_start: 0.7901 (mp0) cc_final: 0.7197 (pp20) REVERT: L 102 LEU cc_start: 0.8289 (mm) cc_final: 0.8067 (mm) REVERT: L 127 ASP cc_start: 0.7137 (t0) cc_final: 0.6564 (t0) REVERT: L 180 GLN cc_start: 0.6913 (tt0) cc_final: 0.6670 (tt0) outliers start: 129 outliers final: 67 residues processed: 796 average time/residue: 1.5652 time to fit residues: 1507.2859 Evaluate side-chains 779 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 697 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 595 GLU Chi-restraints excluded: chain E residue 688 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 185 GLU Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 3.9990 chunk 472 optimal weight: 0.4980 chunk 288 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 328 optimal weight: 1.9990 chunk 496 optimal weight: 0.9990 chunk 456 optimal weight: 0.3980 chunk 395 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 242 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 318 ASN B 242 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN C 660 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 318 ASN D 319 GLN ** D 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 596 GLN G 180 GLN H 180 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39678 Z= 0.202 Angle : 0.634 12.860 53496 Z= 0.315 Chirality : 0.041 0.230 5754 Planarity : 0.004 0.050 7182 Dihedral : 3.908 34.667 5444 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.54 % Allowed : 28.49 % Favored : 68.96 % 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: 0.76 (0.12), residues: 4980 helix: 1.19 (0.09), residues: 3426 sheet: -1.67 (0.67), residues: 60 loop : -0.92 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 351 HIS 0.002 0.001 HIS F 182 PHE 0.011 0.001 PHE D 553 TYR 0.015 0.001 TYR J 138 ARG 0.011 0.000 ARG C 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 713 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LYS cc_start: 0.8143 (ptpp) cc_final: 0.7939 (ptpp) REVERT: A 519 ASP cc_start: 0.6757 (m-30) cc_final: 0.6451 (m-30) REVERT: B 363 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6288 (ttt) REVERT: B 543 LYS cc_start: 0.7175 (tppt) cc_final: 0.6974 (tppt) REVERT: B 550 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7058 (t70) REVERT: B 590 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: B 592 MET cc_start: 0.6565 (tmt) cc_final: 0.6019 (tmt) REVERT: C 335 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: C 363 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6109 (ttt) REVERT: C 550 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7066 (t70) REVERT: C 663 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7170 (ttp) REVERT: D 519 ASP cc_start: 0.6809 (m-30) cc_final: 0.6503 (m-30) REVERT: E 363 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6307 (ttt) REVERT: E 550 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.7055 (t70) REVERT: E 592 MET cc_start: 0.6591 (tmm) cc_final: 0.5382 (tmt) REVERT: E 625 MET cc_start: 0.8191 (mtt) cc_final: 0.7904 (mtt) REVERT: F 335 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: F 550 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7070 (t70) REVERT: F 673 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6388 (tmm) REVERT: H 112 GLU cc_start: 0.7884 (mp0) cc_final: 0.7212 (pp20) REVERT: I 102 LEU cc_start: 0.8236 (mm) cc_final: 0.8024 (mm) REVERT: I 112 GLU cc_start: 0.7712 (mp0) cc_final: 0.7306 (pp20) REVERT: I 127 ASP cc_start: 0.7096 (t0) cc_final: 0.6545 (t0) REVERT: J 112 GLU cc_start: 0.7894 (mp0) cc_final: 0.7233 (pp20) REVERT: L 102 LEU cc_start: 0.8268 (mm) cc_final: 0.8067 (mm) REVERT: L 127 ASP cc_start: 0.7124 (t0) cc_final: 0.6579 (t0) REVERT: L 180 GLN cc_start: 0.6872 (tt0) cc_final: 0.6614 (tt0) outliers start: 102 outliers final: 62 residues processed: 769 average time/residue: 1.5963 time to fit residues: 1496.6436 Evaluate side-chains 770 residues out of total 4218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 696 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 482 LYS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 363 MET Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 490 MET Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 574 GLU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 568 MET Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 363 MET Chi-restraints excluded: chain E residue 550 ASP Chi-restraints excluded: chain E residue 595 GLU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 245 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 411 GLU Chi-restraints excluded: chain F residue 445 MET Chi-restraints excluded: chain F residue 454 SER Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 550 ASP Chi-restraints excluded: chain F residue 574 GLU Chi-restraints excluded: chain F residue 613 VAL Chi-restraints excluded: chain F residue 673 MET Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 194 VAL Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 131 ILE Chi-restraints excluded: chain J residue 143 LEU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain L residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 0.9980 chunk 420 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 364 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 395 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 406 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN E 88 ASN ** E 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN H 180 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.118221 restraints weight = 57598.955| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.35 r_work: 0.3701 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39678 Z= 0.222 Angle : 0.649 12.503 53496 Z= 0.323 Chirality : 0.041 0.237 5754 Planarity : 0.004 0.048 7182 Dihedral : 3.921 33.572 5444 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 28.84 % Favored : 68.44 % 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: 0.81 (0.12), residues: 4980 helix: 1.23 (0.09), residues: 3426 sheet: -1.61 (0.67), residues: 60 loop : -0.91 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 351 HIS 0.002 0.001 HIS F 182 PHE 0.012 0.001 PHE E 167 TYR 0.016 0.001 TYR J 138 ARG 0.009 0.000 ARG D 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19843.87 seconds wall clock time: 351 minutes 39.03 seconds (21099.03 seconds total)